Papers - SHIMODE Shinji
about 73-
Shimode, S., T. Yamaguchi and K. Hidaka
Plankton & Benthos Research 17 ( 3 ) 301 - 311 2022.8 [Reviewed]
Authorship：Lead author, Corresponding author Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Biological traits predict species' time-varying responses to multiple global change drivers
Sasaki T., Iwachido Y., Lam-Gordillo O., Cook K., Douglas E., Gladstone-Gallagher R., Greenfield B. … Show more authors
Sasaki T., Iwachido Y., Lam-Gordillo O., Cook K., Douglas E., Gladstone-Gallagher R., Greenfield B., Hailes S., Carter K., Ishii N., Takayama Y, Shimode S., Kagami M, Hewitt J., Thrush S. and Lohrer A Hide authors
Nature Communications 2026.3 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Single Work
-
Yano, K; Ashenafi, RM; Takayama, Y; Shimode, S; Suzuki, K; Kuwahara, VS
MARINE ECOLOGY PROGRESS SERIES 780 20 - 20 2026.3 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Sugai, Y; Hoshihara, AY; Fujiki, T; Ikuta, T; Yoshizawa, S; Shimode, S; Kuwahara, VS
PLANKTON & BENTHOS RESEARCH 21 ( 1 ) 52 - 62 2026.2 [Reviewed]
DOI Web of Science CiNii Research
Language：English Publishing type：Research paper (scientific journal) Publisher：日本プランクトン学会、日本ベントス学会 Joint Work
<p>To clarify the community compositions and three-dimensional (3D) structure of microbial biofilms on marine plastics, five types of plastic and glass plates were incubated in temperate coastal waters (Sagami Bay, Japan). Metabarcoding analysis showed that both prokaryotic and eukaryotic community structures on plastics and glass were largely different compared to ambient seawater, although similar communities were observed on different types of substrates except for polyethylene. Among the plastic-associated communities, Flavobacteriales (33.5–54.7%) were the most dominant prokaryotes, and microbial eukaryotes were dominated by Exogenida (suctorian ciliates) (74.5–80.3%), particularly the genus <i>Ephelota</i>, followed by Naviculales (pennate diatoms) (17.7–23.3%). Confocal fluorescence microscopy visualized the 3D layered structure of plastic biofilms mainly composed of bacteria and <i>Navicula</i>-like diatoms with the abundant and spatially heterogeneous distribution of the stalked suctorian ciliates. Bacteria and diatoms were found from the inner to outer layers of biofilms with abundant bacterial cells on the plastic surface, whereas the cell bodies of suctorian ciliates were observed exclusively in the outermost layer. Furthermore, chlorophyll autofluorescence was detected abundantly in the cell bodies of the ciliates, indicating their active grazing on diatoms. These combined taxonomic and structural results suggest the formation and developmental processes of microbial biofilms and biological interactions (synergistic and predatory relationships) on marine plastics. The present study indicates the proliferation of suctorian ciliates, which have been reported to cause serious damage to aquaculture, on plastics, implicating the potential ecological roles of marine plastic debris as a dispersal vector transporting harmful hitchhiking microorganisms.</p>
-
Optical water types associated with phytoplankton community structure in temperate coastal waters.
Yano K., Ashenafi R.M., Chang B.A., Suzuki K., Shimode S. and Kuwahara V.S.
The IEEE proceedings of OCEANS 2025 Great Lake 2025.11 [Reviewed]
Language：English Publishing type：Research paper (international conference proceedings) Single Work
-
Satellite-based analysis of physical-biological interactions in the temperate western boundary pacific
Ashenafi R.M., Yano K., Terauchi G., Shimode S. and Kuwahara V.S.
The IEEE proceedings of OCEANS 2025 Great Lake 2025.11 [Reviewed]
Language：English Publishing type：Research paper (international conference proceedings) Single Work
-
20 ( 4 ) 263 - 268 2025.11 [Reviewed]
DOI Web of Science CiNii Research
Language：English Publishing type：Research paper (scientific journal) Publisher：The Plankton Society of Japan, The Japanese Association of Benthology Joint Work
-
Hoshihara, AY; Fujiki, T; Ikuta, T; Shimode, S; Sugai, Y; Kuwahara, VS
HARMFUL ALGAE 148 2025.9 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Coelenterazine-dependent Bioluminescence in the Cyclopoid Copepod, Triconia conifera
Gaku Mizuno , Shinji Shimode , Yuichiro Nishibe , Yuichi Oba
ChemBioChem 26 ( 8 ) e202401051 2025.3 [Reviewed]
DOI Web of Science PubMed CiNii Research
Language：English Publishing type：Research paper (scientific journal) Publisher：Wiley Joint Work
<jats:title>Abstract</jats:title><jats:p>Species in the cyclopoid copepod <jats:italic>Triconia</jats:italic> are known to be bioluminescent, emitting blue light by mechanical stimulus. In this study in <jats:italic>Triconica conifera</jats:italic>, we identified the presence of luciferase activity to coelenterazine, a substrate for the bioluminescence in various marine taxa such as luminous cnidarians, fishes, and crustaceans including calanoid copepods. The molecular size estimated by gel‐filtration chromatography and pH dependency of the luciferase activity were similar to those in calanoid copepods. On the other hand, the reaction rate and inhibitory effect by magnesium ion were much different between them. The presence of coelenterazine in the specimen was confirmed by LC‐ESI‐MS/MS. Taken together with the phylogenetically distant relationship between Cyclopoida and Calanoida, our findings suggested that coelenterazine‐dependent bioluminescence was evolved parallelly at least twice in copepod lineages.</jats:p>
-
A biogenic geodesic dome of the silica skeleton in Phaeodaria
Yamaguchi, M; Nakamura, Y; Watanabe, H; Kimoto, K; Oaki, Y; Shimode, S; Imai, H
SCIENTIFIC REPORTS 14 ( 1 ) 2024.6 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Yano, K., Takayama, Y., Shimode, S., Toratani, M., Mrakami, H. and Kuwahara, V.S.
Plankton & Benthos Research 19 ( 1 ) 37 - 50 2024.2 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Nakamura, Y; Itagaki, H; Tuji, A; Shimode, S; Yamaguchi, A; Hidaka, K; Ogiso-Tanaka, E
ENVIRONMENTAL MICROBIOLOGY 25 ( 12 ) 3630 - 3638 2023.12 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
温帯沿岸域相模湾における植物プランクトンのサイズ組成と光吸収係数の特徴
矢野光一・下出信次・Victor S. Kuwahara
プランクトン工学研究 3 39 - 46 2023.6
Language：Japanese Publishing type：Research paper (bulletin of university, research institution) Joint Work
Other Link： https://www.soka.ac.jp/files/ja/20230914_133642.pdf
-
Sugai, Y., N. Natori, K. Tsuchiya, M. Nakagawa, M. C. Honda, S. Shimode and T. Toda
Journal of Plankton Research 45 ( 2 ) 325 - 337 2023.2 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
25年ぶりに相模湾で発生した円石藻Gephyrocapsa oceanicaによるブルーム
矢野光一・梶正彦・下出信次・村上浩・虎谷充浩・Victor S. Kuwahara
プランクトン工学研究 ( 2 ) 24 - 31 2022.6
Language：Japanese Publishing type：Research paper (bulletin of university, research institution) Single Work
-
カイアシ類1個体からのDNA抽出法の改良とホルマリン固定期間がミトコンドリア遺伝子のPCR増幅に与える影響
小林真輝・髙山佳樹・下出信次・戸田龍樹・黒沢則夫
プランクトン工学研究 ( 2 ) 56 - 65 2022.6
Language：Japanese Publishing type：Research paper (bulletin of university, research institution) Joint Work
-
Ultrastructures of setae of a planktonic diatom, Chaetoceros coarctatus
Owari,Y., F. Nakamura, Y. Oaki, H. Tsuda, S. Shimode and H. Imai
Scientific Reports 12 ( 5768 ) 1 - 9 2022.5 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
Other Link： https://doi.org/10.1038/s41598-022-11484-2
-
Characterization of calcite spines of planktonic foraminifers (Globigerinidae)
Izumida, K., T. Mihiro, R. Fujimaki, Y. Nagai, Y. Oaki, K. Nito, Y. Tanaka, S. Shimode, T. Toyofuku … Show more authors
Izumida, K., T. Mihiro, R. Fujimaki, Y. Nagai, Y. Oaki, K. Nito, Y. Tanaka, S. Shimode, T. Toyofuku and H. Imai Hide authors
CrystEngComm 24 ( 13 ) 2446 - 2450 2022.3 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
Other Link： https://pubs.rsc.org/en/content/articlelanding/2022/ce/d2ce00110a
-
Sayaka Sogawa, Kenji Tsuchiya, Satoshi Nagai, Shinji Shimode, Victor S. Kuwahara
Metabarcoding and Metagenomics 6 41 - 58 2022.2 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
Other Link： https://mbmg.pensoft.net/article/78181/
-
Fujimaki, R., N. Suzuki, K. Kimoto, Y. Nagai, Y. Oaki, S. Shimode, T. Toyofuku and H. Imai
Scientific Reports 12 ( 2848 ) 2022.2 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
Other Link： https://www.nature.com/articles/s41598-022-06974-2
-
Feeding and growth efficiency in a pelagic chaetognath, Zonosagitta nagae reared in the laboratory
Otake, S., Takahashi, K. and Shimode, S.
Journal of Plankton Research 42 265 - 273 2020.4 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
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 rates of Zonosagitta nagae under laboratory rearing condition. A total of 54 field-collected chaetognaths with maturity Stage I and II ranging from 5 to 12 mm in body length collected in June, August and October were individually incubated at 20–22°C with excess copepod prey and growth parameters were obtained from 26 individuals that survived ~10–46 days. For Z. nagae, ingestion and growth rates increased with body dry weight, and both parameters were significantly related, indicating that gross growth efficiency was ~47%. Specific ingestion rates ranged from 0.03 to 0.43 d−1 and tended to decrease with an increase of size of the chaetognaths. Individual specific growth rate varied widely in small-sized individuals (~6 mm), ranging from −0.103 to 0.135, but became relatively constant (~0.032) with increasing size. Overall the study results suggest that Z. nagae is characterized by high gross growth efficiency, which is in striking contrast with previously studied inshore species.
Other Link： https://academic.oup.com/plankt
-
Sugai, Y., K. Tsuchiya, S. Shimode and T. Toda
Journal of Geophysical Research: Oceans 125 ( 4 ) e2019JC015505 2020.3 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
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 biological processes are expected, in air‐sea CO exchange, the production and consumption of CO in the SML and its sea‐air emission were investigated in temperate coastal waters. In the SML, the light‐normalized photochemical CO production rate was relatively high from spring to autumn (median: 2.57 nM [kWh m−2]−1) when relatively high absorbance of chromophoric dissolved organic matter (0.55 m−1) was observed. Biological CO consumption rate constant in the SML showed relatively high values from spring to autumn (mean ± standard deviation: 0.060 ± 0.010 h−1) during the period of relatively high water temperature (22.3 ± 2.7 °C). The calculated sea‐air CO flux (F) varied similarly to CO concentration in the subsurface water. Comparison among the production, consumption, and sea‐air emission of CO in the SML suggests that biological consumption in the SML can be ignored in air‐sea CO exchange throughout the year whereas photochemical production in the SML enhances F during summer under intense light, active biological production, and weak wind conditions. Further, seawater warming experiments found the tendency of the stimulation of biological CO consumption by water temperature increase from spring to autumn, which suggests negative but insignificant feedback on global warming.
-
Tsuchiya, K., T. Sano, T. Tomioka, A. Kohzu, K. Komatsu, R. Shinohara, S. Shimode, T. Toda, A. Imai
PLoS ONE 15 ( 2 ) e0229740 2020.2 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
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 deoxyribonucleosides for evaluating bacterial production of natural bacterial communities from the viewpoint of DNA synthesis, incorporation rates of four deoxyribonucleosides (thymidine, deoxyadenosine, deoxyguanosine and deoxycytidine) labeled by nitrogen stable isotope (15N) into bacterial DNA were examined in both ocean (Sagami Bay) and freshwater (Lake Kasumigaura) ecosystems in July 2015 and January 2016. In most stations in Sagami Bay and Lake Kasumigaura, we found that incorporation rates of deoxyguanosine were the highest among those of the four deoxyribonucleosides, and the incorporation rate of deoxyguanosine was approximately 2.5 times higher than that of thymidine. Whereas, incorporation rates of deoxyadenosine and deoxycytidine were 0.9 and 0.2 times higher than that of thymidine. These results clearly suggest that the numbers of bacterial species which can incorporate exogenous deoxyguanosine into their DNA are relatively greater as compared to the other deoxyribonucleosides, and measurement of bacterial production using deoxyguanosine more likely reflects larger numbers of bacterial species productions.
Other Link： https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0229740
-
Guanine crystals regulated by chitin-based honeycomb frameworks for tunable structural colors of sapphirinid copepod, Sapphirina nigromaculata
Kimura Tsubasa, Takasaki Mihiro, Hatai Ryosuke, Nagai Yukiko, Uematsu Katsuyuki, Oaki Yuya, Osada M … Show more authors
Kimura Tsubasa, Takasaki Mihiro, Hatai Ryosuke, Nagai Yukiko, Uematsu Katsuyuki, Oaki Yuya, Osada Minoru, Tsuda Hiroyuki, Ishigure Takaaki, Toyofuku Takashi, Shimode Shinji, Imai Hiroaki Hide authors
SCIENTIFIC REPORTS 10 ( 1 ) 2020.2 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
相模湾における寄生性渦鞭毛藻類の浮遊性カイアシ類Calanus sinicusの卵生産に与える影響
下出信次
日本プランクトン学会報 66 ( 2 ) 106 - 108 2019.8
Language：English Publishing type：Research paper (research society, symposium materials, etc.) Single Work
-
Nakamura Ken-ichi, Takahashi Kazutaka, Shimode Shinji, Shimizu Yugo, Furuya Ken
PLANKTON & BENTHOS RESEARCH 14 ( 2 ) 62 - 70 2019.5 [Reviewed]
DOI Web of Science CiNii Research
Language：English Publishing type：Research paper (scientific journal) Publisher：日本プランクトン学会、日本ベントス学会 Joint Work
<p>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, or a long incubation for ammonium excretion measurements. Therefore, most of the estimated ammonium excretion rates are potentially linked to stresses on the experimental animals during incubation. In this study, the effects of container size, density, and incubation period on the ammonium excretion rates of five copepod species (<i>Calanus sinicus, Eucalanus californicus, Metridia pacifica, Pleuromamma abdominalis, P. gracilis</i>) were examined using a highly sensitive analytical method that has recently been developed to measure ammonium concentration at the nanomolar level. The results indicate that responses to experimental stresses are species-specific, while incubation in a small container was generally the most significant factor causing overestimation (up to 2.6 times) of the excretion rates. This study shows that this highly sensitive analysis method, which allows short incubations with a single individual in a relatively large-sized container is an appropriate method to estimate ammonium excretion of pelagic copepods in the field using the sealed chamber method.</p>
Other Link： https://ci.nii.ac.jp/naid/130007652795
-
Identification of molecular markers associated with starvation in female Calanus sinicus (Copepoda: Calanoida)
Ohnishi Takuya, Hirai Junya, Shimode Shinji, Tsuda Atsushi
MARINE ECOLOGY PROGRESS SERIES 614 51 - 65 2019.4 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Dead heat: copepod carcass occurrence along the Japanese coasts and implications for a warming ocean
Tang, K. W., Ivory, J. A., Shimode, S., Nishibe, Y., K. Takahashi
ICES Journal of Marine Science 2019.3 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
Other Link： https://doi.org/10.1093/icesjms/fsz017
-
Digestion time and feeding of the pelagic chaetognath Zonosagitta nagae in the laboratory
OTAKE SHIORI, TAKAHASHI KAZUTAKA, SHIMODE SHINJI
Plankton and Benthos Research 14 ( 1 ) 39 - 44 2019 [Reviewed]
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：日本プランクトン学会、日本ベントス学会 Joint Work
<p>Digestion time and feeding of the pelagic chaetognath <i>Zonosagitta nagae</i>, which occurs predominantly in warm waters around Japan, were investigated in the laboratory. Young individuals of <i>Z. nagae</i> ranging from 4.1–7.6 mm in body length were used for the experiments with adult females of the copepod <i>Acartia steueri</i> as prey. The mean digestion time of <i>Z. nagae</i> was 115±3 minutes at 20°C. Temporal change in individual's feeding intensity was observed every 1.5 h for 24 h to determine the diel feeding pattern, feeding interval, feeding rates and daily ration. Almost all individuals showed no clear diel rhythm within 24-h at 20°C under 12L:12D cycle; time interval between feeding was 4.5–6 h (mode) for individuals that ingested multiple copepods. The number of copepods ingested by a chaetognath ranged from 0 to 5 and on average 2.6 copepods were consumed a day per individual. Specific daily ration in most individuals corresponded to ca. 50% of its dry weight while some individuals showed the extremes of non-feeding or voracious feeding (>200% d<sup>−1</sup>), indicating that some of the young <i>Z. nagae</i> had an intermittent feeding mode, which would be adaptive to save energy expenditure at low prey densities and to reduce mortality by lowering the risk of predation.</p>
Other Link： https://ci.nii.ac.jp/naid/130007610807
-
プランクトンとアウトリーチツールとしてのInstagram
下出信次
日本プランクトン学会報 65 ( 2 ) 48 - 49 2018.8
Language：English Publishing type：Research paper (research society, symposium materials, etc.) Single Work
-
Takayama Yoshiki, Nakamura Ken-ichi, Shimode Shinji, Toda Tatsuki
Coastal Marine Science 41 ( 1 ) 11 - 14 2018.8 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Seasonal variations in microbial abundance and transparent exopolymer particle concentration in the sea surface microlayer of temperate coastal waters
Sugai Youta, Tsuchiya Kenji, Shimode Shinji, Toda Tatsuki
AQUATIC MICROBIAL ECOLOGY 81 ( 3 ) 201 - 211 2018
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Response of phytoplankton and enhanced biogeochemical activity to an episodic typhoon event in the coastal waters of Japan
Tsuchiya Kenji, Kuwahara Victor S., Yoshiki Tomoko M., Nakajima Ryota, Shimode Shinji, Kikuchi Tomo … Show more authors
Tsuchiya Kenji, Kuwahara Victor S., Yoshiki Tomoko M., Nakajima Ryota, Shimode Shinji, Kikuchi Tomohiko, Toda Tatsuki Hide authors
ESTUARINE COASTAL AND SHELF SCIENCE 194 30 - 39 2017.7
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Feeding habits of six species of euphausiids (Decapoda: Euphausiacea) in the northwestern Pacific Ocean determined by carbon and nitrogen stable isotope ratios
Sogawa Sayaka, Sugisaki Hiroya, Tadokoro Kazuaki, Ono Tsuneo, Sato Erika, Shimode Shinji, Kikuchi T … Show more authors
Sogawa Sayaka, Sugisaki Hiroya, Tadokoro Kazuaki, Ono Tsuneo, Sato Erika, Shimode Shinji, Kikuchi Tomohiko Hide authors
JOURNAL OF CRUSTACEAN BIOLOGY 37 ( 1 ) 29 - 36 2017.1
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Sugai Youta, Tsuchiya Kenji, Kuwahara Victor S., Shimode Shinji, Komatsu Kazuhiro, Imai Akio, Toda … Show more authors
Sugai Youta, Tsuchiya Kenji, Kuwahara Victor S., Shimode Shinji, Komatsu Kazuhiro, Imai Akio, Toda Tatsuki Hide authors
JOURNAL OF OCEANOGRAPHY 72 ( 4 ) 577 - 587 2016.8
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Seasonal and regional change in vertical distribution and diet vertical migration of four euphausiid species (Euphausia pacifica, Thysanoessa inspinata, T-longipes, and Tessarabrachion oculatum) in the northwestern Pacific
Sogawa Sayaka, Sugisaki Hiroya, Saito Hiroaki, Okazaki Yuji, Ono Tsuneo, Shimode Shinji, Kikuchi To … Show more authors
Sogawa Sayaka, Sugisaki Hiroya, Saito Hiroaki, Okazaki Yuji, Ono Tsuneo, Shimode Shinji, Kikuchi Tomohiko Hide authors
DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS 109 1 - 9 2016.3
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Typhoon-induced response of phytoplankton and bacteria in temperate coastal waters
Tsuchiya Kenji, Kuwahara Victor S., Hamasaki Koji, Tada Yuya, Ichikawa Tadafumi, Yoshiki Tomoko, Na … Show more authors
Tsuchiya Kenji, Kuwahara Victor S., Hamasaki Koji, Tada Yuya, Ichikawa Tadafumi, Yoshiki Tomoko, Nakajima Ryota, Imai Akio, Shimode Shinji, Toda Tatsuki Hide authors
ESTUARINE COASTAL AND SHELF SCIENCE 167 458 - 465 2015.12
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
New radioisotope-free method for measuring bacterial production using [N-15(5)]-2'-deoxyadenosine and liquid chromatography mass spectrometry (LC-MS) in aquatic environments
Tsuchiya Kenji, Sano Tomoharu, Kawasaki Nobuyuki, Fukuda Hideki, Tomioka Noriko, Hamasaki Koji, Tad … Show more authors
Tsuchiya Kenji, Sano Tomoharu, Kawasaki Nobuyuki, Fukuda Hideki, Tomioka Noriko, Hamasaki Koji, Tada Yuya, Shimode Shinji, Toda Tatsuki, Imai Akio Hide authors
JOURNAL OF OCEANOGRAPHY 71 ( 6 ) 675 - 683 2015.12
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Model tests of the buoyancy-control type ballast-free ship at sea.
Arai, M., Yoneyama, S., Quan, H., Kikuchi, T. and Shimode, S.
12th International Marine Design Conference 2015 569 - 577 2015.5 [Reviewed]
Language：English Publishing type：Research paper (international conference proceedings) Joint Work
-
Short-term variation in the Calanus sinicus ammonium excretion rate during the post-capture period
Kodama Taketoshi, Takahashi Kazutaka, Nakamura Ken-ichi, Shimode Shinji, Yamaguchi Takafumi, Ichika … Show more authors
Kodama Taketoshi, Takahashi Kazutaka, Nakamura Ken-ichi, Shimode Shinji, Yamaguchi Takafumi, Ichikawa Tadafumi Hide authors
PLANKTON & BENTHOS RESEARCH 10 ( 1 ) 75 - 79 2015.3
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Metagenetic community analysis of copepods using high throughput sequencing
Hirai Junya, Shimode Shinji, Kuriyama Mikiko, Ichikawa Tadafumi, Hidaka Kiyotaka, Tsuda Atsushi
Bulletin of the Plankton Society of Japan 62 ( 1 ) 73 - 78 2015.2
Language：English Publishing type：Research paper (scientific journal) Publisher：The Plankton Society of Japan Joint Work
<p>Marine planktonic copepods are an ecologically important group with high species richness and abundance. Here, we propose a metagenetic approach for revealing the community structure of marine planktonic copepods using 454 pyrosequencing of nuclear large subunit ribosomal DNA. We determined an appropriate similarity threshold for clustering pyrosequencing data into molecular operational taxonomic units (MOTUs) using an artificial community containing 33 morphologically identified species. The artificial community was appropriately clustered into MOTUs at 97% similarity, with little inflation in MOTU numbers and with relatively high species-level resolution. Next, we applied the method to field-collected samples, and the results corresponded reasonably well with morphological analysis of these communities. Numbers of MOTUs were well correlated with species richness at 97% similarity, and large numbers of sequence reads were generally observed in MOTUs derived from species with large biomass. Further, MOTUs were successfully classified into taxonomic groups at the family level at 97% similarity; similar patterns of species richness and biomass were revealed within families with metagenetic and morphological analyses. The metagenetic approach reported here can be an effective tool for rapid and comprehensive assessment of copepod community structure. In this paper, we also introduce an example of metagenetic community study of copepods in the tropical and subtropical Pacific.</p>
Other Link： https://ci.nii.ac.jp/naid/130007618105
-
浮力制御方式バラストフリー船の海水交換性能に関する洋上模型実験について
荒井 誠, 若林康太, 菊池知彦, 下出信次
日本船舶海洋工学会論文集 17 177 - 184 2013.6 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Evaluation of ITS2-28S as a molecular marker for identification of calanoid copepods in the subtropical western North Pacific
Hirai Junya, Shimode Shinji, Tsuda Atsushi
JOURNAL OF PLANKTON RESEARCH 35 ( 3 ) 644 - 656 2013.5
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Congruence between euphausiid community and water region in the northwestern Pacific: particularly in the Oyashio-Kuroshio Mixed Water Region
Sogawa Sayaka, Sugisaki Hiroya, Saito Hiroaki, Okazaki Yuji, Shimode Shinji, Kikuchi Tomohiko
JOURNAL OF OCEANOGRAPHY 69 ( 1 ) 71 - 85 2013.2
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Distribution and life history of two planktonic copepods, Rhincalanus nasutus and Rhincalanus rostrifrons, in the northwestern Pacific Ocean.
Shimode, S., Takahashi, K., Shimizu, Y., Nonomura, T. and Tsuda, T.
Deep-Sea Research I 65 133 - 145 2012.7 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
istribution and life history of the planktonic copepod, Eucalanus californicus, in the northwestern Pacific: Mechanisms for population maintenance within a high primary production area.
Shimode, S., Takahashi, K., Shimizu, Y., Nonomura, T. and Tsuda, T.
Progress in Oceanography 96 ( 1 ) 1 - 13 2012.4 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Ecological behavior of the dinoflagellate Ceratium furca in Jangmok harbor of Jinhae Bay, Korea.
Baek, S.H., Shin, H.H., Choi, H.W., Shimode, S., Hwang, O.M., Shin, K., and Kim, Y.O.
Journal of Plankton Research 33 ( 12 ) 1842 - 1846 2011.12 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Meso- and microzooplankton responses to an in situ iron fertilization experiment (SEEDS II) in the northwest subarctic Pacific.
Tsuda, A., Saito, H., Machida, R. J. and Shimode, S.
Deep-Sea Research II 56 2767 - 2778 2009.12 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Life history and ontogenetic vertical migration of Neocalanus gracilis in the western North Pacific Ocean.
Shimode, S., Hirose, Y., Hidaka, K., Takahashi, K. and Tsuda, A.
Aquatic Biology 7 295 - 306 2009.12 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Growth of dinoflagellates, Ceratium furca and Ceratium fusus in Sagami Bay, Japan: The role of vertical migration and cell division
Baek Seung Ho, Shimode Shinji, Shin Kyoungsoon, Han Myung-Soo, Kikuchi Tomohiko
HARMFUL ALGAE 8 ( 6 ) 843 - 856 2009.9 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Temporal changes in chlorophyll a cocentrations and bacterial, viral, and heterotrophic nanoflagellate abundances in the coastal zone of Sagami Bay, Japan: implications of top-down and bottom-up effects
Baki, M.A., Motegi, C., Shibata, A., Fukuda, H., Shimode, S. and Kikuchi, T.
Coastal Marine Science 33 ( 1 ) 29 - 38 2009.8
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
相模湾北西部における栄養塩類およびプランクトン群集の中長期的な動態.
下出信次, 白承鎬, 大曽根智暁, 菊池知彦
月刊海洋 41 ( 2 ) 86 - 97 2009.2
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Strong bottom-up effects on phytoplankton community caused by a rainfall during spring and summer in Sagami Bay, Japan
Baek Seung Ho, Shimode Shinji, Kim Hyun-Cheol, Han Myung-Soo, Kikuchi Tomohiko
JOURNAL OF MARINE SYSTEMS 75 ( 1-2 ) 253 - 264 2009.1
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
The influence of nutrients concentration and the ratio on phytoplankton community structure during late spring and early summer in Sagami Bay, Japan.
Baek, S.H., Shimode, S., Han S.M. and Kikuchi, T.
Algae 7 ( 6 ) 729 - 739 2008.12 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Growth of dinoflagellates, Ceratium furca and Ceratium fusus in Sagami Bay, Japan: The role of nutrients
Baek Seung Ho, Shimode Shinji, Han Myung-Soo, Kikuchi Tomohiko
HARMFUL ALGAE 7 ( 6 ) 729 - 739 2008.10
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
SOUGAWA Hiroshi, SHIMODE Shinji, HASHIMOTO Takashi, KIKUCHI Tomohiko
Japanese Journal of Benthology 63 11 - 22 2008.7
Language：English Publishing type：Research paper (scientific journal) Publisher：JAPANESE ASSOCIATION OF BENTHOLOGY Joint Work
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 a simple cylindrical dredge. In addition, chloroplastic pigment equivalents (from October, 2003, to March, 2004), organic carbon and nitrogen content (in April and June, 2004), and grain size composition (in April, 2004) of the sediment were analyzed. Organic carbon and nitrogen were much higher at St. MP2 than at the other three stations. The sediment samples at St. MP2 frequently included dead fish and shellfish, evidently dumped from a nearby fish market. Station MP2 thus was subject to heavy organic loading. Multivariate community structure analyses using only higher taxonomic levels (phylum, order and/or class) of the meiobenthos did not show significant differences among the stations and sampling months. In contrast, based on species and feeding-types of nematodes, a distinct sample group form St. MP2 was revealed by multidimensional scaling (MDS) and cluster analyses. R-type analysis of the species association of dominant nematodes and correspondence analysis of dominant species and feeding-types of nematodes both also clearly showed the distinctness of the sample group from this station, which mainly consisted of facultative predators collected exclusively there. These results suggest that two species of facultative predators, <i>Meyersia</i> sp. and <i>Metaparoncholaimus</i> sp. belonging to the family Oncholaimidae, and four other nematode species are good indicators of a harbor environment affected by heavy organic loading.
Other Link： https://ci.nii.ac.jp/naid/10027166902
-
Population development of the dinoflagellates Ceratium furca and Ceratium fusus during spring and early summer in Iwa harbor, Sagami Bay, Japan
Baek, S.H., Shimode, S., Han, M.S. and Kikuchi, T.
Ocean Science Journal 43 ( 1 ) 49 - 59 2008.4 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Growth of dinoflagellates, Ceratium furca and Ceratium fusus in Sagami Bay, Japan: The role of temperature, light intensity and photoperiod
Baek Seung Ho, Shimode Shinji, Kikuchi Tomohiko
HARMFUL ALGAE 7 ( 2 ) 163 - 173 2008.2
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Baek Seung Ho, Shimode Shinji, Kikuchi Tomohiko
Journal of oceanography 63 ( 1 ) 35 - 45 2007.2
Language：English Publishing type：Research paper (scientific journal) Publisher：Oceanographic Society of Japan Joint Work
Other Link： https://ci.nii.ac.jp/naid/10018463422
-
Baek, SH; Shimode, S; Kikuchi, T
JOURNAL OF OCEANOGRAPHY 63 ( 1 ) 35 - 45 2007.2
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
生態リスクマネジメントの基本手順と事例比較
松田裕之・浦野紘平，Axel Rossberg，小池文人，雨宮隆，牧野光琢，森野真理，久保隆，下出信次，中井里史，加藤峰夫，茂岡忠義
生物科学 58 41 - 47 2006.7
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Reproductive ecology of dominant dinoflagellate, Ceratium furca, in the coastal area of Sagami Bay
Baek Seung Ho, Shimode Shinji, Kikuchi Tomohiko
Coastal marine science ( 30 ) 344 - 352 2006.4
Language：English Publishing type：Research paper (scientific journal) Publisher：東京大学 Joint Work
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 from April to September and was decreased in November. In particular, the population increased during the spring when the water column was weakly stratified and relatively low nutrient conditions were observed in the surface layer. High growth rates of C. furca were observed at the conditions of 20-28℃, 17-34 PSU and 216-800μEm^<-2>s^<-1> with the highest growth rate (μ=0.72d^<-1>) being observed at 24℃, 30 PSU and 600μEm^<-2>s^<-1>. In addition, the growth rates increased gradually with increasing irradiance from 58 to 216μEm^<-2>s^<-1> in the all salinity conditions, and afterwards the rates reached plateaus between 216 and 796μEm^<-2>s^<-1>. The field survey and laboratory experiments indicated that the species is distributed throughout the year and adapted to a wide-range of environmental fluctuations such as water temperature, salinity, irradiance and nutrients. These specific characteristics make C. furca one of the dominant dinoflagellates in the coastal area.
Other Link： https://ci.nii.ac.jp/naid/110004782877
-
Reproductive strategy of Acartia steueri in Sagami Bay, Japan
Onoue Yasuko, Shimode Shinji, Toda Tatsuki, KIKUCHI Tomohiko
Coastal marine science ( 30 ) 353 - 359 2006.4
Language：English Publishing type：Research paper (scientific journal) Publisher：東京大学 Joint Work
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 experimental period, whereas diapausing ones were restricted from February to August in both years. Population egg production rate (EPR) increased with the abundance of adult males and females from February and reached maximum in June. However, planktonic population of A. steueri did not increase during summer to winter because diapausing eggs occupied a great part of their reproduction (～98%). Recruitment rates in October to December 2002 and September 2003 were higher than population EPR, implying that diapausing eggs of A. steueri had a key role to support the recruitment into water column when the reproductive ability of the population diminished rather than to contribute to an increase of the planktonic population rapidly in their favorable seasons.
Other Link： https://ci.nii.ac.jp/naid/110004782878
-
Free-living Marine Nematodes in the Shallow Area off Manazuru Peninsula in Sagami Bay, Japan
Hashimoto Takashi, Shimode Shinji, Kikuchi Tomohiko
Memoirs of the National Science Museum ( 41 ) 209 - 215 2006.3
Language：English Publishing type：Research paper (scientific journal) Publisher：National Science Museum Joint Work
Other Link： https://ci.nii.ac.jp/naid/110005998868
-
Shimode Senji, Shirayama Yoshihisa
Plankton & benthos research 1 ( 1 ) 42 - 53 2006.2
Language：English Publishing type：Research paper (scientific journal) Publisher：日本プランクトン学会、日本ベントス学会 Joint Work
Seasonal occurrence, diel vertical migration (DVM), biomass (dry weight, carbon and nitrogen contents), growth and behavior of the two phytal-dwelling harpacticoid copepods, <i>Ambunguipes rufocincta</i> and <i>Eudactylops spectabilis</i>, were investigated using field samplings and laboratory experiments. The field samplings were conducted at a subtidal station (St. M; ca. 6.5 m depth) in Tanabe Bay, Japan from March 1999 to January 2000. The results from the field revealed that the two species performed DVM between the water column and macroalgal beds of <i>Colpomenia sinuosa</i> (brown algae), and the seasonal occurrence of the two species at St. M were almost identical to that of <i>C. sinuosa</i>, which bloomed only between December and May. The carbon/nitrogen ratios of <i>A. rufocincta</i> (5.00±0.60) and <i>E. spectabilis</i> (3.95±0.66) differed, probably due to the differences in their foods. Laboratory incubation showed that <i>E. spectabilis</i> needed both <i>C. sinuosa</i> and sediments as food for growth, whereas <i>A. rufocincta</i> that was fed only with the macroalgae was able to grow to maturity. Our results suggested that their DVM behaviors of both species were related to the dispersal of copepodids and adults, because 1) the nauplii grew on <i>C. sinuosa</i>, 2) their main food items were <i>C. sinuosa</i> and sediments, and 3) mating might not be the main purpose of the DVM since females with egg sacs emerged into the water column. Moreover, in later field investigations during summer, refuge populations of <i>A. rufocincta</i> were collected from the seagrass <i>Halophila ovalis</i> in an area shallower than St. M, indicating that <i>A. rufocincta</i> might sustain its population by moving to different habitats though the DVM behavior and changing food items from <i>C. sinuosa</i> to <i>H. ovalis</i> during summer. Therefore, at least for <i>A. rufocincta</i>, the DVM behavior might be indispensable in their life strategy for sustaining their population year round.
Other Link： https://ci.nii.ac.jp/naid/10017410931
-
Spatio-temporal changes in diversity and community structure of planktonic copepods in Sagami Bay, Japan
Shimode S, Toda T, Kikuchi T
MARINE BIOLOGY 148 ( 3 ) 581 - 597 2006.1
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
A guideline for ecological risk management procedures
Rossberg, A.G., Matsuda, H., Koike, F., Amemiya, T., Makino, M., Morino, M., Kubo, T., Shimoide, S. … Show more authors
Rossberg, A.G., Matsuda, H., Koike, F., Amemiya, T., Makino, M., Morino, M., Kubo, T., Shimoide, S., Nakai, S., Katoh, M., Shigeoka, T., and Urano, K. Hide authors
Landscape and Ecological Engineering 1 ( 2 ) 221 - 228 2005.11 [Reviewed]
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Effects of raised CO2 concentration on the egg production rate and early development of two marine copepods (Acartia steueri and Acartia erythraea)
Kurihara H, Shimode S, Shirayama Y
MARINE POLLUTION BULLETIN 49 ( 9-10 ) 721 - 727 2004.11
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Sub-lethal effects of elevated concentration of CO2 on planktonic copepods and sea urchins
Kurihara H, Shimode S, Shirayama Y
JOURNAL OF OCEANOGRAPHY 60 ( 4 ) 743 - 750 2004.8
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Diel changes in vertical distribution of copepods community in Tanabe Bay, Japan
Shimode S, Shirayama Y
JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM 84 ( 3 ) 607 - 615 2004.6
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
夜間水柱内に出現する葉上性ハルパクチコイダ類２種の日周鉛直移動
下出信次, 白山義久
大槌臨海研究センター研究報告 28 13 - 13 2003.3
Language：English Publishing type：Research paper (bulletin of university, research institution) Joint Work
-
Ryocalanus spinifrons, a new species of Ryocalanidae (Copepoda : Calanoida), from the southwestern part of Sagami Bay, Japan
Shimode S, Toda T, Kikuchi T
HYDROBIOLOGIA 432 ( 1-3 ) 127 - 133 2000.8
Language：English Publishing type：Research paper (scientific journal) Joint Work
-
Pelagic Copepods (Crustacea, Maxillopoda) from Neighbouring Sea of Manazuru Peninsula in Sagami Bay
SHIMODE Shinji, TODA Tatsuki, KIKUCHI Tomohiko
Reports of the Manazuru Marine Laboratory for Science Education, Faculty of Education and Human Sciences, Yokohama National University ( 11 ) 1 - 11 1998.3
Language：English Publishing type：Research paper (scientific journal) Publisher：Yokohama National University Joint Work
Ninety species (including 21 unidentyfied and 2 copepodite species) of pelagic copepods (Crustacea, Maxillopoda) from the monthly sampling at station M off Manazuru Peninsula in the northwestern part of Sagami Bay. These species were categorized into 12 seasonal occurrence patterns.
Other Link： https://ci.nii.ac.jp/naid/110006151586