Article
Environmental Sciences
Yuzhuo Liao, Xing Miao, Rui Wang, Ran Zhang, Hai Li, Longshan Lin
Summary: In this study, eDNA metabarcoding was used to analyze the fish biodiversity in the Cosmonaut Sea of East Antarctica. The results showed a higher fish biodiversity than previous studies and the eDNA composition of fish was related to environmental factors. The study demonstrated the potential of eDNA technique as a powerful tool for polar ecology research, especially in the context of climate change.
MARINE ENVIRONMENTAL RESEARCH
(2023)
Article
Environmental Sciences
Zeshu Yu, Marty Kwok-Shing Wong, Jun Inoue, Sk Istiaque Ahmed, Tomihiko Higuchi, Susumu Hyodo, Sachihiko Itoh, Kosei Komatsu, Hiroaki Saito, Shin-ichi Ito
Summary: Using environmental DNA monitoring, we were able to reveal the spatial distribution patterns of small pelagic fishes in the Kuroshio Current system and hypothesize that predator-prey relationships influence their distribution in these fish communities.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Avery McCarthy, Hoda Rajabi, Beverly McClenaghan, Nicole A. Fahner, Emily Porter, Gregory A. C. Singer, Mehrdad Hajibabaei
Summary: Environmental DNA (eDNA)-based methods, particularly next generation sequencing (NGS), have higher sensitivity than qPCR for species detection, and can detect multiple fish species simultaneously from eDNA samples.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Leonie Suter, Andrea Maree Polanowski, Laurence John Clarke, John Andrew Kitchener, Bruce Emerson Deagle
Summary: eDNA metabarcoding is a promising tool for monitoring marine metazoan biodiversity compared to conventional methods. It can detect more zooplankton species, but may have limitations in amplifying non-metazoan organisms. Further refinement and standardization of methodology is needed for its wider application in open ocean biodiversity monitoring.
Article
Engineering, Marine
Hae-Young Choi, Sung Kim
Summary: This study observed hydroids consuming pelagic fish eggs and used COI metabarcoding to identify the predator and prey species. The predator was determined to be Ectopleura crocea, and the prey species were Sillago japonica and Parajulis poecilepterus. Additionally, four arthropod species were consumed.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Cory Dick, Wesley A. Larson, Kirby Karpan, Diana S. Baetscher, Yue Shi, Suresh Sethi, Nann A. Fangue, Mark J. Henderson
Summary: Ration size, temperature, and predator species all influence digestion rate, with ration size having the largest influence. Molecular analyses can identify prey items for a longer period of time compared to visual analysis. Our study suggests that using a small set of controlling variables, it may be possible to model the persistence of prey DNA in predator guts for molecular diet analyses in many fish systems.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Didier Pont, Paul Meulenbroek, Vincenz Bammer, Tony Dejean, Tibor Eros, Pauline Jean, Mirjana Lenhardt, Christoffer Nagel, Ladislav Pekarik, Michael Schabuss, Bernhard C. Stoeckle, Elena Stoica, Horst Zornig, Alexander Weigand, Alice Valentini
Summary: Environmental DNA (eDNA) metabarcoding combined with qPCR can be used to infer the absolute abundance of fish species. A survey in the Danube catchment found a high correlation between total fish eDNA concentrations and total fish abundance. This method can also be used for biomonitoring and bioassessment surveys in large rivers, providing rough estimates of absolute species abundance.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biodiversity Conservation
Manabu Kume, Edouard Lavergne, Hyojin Ahn, Yuki Terashima, Kohmei Kadowaki, Feng Ye, Satoshi Kameyama, Yoshiaki Kai, Yumi Henmi, Yoh Yamashita, Akihide Kasai
Summary: Estuarine and coastal ecosystems are important habitats for many fish species. Patterns of fish communities in these ecosystems are influenced by geographical factors such as latitude and water temperature, as well as human activities. Environmental DNA metabarcoding has provided insights into the structure of these communities, revealing the impact of red-listed and alien species, as well as human population density, on fish diversity. These findings can inform conservation efforts for estuarine and coastal ecosystems.
ECOLOGICAL INDICATORS
(2021)
Article
Biodiversity Conservation
Ida Hartvig, Chatchai Kosawang, Erik Dahl Kjaer, Lene Rostgaard Nielsen
Summary: This study tested the feasibility of using environmental DNA to detect orchid tissue from soil samples and developed species-specific probe-based qPCR assays. Although the assays were highly efficient and specific, orchid DNA was only detected in a subset of samples, mostly in close vicinity to the nearest orchid.
BIODIVERSITY AND CONSERVATION
(2021)
Article
Environmental Sciences
Hye-Eun Kang, Tae-Ho Yoon, Jong-Woo Park, Weol-Ae Lim, Chang-Keun Kang, Hyun-Woo Kim
Summary: This study aimed to investigate the possibility of early warning for Cochlodinium polykrikoides blooms in southern Korean waters using qPCR and metabarcoding analysis. The early warning potential of C. polykrikoides was confirmed through qPCR, and metabarcoding analysis identified microbial organisms related to the blooms. Although no single group could explain the successive blooms, four taxa were found to be related to C. polykrikoides blooms. Additionally, a multi-year metabarcoding analysis revealed differentiation in the phytoplankton community structure.
Article
Environmental Sciences
Annalisa Sambolino, Eva Iniguez, Inma Herrera, Manfred Kaufmann, Ana Dinis, Nereida Cordeiro
Summary: This study investigates the ingestion of microplastics (MPs) and phthalate esters (PAEs) in two fish species and three squid species in an open oceanic region of the Northeast Atlantic. MPs were found in the digestive tract of all species and in the gills and ink sacs of squid. The study identifies gastrosomatic index (GSI) and season as significant predictors of MPs ingestion in fish species, with higher ingestion rates in the cold season and in individuals with higher GSI values.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Biochemistry & Molecular Biology
Wang Cai, Lynsey R. Harper, Erika F. Neave, Peter Shum, Jamie Craggs, Maria Belen Arias, Ana Riesgo, Stefano Mariani
Summary: Large and diverse marine ecosystems present challenges for biodiversity monitoring. Recent studies have shown that sponges can serve as natural samplers for detecting marine vertebrates. However, little is known about the dynamics of eDNA particles in sponge tissue and how effective sponge sampling is compared to water samples. This study found that sponges and water samples have similar detectability for fish, but different sponge species vary in performance. Some sponges are suitable as natural samplers, while others may introduce difficulties in laboratory processing. An initial optimization phase is recommended for future studies using sponges for biodiversity assessment.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Environmental Sciences
Eun-Bi Kim, Hyun Sagong, Ji-Hyun Lee, Gyungryul Kim, Dae-Hyeon Kwon, Yeonghye Kim, Hyun-Woo Kim
Summary: This study analyzed the impact of aggregate mining on fish assemblages and phytoplankton communities using environmental DNA metabarcoding. The results showed significant differences in fish assemblages and phytoplankton between the mining area and its surroundings, indicating the impact of mining activities on marine ecosystems.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Ecology
Annette F. Govindarajan, Rene D. Francolini, J. Michael Jech, Andone C. Lavery, Joel K. Llopiz, Peter H. Wiebe, Weifeng (Gordon) Zhang
Summary: Environmental DNA (eDNA) analysis shows potential for efficiently identifying animal taxa in the ocean's mesopelagic zone, especially those missed by traditional net sampling. Results indicate a significantly higher number of taxa detected per liter of water sampled in eDNA samples, particularly useful for detecting delicate gelatinous animals.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Masaaki Sato, Nariaki Inoue, Ryogen Nambu, Naoki Furuichi, Tomohito Imaizumi, Masayuki Ushio
Summary: The study utilized qMiSeq and echo sounder survey to investigate the distribution of marine fishes at artificial reefs (ARs) and surrounding stations in Tateyama Bay, Japan. The results showed higher fish eDNA quantities at ARs compared to surrounding stations, as well as different fish species compositions between them. Positive correlations were found between fish eDNA concentration and echo intensity, indicating a highly localized signal of eDNA at each sampling station. These findings suggest that qMiSeq is a promising technique to complement conventional methods for monitoring the distributions of multiple fish species.
SCIENTIFIC REPORTS
(2021)
Article
Geosciences, Multidisciplinary
Takaaki Yokoi, Shin-ichi Ito, Enrique Curchitser
Summary: This study examines the seasonal and interannual variability in vertical nutrient supply above the Seychelles Dome in the southwestern tropical Indian Ocean. The results show that seasonal phytoplankton blooms are mainly controlled by vertical processes, with nutrient concentrations increasing during blooming season due to vertical diffusion and entrainment. Interannual variations in nutrient concentrations and surface chlorophyll are strongly related to the intensity of the subsurface Seychelles Dome.
JOURNAL OF MARINE SYSTEMS
(2022)
Review
Oceanography
Chenying Guo, Shin-ichi Ito, Yasuhiro Kamimura, Peng Xiu
Summary: Chub mackerel is an important fisheries target species, and this study used a bioenergetics model to investigate the factors influencing their early life history. The results showed that the growth and migration of chub mackerel are closely related to the prey environment, with individuals experiencing higher growth in better prey fields. The distance between the Kuroshio axis and the Boso Peninsula also affected coastal water temperature and prey species, thereby influencing the early growth of chub mackerel.
PROGRESS IN OCEANOGRAPHY
(2022)
Article
Fisheries
Zhen Lin, Toshihide Kitakado, Naoki Suzuki, Shin-ichi Ito
Summary: The impact of stock enhancement on increasing biomass is not well understood. This study developed a state-space production model to evaluate the impact of stock enhancement on population dynamics. The results showed that the use of valid prior biomass reference data improved the performance of the model. As a case study, the study examined the impact of stock enhancement on Japanese flounder in the Seto Inland Sea and found limited contribution. Future projections showed that stock enhancement was more effective at augmenting biomass under higher fishing pressure, but total biomass decreased simultaneously.
FISHERIES RESEARCH
(2022)
Article
Oceanography
Sebastian Essink, Eric Kunze, Ren-Chieh Lien, Ryuichiro Inoue, Shin-Ichi Ito
Summary: The interaction between near-inertial waves and balanced eddy fields affects the intensity and location of turbulent dissipation and mixing. This study used profiling floats and ray-tracing simulations to investigate the propagation and turbulence characteristics of near-inertial waves near a mesoscale anticyclonic eddy. The results suggest that radial vorticity gradients and Doppler shifting play a major role in governing wave dynamics and turbulence in the eddy region.
JOURNAL OF PHYSICAL OCEANOGRAPHY
(2022)
Article
Ecology
Shinnosuke Kaga, Shigeho Kakehi, Kimiaki Naiki, Takuya Kodama, Taku Wagawa, Satoshi Segawa, Shiho Watanabe, Tatsuya Musashi, Hiroshi Kuroda, Shin-ichi Ito
Summary: An intensive aquaculture industry in Sanriku coastal waters produces a significant amount of Japan's wakame seaweed. This study examined nutrient fluctuations and found that the Tsugaru Warm Current plays a crucial role in nutrient supply to the wakame farms.
REGIONAL STUDIES IN MARINE SCIENCE
(2022)
Article
Oceanography
Shuhao Liu, Yongjun Tian, Yang Liu, Irene D. Alabia, Jiahua Cheng, Shin-ichi Ito
Summary: One major challenge in species distribution models (SDMs) is incorporating the influence of prey on the predator. This study utilizes a prey-predator species distribution model (PPSDM) to predict the habitat of Japanese Spanish mackerel in the China Seas. The PPSDM considers environmental variables such as sea surface temperature, bathymetry, and sea surface current, as well as a biotic variable, the predicted prey distribution (Japanese anchovy). The results show the importance of wintering ground temperature, salinity, and bottom topography in determining the habitat of Japanese Spanish mackerel.
DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY
(2023)
Editorial Material
Fisheries
Steven J. Bograd, Martin Edwards, Shin-ichi Ito, Janet Nye, Emily Chappell
Summary: The journal Fisheries Oceanography serves as a global platform for fisheries scientists and oceanographers to understand the impact of environmental variability and climate change on marine ecosystems and the services they provide to society. In this special issue and the 30th Anniversary Virtual Issue, the journal commemorates 30 years of publishing influential research in the field, showcasing the extent, depth, and impact of their publications. The journal also reflects on the evolution of research themes and highlights emerging themes in the field.
FISHERIES OCEANOGRAPHY
(2023)
Article
Microbiology
Md Mehedi Iqbal, Masahiko Nishimura, Md. Nurul Haider, Susumu Yoshizawa
Summary: This study investigated the microbial community structure and diversity of Zostera marina growing in Futtsu bathing water, Chiba prefecture, Japan. The composition of leaf-attached microbes changed with the relative age of the eelgrass leaf. The microbial communities of marine particles resembled those of eelgrass leaves, suggesting that leaf-attached microbes may derive from suspended particles and move between eelgrass leaves and the water column.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Fisheries
Qinwang Xing, Haiqing Yu, Hui Wang, Shin-ichi Ito, Fei Chai
Summary: Frequent fishing activities are causing overfishing, destroying the habitat of marine life, and threatening global marine biodiversity. Understanding the dynamics of fishing activities and their drivers is crucial for designing and implementing effective ocean management. Global fishing activities primarily targeting tuna were found to be closely related to mesoscale eddies in the global midlatitude ocean, with activities aggregated in anticyclonic eddy cores.
FISH AND FISHERIES
(2023)
Article
Ecology
Shiozaki Takuhei, Yosuke Nishimura, Susumu Yoshizawa, Hideto Takami, Koji Hamasaki, Amane Fujiwara, Shigeto Nishino, Naomi Harada
Summary: Dinitrogen (N-2) fixation is considered to occur only in low-latitude oceans, but recent studies have found that it also occurs in polar regions, indicating it is a global process. This study successfully reconstructed diazotroph genomes from samples in the Arctic Ocean and found that they are highly abundant and play important roles in the Arctic ecosystem and biogeochemical cycles. Diazotrophs in the Arctic Ocean are either Arctic-endemic or cosmopolitan species and have unique gene sets that enable them to adapt to Arctic-specific conditions.
Correction
Ecology
Takuhei Shiozaki, Yosuke Nishimura, Susumu Yoshizawa, Hideto Takami, Koji Hamasaki, Amane Fujiwara, Shigeto Nishino, Naomi Harada
Article
Multidisciplinary Sciences
Ariel Chazan, Ishita Das, Takayoshi Fujiwara, Shunya Murakoshi, Andrey Rozenberg, Ana Molina-Marquez, Fumiya K. Sano, Tatsuki Tanaka, Patricia Gomez-Villegas, Shirley Larom, Alina Pushkarev, Partha Malakar, Masumi Hasegawa, Yuya Tsukamoto, Tomohiro Ishizuka, Masae Konno, Takashi Nagata, Yosuke Mizuno, Kota Katayama, Rei Abe-Yoshizumi, Sanford Ruhman, Keiichi Inoue, Hideki Kandori, Rosa Leon, Wataru Shihoya, Susumu Yoshizawa, Mordechai Sheves, Osamu Nureki, Oded Beja
Summary: Light-harvesting carotenoids, such as zeaxanthin and lutein, transfer energy to the retinal chromophore of xanthorhodopsins and proteorhodopsins, indicating their potential role in rhodopsin phototrophy in lakes, seas, and oceans.
Article
Multidisciplinary Sciences
Keiichi Kojima, Shiho Kawanishi, Yosuke Nishimura, Masumi Hasegawa, Shin Nakao, Yuya Nagata, Susumu Yoshizawa, Yuki Sudo
Summary: Microbial rhodopsins are photoreceptive membrane proteins that exhibit various light-dependent molecular functions. In this study, two channelrhodopsin-like rhodopsins were identified from the alga Vitrella brassicaformis, which are phylogenetically distinct. These rhodopsins function as green- and blue-sensitive pigments and show light-dependent ion channeling activities. One of them, named VbACR2, acts as a monovalent anion channel. This study expands the molecular diversity of anion channelrhodopsins.
SCIENTIFIC REPORTS
(2023)
Article
Chemistry, Medicinal
Marie Kurihara, Vera Thiel, Hirona Takahashi, Keiichi Kojima, David M. Ward, Donald A. Bryant, Makoto Sakai, Susumu Yoshizawa, Yuki Sudo
Summary: In this study, a newly identified rhodopsin called Bellilinea Na+-pumping rhodopsin (BeNaR) was characterized. BeNaR has a significantly higher Na+-pumping activity compared to known Na+-pumping rhodopsin KR2. The findings provide a useful model for studying ion transporters and optogenetic tools.
CHEMICAL & PHARMACEUTICAL BULLETIN
(2023)