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Chen S, Xie ZX, Yan KQ, Chen JW, Li DX, Wu PF, Peng L, Lin L, Dong CM, Zhao Z, Fan GY, Liu SQ, Herndl GJ, Wang DZ. Functional vertical connectivity of microbial communities in the ocean. SCIENCE ADVANCES 2024; 10:eadj8184. [PMID: 38781332 PMCID: PMC11114224 DOI: 10.1126/sciadv.adj8184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
Abstract
Sinking particles are a critical conduit for the transport of surface microbes to the ocean's interior. Vertical connectivity of phylogenetic composition has been shown; however, the functional vertical connectivity of microbial communities has not yet been explored in detail. We investigated protein and taxa profiles of both free-living and particle-attached microbial communities from the surface to 3000 m depth using a combined metaproteomic and 16S rRNA amplicon sequencing approach. A clear compositional and functional vertical connectivity of microbial communities was observed throughout the water column with Oceanospirillales, Alteromonadales, and Rhodobacterales as key taxa. The surface-derived particle-associated microbes increased the expression of proteins involved in basic metabolism, organic matter processing, and environmental stress response in deep waters. This study highlights the functional vertical connectivity between surface and deep-sea microbial communities via sinking particles and reveals that a considerable proportion of the deep-sea microbes might originate from surface waters and have a major impact on the biogeochemical cycles in the deep sea.
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Affiliation(s)
- Shi Chen
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
| | - Zhang-Xian Xie
- School of Resource and Environmental Sciences, Quanzhou Normal University, Quanzhou 362000, China
| | - Ke-Qiang Yan
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian-Wei Chen
- Qingdao Key Laboratory of Marine Genomics, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao 266555, China
| | - Dong-Xu Li
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Peng-Fei Wu
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Ling Peng
- Qingdao Key Laboratory of Marine Genomics, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
| | - Chun-Ming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen 361005, Fujian, China
| | - Zihao Zhao
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Guang-Yi Fan
- BGI-Shenzhen, Shenzhen 518083, China
- Qingdao Key Laboratory of Marine Genomics, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao 266555, China
| | - Si-Qi Liu
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gerhard J. Herndl
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, 1790 AB Den Burg, Texel, Netherlands
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
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2
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Karthäuser C, Fucile PD, Maas AE, Blanco-Bercial L, Gossner H, Lowenstein DP, Niimi YJ, Van Mooy BAS, Bernhard JM, Buesseler KO, Sievert SM. RotoBOD─Quantifying Oxygen Consumption by Suspended Particles and Organisms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:8760-8770. [PMID: 38717860 PMCID: PMC11112748 DOI: 10.1021/acs.est.4c03186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 05/22/2024]
Abstract
Sinking or floating is the natural state of planktonic organisms and particles in the ocean. Simulating these conditions is critical when making measurements, such as respirometry, because they allow the natural exchange of substrates and products between sinking particles and water flowing around them and prevent organisms that are accustomed to motion from changing their metabolism. We developed a rotating incubator, the RotoBOD (named after its capability to rotate and determine biological oxygen demand, BOD), that uniquely enables automated oxygen measurements in small volumes while keeping the samples in their natural state of suspension. This allows highly sensitive rate measurements of oxygen utilization and subsequent characterization of single particles or small planktonic organisms, such as copepods, jellyfish, or protists. As this approach is nondestructive, it can be combined with several further measurements during and after the incubation, such as stable isotope additions and molecular analyses. This makes the instrument useful for ecologists, biogeochemists, and potentially other user groups such as aquaculture facilities. Here, we present the technical background of our newly developed apparatus and provide examples of how it can be utilized to determine oxygen production and consumption in small organisms and particles.
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Affiliation(s)
- Clarissa Karthäuser
- Woods
Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Paul D. Fucile
- Woods
Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Amy E. Maas
- Bermuda
Institute of Ocean Sciences, Arizona State
University, 17 Biological
Station, St. George’s GE01, Bermuda
| | - Leocadio Blanco-Bercial
- Bermuda
Institute of Ocean Sciences, Arizona State
University, 17 Biological
Station, St. George’s GE01, Bermuda
| | - Hannah Gossner
- Bermuda
Institute of Ocean Sciences, Arizona State
University, 17 Biological
Station, St. George’s GE01, Bermuda
| | - Daniel P. Lowenstein
- Woods
Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Yuuki J. Niimi
- Bermuda
Institute of Ocean Sciences, Arizona State
University, 17 Biological
Station, St. George’s GE01, Bermuda
| | - Benjamin A. S. Van Mooy
- Woods
Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Joan M. Bernhard
- Woods
Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Ken O. Buesseler
- Woods
Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Stefan M. Sievert
- Woods
Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, Falmouth, Massachusetts 02543, United States
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Franco-Cisterna B, Stief P, Glud RN. Hydrostatic pressure impedes the degradation of sinking copepod carcasses and fecal pellets. JOURNAL OF PLANKTON RESEARCH 2024; 46:219-223. [PMID: 38572121 PMCID: PMC10987097 DOI: 10.1093/plankt/fbae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/05/2024] [Indexed: 04/05/2024]
Abstract
Fast-sinking zooplankton carcasses and fecal pellets appear to contribute significantly to the vertical transport of particulate organic carbon (POC), partly because of low temperature that decreases microbial degradation during the descent into the deep ocean. Increasing hydrostatic pressure could further reduce the degradation efficiency of sinking POC, but this effect remains unexplored. Here, the degradation of carcasses and fecal pellets of the abundant marine copepod Calanus finmarchicus was experimentally studied as a function of pressure (0.1-100 MPa). Samples were either exposed to elevated pressure in short 1-day incubations or a gradual pressure increase, simulating continuous particle sinking during a 20-day incubation. Both experiments revealed gradual inhibition of microbial respiration in the pressure range of 20-100 MPa, corresponding to 2-10-km depth. This suggests that hydrostatic pressure impedes carbon mineralization of fast-sinking carcasses and fecal pellets and enhances the deep-sea deposition rate of zooplankton-derived organic material.
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Affiliation(s)
- Belén Franco-Cisterna
- HADAL & Nordcee, Department of Biology, University of Southern Denmark, Odense 5230, Denmark
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen 6708 PB, The Netherlands
| | - Peter Stief
- HADAL & Nordcee, Department of Biology, University of Southern Denmark, Odense 5230, Denmark
| | - Ronnie N Glud
- HADAL & Nordcee, Department of Biology, University of Southern Denmark, Odense 5230, Denmark
- Danish Institute for Advanced Study (DIAS), University of Southern Denmark, Odense 5230, Denmark
- Department of Ocean and Environmental Sciences, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
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Kholssi R, Stefanova S, González-Ortegón E, Araújo CVM, Moreno-Garrido I. Population and functional changes in a multispecies co-culture of marine microalgae and cyanobacteria under a combination of different salinity and temperature levels. MARINE ENVIRONMENTAL RESEARCH 2024; 193:106279. [PMID: 38016302 DOI: 10.1016/j.marenvres.2023.106279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023]
Abstract
Changes in the temperature or salinity of ocean waters can affect marine organisms at multiple trophic levels. Both environmental variables could have an impact on marine microalgae populations. Therefore, the effect of the combination of three levels of temperature (20, 24 and 28 °C), and three levels of salinity (33, 36, and 39 PSU) were evaluated on the growth of a multispecies community of five common species of phytoplankton: (one cyanobacteria, Synechococcus sp., and four microalgae, Chaetoceros gracilis, Amphidinium carterae, Pleurochrysis roscoffensis and Rhodomonas baltica). The co-culture was monitored by flow cytometry under controlled conditions in a 96 h study. The effect of both variables on dissolved oxygen concentrations was measured using the SDR SensorDish Reader system. The results demonstrated that Synechococcus sp., C. gracilis, and A. carterae displayed a high growth at the temperature of 28 °C combined with the lowest salinity assayed. However, salinity increases negatively affected the growth of P. roscoffensis and R. baltica. Decreased salinity combined with decreased temperature exhibited a higher net O2 production. The interaction of two environmental factors related to global change such as temperature and salinity can cause structural (community growth) and functional (net oxygen production) changes in a phytoplanktonic community.
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Affiliation(s)
- Rajaa Kholssi
- Composting Research Group, Faculty of Sciences, University of Burgos, Burgos, Spain; Institute of Marine Sciences of Andalusia (ICMAN-CSIC), Campus Río San Pedro, 11510 Puerto Real, Cádiz, Spain
| | - Sara Stefanova
- Institute of Marine Sciences of Andalusia (ICMAN-CSIC), Campus Río San Pedro, 11510 Puerto Real, Cádiz, Spain
| | - Enrique González-Ortegón
- Institute of Marine Sciences of Andalusia (ICMAN-CSIC), Campus Río San Pedro, 11510 Puerto Real, Cádiz, Spain
| | - Cristiano V M Araújo
- Institute of Marine Sciences of Andalusia (ICMAN-CSIC), Campus Río San Pedro, 11510 Puerto Real, Cádiz, Spain
| | - Ignacio Moreno-Garrido
- Institute of Marine Sciences of Andalusia (ICMAN-CSIC), Campus Río San Pedro, 11510 Puerto Real, Cádiz, Spain.
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Amano C, Reinthaler T, Sintes E, Varela MM, Stefanschitz J, Kaneko S, Nakano Y, Borchert W, Herndl GJ, Utsumi M. A device for assessing microbial activity under ambient hydrostatic pressure: The in situ microbial incubator (ISMI). LIMNOLOGY AND OCEANOGRAPHY, METHODS 2023; 21:69-81. [PMID: 38505832 PMCID: PMC10946486 DOI: 10.1002/lom3.10528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/22/2022] [Accepted: 11/22/2022] [Indexed: 03/21/2024]
Abstract
Microbes in the dark ocean are exposed to hydrostatic pressure increasing with depth. Activity rate measurements and biomass production of dark ocean microbes are, however, almost exclusively performed under atmospheric pressure conditions due to technical constraints of sampling equipment maintaining in situ pressure conditions. To evaluate the microbial activity under in situ hydrostatic pressure, we designed and thoroughly tested an in situ microbial incubator (ISMI). The ISMI allows autonomously collecting and incubating seawater at depth, injection of substrate and fixation of the samples after a preprogramed incubation time. The performance of the ISMI was tested in a high-pressure tank and in several field campaigns under ambient hydrostatic pressure by measuring prokaryotic bulk 3H-leucine incorporation rates. Overall, prokaryotic leucine incorporation rates were lower at in situ pressure conditions than under to depressurized conditions reaching only about 50% of the heterotrophic microbial activity measured under depressurized conditions in bathypelagic waters in the North Atlantic Ocean off the northwestern Iberian Peninsula. Our results show that the ISMI is a valuable tool to reliably determine the metabolic activity of deep-sea microbes at in situ hydrostatic pressure conditions. Hence, we advocate that deep-sea biogeochemical and microbial rate measurements should be performed under in situ pressure conditions to obtain a more realistic view on deep-sea biotic processes.
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Affiliation(s)
- Chie Amano
- Department of Functional and Evolutionary Ecology, Bio‐Oceanography UnitUniversity of ViennaViennaAustria
| | - Thomas Reinthaler
- Department of Functional and Evolutionary Ecology, Bio‐Oceanography UnitUniversity of ViennaViennaAustria
| | - Eva Sintes
- Instituto Español de Oceanografía‐CSIC, Centro Oceanográfico de BalearesPalma de MallorcaSpain
| | - Marta M. Varela
- Instituto Español de Oceanografia‐CSIC, Centro Oceanografico de A CoruñaA CoruñaSpain
| | - Julia Stefanschitz
- Department of Functional and Evolutionary Ecology, Bio‐Oceanography UnitUniversity of ViennaViennaAustria
- Present address:
Marine Evolutionary Ecology, Deep‐Sea Biology Group, GEOMAR Helmholtz Centre for Ocean Research KielKielGermany
| | | | - Yoshiyuki Nakano
- Japan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaJapan
| | | | - Gerhard J. Herndl
- Department of Functional and Evolutionary Ecology, Bio‐Oceanography UnitUniversity of ViennaViennaAustria
- NIOZ, Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research, Utrecht UniversityTexelThe Netherlands
| | - Motoo Utsumi
- Faculty of Life and Environmental SciencesUniversity of TsukubaIbarakiJapan
- Microbiology Research Center for SustainabilityUniversity of TsukubaIbarakiJapan
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6
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Herndl GJ, Bayer B, Baltar F, Reinthaler T. Prokaryotic Life in the Deep Ocean's Water Column. ANNUAL REVIEW OF MARINE SCIENCE 2023; 15:461-483. [PMID: 35834811 DOI: 10.1146/annurev-marine-032122-115655] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The oceanic waters below a depth of 200 m represent, in terms of volume, the largest habitat of the biosphere, harboring approximately 70% of the prokaryotic biomass in the oceanic water column. These waters are characterized by low temperature, increasing hydrostatic pressure, and decreasing organic matter supply with depth. Recent methodological advances in microbial oceanography have refined our view of the ecology of prokaryotes in the dark ocean. Here, we review the ecology of prokaryotes of the dark ocean, present data on the biomass distribution and heterotrophic and chemolithoautotrophic prokaryotic production in the major oceanic basins, and highlight the phylogenetic and functional diversity of this part of the ocean. We describe the connectivity of surface and deep-water prokaryotes and the molecular adaptations of piezophilic prokaryotes to high hydrostatic pressure. We also highlight knowledge gaps in the ecology of the dark ocean's prokaryotes and their role in the biogeochemical cycles in the largest habitat of the biosphere.
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Affiliation(s)
- Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria;
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Burg, The Netherlands
| | - Barbara Bayer
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Federico Baltar
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria;
| | - Thomas Reinthaler
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria;
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7
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Microbial Community Structure and Ecological Networks during Simulation of Diatom Sinking. Microorganisms 2022; 10:microorganisms10030639. [PMID: 35336213 PMCID: PMC8949005 DOI: 10.3390/microorganisms10030639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 11/17/2022] Open
Abstract
Microbial-mediated utilization of particulate organic matter (POM) during its downward transport from the surface to the deep ocean constitutes a critical component of the global ocean carbon cycle. However, it remains unclear as to how high hydrostatic pressure (HHP) and low temperature (LT) with the sinking particles affects community structure and network interactions of the particle-attached microorganisms (PAM) and those free-living microorganisms (FLM) in the surrounding water. In this study, we investigated microbial succession and network interactions in experiments simulating POM sinking in the ocean. Diatom-derived 13C- and 12C-labeled POM were used to incubate surface water microbial communities from the East China Sea (ECS) under pressure (temperature) of 0.1 (25 °C), 20 (4 °C), and 40 (4 °C) MPa (megapascal). Our results show that the diversity and species richness of the PAM and FLM communities decreased significantly with HHP and LT. Microbial community analysis indicated an increase in the relative abundance of Bacteroidetes at high pressure (40 MPa), mostly at the expense of Gammaproteobacteria, Alphaproteobacteria, and Gracilibacteria at atmospheric pressure. Hydrostatic pressure and temperature affected lifestyle preferences between particle-attached (PA) and free-living (FL) microbes. Ecological network analysis showed that HHP and LT enhanced microbial network interactions and resulted in higher vulnerability to networks of the PAM communities and more resilience of those of the FLM communities. Most interestingly, the PAM communities occupied most of the module hubs of the networks, whereas the FLM communities mainly served as connectors of the modules, suggesting their different ecological roles of the two groups of microbes. These results provided novel insights into how HHP and LT affected microbial community dynamics, ecological networks during POM sinking, and the implications for carbon cycling in the ocean.
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Nagata T, Yamada Y, Fukuda H. Transparent Exopolymer Particles in Deep Oceans: Synthesis and Future Challenges. Gels 2021; 7:75. [PMID: 34206532 PMCID: PMC8293251 DOI: 10.3390/gels7030075] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/16/2021] [Accepted: 06/19/2021] [Indexed: 11/17/2022] Open
Abstract
Transparent exopolymer particles (TEP) are a class of abundant gel-like particles that are omnipresent in seawater. While versatile roles of TEP in the regulation of carbon cycles have been studied extensively over the past three decades, investigators have only recently begun to find intriguing features of TEP distribution and processes in deep waters. The emergence of new research reflects the growing attention to ecological and biogeochemical processes in deep oceans, where large quantities of organic carbon are stored and processed. Here, we review recent research concerning the role of TEP in deep oceans. We discuss: (1) critical features in TEP distribution patterns, (2) TEP sources and sinks, and (3) contributions of TEP to the organic carbon inventory. We conclude that gaining a better understanding of TEP-mediated carbon cycling requires the effective application of gel theory and particle coagulation models for deep water settings. To achieve this goal, we need a better recognition and determination of the quantities, turnover, transport, chemical properties, and microbial processing of TEP.
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Affiliation(s)
- Toshi Nagata
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa 277-8564, Japan
| | - Yosuke Yamada
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son 904-0495, Japan;
| | - Hideki Fukuda
- International Coastal Research Center, Atmosphere and Ocean Research Institute, The University of Tokyo, Otsuchi 028-1102, Japan;
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