Researchers Database

Obayashi, Yumiko

    Center for Marine Environmental Studies Assistant Professor
Last Updated :2021/03/05

Researcher Information

Research funding number

  • 60380284

J-Global ID

Research Interests

  • Biogeochemistry   Microbial ecology   物質循環   海洋   

Research Areas

  • Life sciences / Aquaculture
  • Environmental science/Agricultural science / Environmental dynamics

Academic & Professional Experience

  • 2015/08 - Today  Ehime UniversityCenter for Marine Environmental Studies助教
  • 2014/07 - 2015/07  筑波大学 生命・環境系研究員
  • 2009/05 - 2014/06  Yokohama National University Faculty of Engineering研究教員

Association Memberships

  • JAPAN GEOSCIENCE UNION   Association for the Sciences of Limnology and Oceanography   THE JAPANESE SOCIETY OF MICROBIAL ECOLOGY   THE OCEANOGRAPHIC SOCIETY OF JAPAN   日本プランクトン学会   

Published Papers

  • Yumiko Obayashi, Aya Kadoya, Naoto Kataoka, Kazuki Kanda, Su-Min Bak, Hisato Iwata, Satoru Suzuki
    Frontiers in Microbiology 11 2020/08 [Peer-reviewed]
     Scientific journal
  • Walaa Elmasry, Yoko Kebukawa, Takeo Kaneko, Yumiko Obayashi, Hitoshi Fukuda, Yoshiyuki Oguri, Kensei Kobayashi
    Origins of Life and Evolution of Biospheres 50 15 - 33 0169-6149 2020/04 [Peer-reviewed]
     Scientific journal
  • Yumiko Obayashi, Satoru Suzuki
    Plankton and Benthos Research 14 (4) 276 - 286 1880-8247 2019/11 [Peer-reviewed]
     Scientific journal
  • Yukie Narasaki, Yumiko Obayashi, Sayami Ito, Shoko Murakami, Jun-Young Song, Kei Nakayama, Shin-Ichi Kitamura
    Fish Pathology 53 (1) 1 - 9 1881-7335 2018 [Peer-reviewed]
     Scientific journal 
    Miamiensis avidus is the causative agent of scuticociliatosis in various marine fish species. The virulence factors of the parasite have not been identified, so far. In this study, we examined M. avidus extracellular proteinases (ECPs) as potential virulence factors, using culture supernatants as an ECPs source. We investigated the substrate specificity of ECPs using artificial peptides, and the cytotoxicity of the ECPs was examined using CHSE-214 cells. To elucidate the role of ECPs in ciliate growth, M. avidus was cultured on CHSE-214 cells in the presence of proteinase inhibitors. We detected proteinase activities from the supernatant of M. avidus. Viable CHSE-214 cells decreased significantly in number, when incubated in a medium supplemented with the culture supernatant of M. avidus. The growth of ciliates on CHSE-214 cells was delayed in the presence of PMSF (serine proteinase inhibitor) and E-64 (cysteine proteinase inhibitor). These results suggested that the culture supernatant contained ECPs showing cytotoxicity, and the proteinases facilitated nutrient uptake by the ciliates. Thus, ECPs may be responsible for virulence factors of M. avidus.
  • Yumiko Obayashi, Chui Wei Bong, Satoru Suzuki
    FRONTIERS IN MICROBIOLOGY 8 1664-302X 2017/10 [Peer-reviewed]
     Scientific journal 
    Microbial extracellular hydrolytic enzymes that degrade organic matter in aquatic ecosystems play key roles in the biogeochemical carbon cycle. To provide linkages between hydrolytic enzyme activities and genomic or metabolomic studies in aquatic environments, reliable measurements are required for many samples at one time. Extracellular proteases are one of the most important classes of enzymes in aquatic microbial ecosystems, and protease activities in seawater are commonly measured using fluorogenic model substrates. Here, we examined several concerns for measurements of extracellular protease activities (aminopeptidases, and trypsin-type, and chymotrypsin-type activities) in seawater. Using a fluorometric microplate reader with low protein binding, 96-well microplates produced reliable enzymatic activity readings, while use of regular polystyrene microplates produced readings that showed significant underestimation, especially for trypsin-type proteases. From the results of kinetic experiments, this underestimation was thought to be attributable to the adsorption of both enzymes and substrates onto the microplate. We also examined solvent type and concentration in the working solution of oligopeptide-analog fluorogenic substrates using dimethyl sulfoxide (DMSO) and 2-methoxyethanol (MTXE). The results showed that both 2% (final concentration of solvent in the mixture of seawater sample and substrate working solution) DMSO and 2% MTXE provide similarly reliable data for most of the tested substrates, except for some substrates which did not dissolve completely in these assay conditions. Sample containers are also important to maintain the level of enzyme activity in natural seawater samples. In a small polypropylene containers (e.g., standard 50-mL centrifugal tube), protease activities in seawater sample rapidly decreased, and it caused underestimation of natural activities, especially for trypsin-type and chymotrypsin-type proteases. In conclusion, the materials and method for measurements should be carefully selected in order to accurately determine the activities of microbial extracellular hydrolytic enzymes in aquatic ecosystems; especially, low protein binding materials should be chosen to use at overall processes of the measurement.
  • Thi Lan Thanh Bien, Ngo Vy Thao, Shin-Ichi Kitamura, Yumiko Obayashi, Satoru Suzuki
    MICROBES AND ENVIRONMENTS 32 (2) 174 - 179 1342-6311 2017/06 [Peer-reviewed]
     Scientific journal 
    Extracellular DNA (exDNA) is released from bacterial cells through various processes. The antibiotic resistance genes (ARGs) coded on exDNA may be horizontally transferred among bacterial communities by natural transformation. We quantitated the released/leaked tetracycline resistance gene, tet(M) over time under grazing stress by ciliates and heterotrophic nanoflagellates (HNFs), and found that extracellular tet(M) (ex-tetM) increased with bacterial grazing. Separate microcosms containing tet(M)-possessing bacteria with ciliates or HNFs were prepared. The copy number of ex-tetM in seawater in the ciliate microcosm rapidly increased until 3 d after the incubation, whereas that in the HNF microcosm showed a slower increase until 20 d. The copy number of ex-tetM was stable in both cases throughout the incubation period, suggesting that extracellular ARGs are preserved in the environment, even in the presence of grazers. Additionally, ARGs in bacterial cells were constant in the presence of grazers. These results suggest that ARGs are not rapidly extinguished in a marine environment under grazing stress.
  • Ngo Vy Thao, Akino Nozawa, Yumiko Obayashi, Shin-Ichi Kitamura, Taichi Yokokawa, Satoru Suzuki
    MARINE ENVIRONMENTAL RESEARCH 109 95 - 102 0141-1136 2015/08 [Peer-reviewed]
     Scientific journal 
    The biodegradation of proteins in seawater requires various proteases which are commonly thought to be mainly derived from heterotrophic bacteria. We, however, found that protists showed a high protease activity and continuously produced trypsin-type enzymes. The free-living marine heterotrophic ciliate Paranophrys marina together with an associated bacterium was isolated and used for microcosm incubation with different concentrations of killed bacteria as food for 10 days. The results showed that the coexistence of the ciliate with its associated bacterium produced a significant protease activity in both cell-associated and cell-free fractions while that in the associated bacterium only microcosm was negligible. The protease profiles are different between cell-associated and cell-free fractions, and a trypsin-type enzyme hydrolyzing Boc-Val-Leu-Lys-MCA was detected throughout the period in the presence of ciliates. This suggests that ciliates release proteases into the surrounding environment which could play a role in protein digestion outside cells. It has been previously suggested that bacteria are the major transformers in seawater. We here present additional data which indicates that protists, or at least ciliates with their specific enzymes, are a potential player in organic matter degradation in water columns. (C) 2015 Elsevier Ltd. All rights reserved.
  • Ngo V. Thao, Yumiko Obayashi, Taichi Yokokawa, Satoru Suzuki
    Frontiers in Marine Science 1 2296-7745 2014 [Peer-reviewed]
     Scientific journal 
    Proteins constitute the major portion of labile substances in the marine environment and are an important source of organic matter supporting marine ecosystems. However, previous studies have revealed that specific bacterial membrane proteins are refractory in the oceans. We here show by kinetic analyses of protease degradation activity using inactivated Pseudomonas aeruginosa (Pa) cells as a proteinaceous substrate that bacterial proteases are insufficient to completely hydrolyze proteins, which may partially cause the protein accumulation in seawater. Protease activity was monitored simultaneously in 8 microcosms subjected to differing conditions. Some Pa proteins were retained for 30 days in the presence of bacteria without protists, whereas the Pa proteins were completely disappeared in the presence of both, indicating that these proteins were substantially incorporated into protist biomass. Our result suggests that protists play an important role in the transformation of bacterial proteins in seawater. Our experiments also imply that the functional/taxonomic diversity should be taken into account when considering decomposition activity in marine environments.
  • Kensei Kobayashi, Hajime Mita, Hikaru Yabuta, Kazumichi Nakagawa, Yukinori Kawamoto, Takeo Kaneko, Yumiko Obayashi, Kazuhiro Kanda, Satoshi Yoshida, Issay Narumi, Eiichi Imai, Hirofumi Hashimoto, Shin-ichi Yokobori, Akihiko Yamagishi, Tanpopo WG
    Transactions of the Japan Society for Aeronautical and Space Sciences, Aerospace Technology Japan 12 (ists29) Pp_1 - 6 2014 [Peer-reviewed]
  • Jun Kawai, Seema Jagota, Takeo Kaneko, Yumiko Obayashi, Yoshitaka Yoshimura, Bishun N. Khare, David W. Deamer, Christopher P. McKay, Kensei Kobayashi
    International Journal of Astrobiology 12 (4) 282 - 291 1473-5504 2013/10 [Peer-reviewed]
     Scientific journal 
    Abstract Titan, the largest satellite of Saturn, has a thick atmosphere containing nitrogen and methane. A variety of organic compounds have been detected in the atmosphere, most likely produced when atmospheric gases are exposed to ultraviolet light, electrons captured by the magnetosphere of Saturn and cosmic rays. The Cassini/Huygens probe showed that the average temperature on the surface of Titan is 93.7 K, with lakes of liquid ethane and methane. Sub-surface mixtures of liquid ammonia and water may also be present. We have synthesized complex organic compounds (tholins) by exposing a mixture of nitrogen and methane to plasma discharges, and investigated their interactions with several different liquids that simulate Titan's liquidosphere. We found that coacervates formed when tholins were extracted in non-polar solvents followed by exposure to aqueous ammonia solutions. The results suggest that coacervates can self-assemble in Titan's liquidosphere which have the potential to undergo further chemical evolution. Similar processes are likely to occur in the early evolution of habitable planets when tholin-like compounds undergo phase separation into microscopic structures dispersed in a suitable aqueous environment. Copyright © Cambridge University Press 2013Â.
  • Jun Kawai, Seema Jagota, Takeo Kaneko, Yumiko Obayashi, Bishun N. Khare, Christopher P. McKay, Kensei Kobayashi
    CHEMISTRY LETTERS 42 (6) 633 - 635 0366-7022 2013/06 [Peer-reviewed]
     Scientific journal 
    Experimental simulations have previously shown that tholins (complex solid organics) can be abundantly formed in Titan's atmosphere and that they contain precursors of amino acids. In this study, we investigated their relevance to possible chemical evolution toward the generation of life in various potential Titan environments (liquidospheres), using tholins synthesized by plasma discharge at low pressure (LP, 26 Pa) and high pressure (HP, 133 Pa). We focused our study on composition of amino acids recovered from LP and HP tholins, as well as on the solubility of these tholins in solvents such as hexane, acetonitrile, ethanol, methanol, water, and ammonia water. Both hydrolyzed extracts of LP and HP tholins were composed of a wide variety of amino acids. Tholins were dissolved more easily in polar solvents than in nonpolar ones: Ammonia water, simulating a potential Titan subsurface ocean, could dissolve tholins quite efficiently. These results show thus the possibility of starting chemical evolution toward life's origin in Titan's environment.
  • Palash K. Sarker, Jun-ichi Takahashi, Yumiko Obayashi, Takeo Kaneko, Kensei Kobayashi
    ADVANCES IN SPACE RESEARCH 51 (12) 2235 - 2240 0273-1177 2013/06 [Peer-reviewed]
     Scientific journal 
    Aqueous solutions of 5-substituted hydantoins were irradiated with ultraviolet (UV) light, to investigate their structural stability against UV radiation as well as the possible photolysis products. The photolysis products were identified and the degree of photolysis was measured using reversed-phase and ion-exchange high-performance liquid chromatography. Hydantoin (2,4-imidazolidinedione) was dominantly detected as a photolysis product of 5-substituted hydantoins. With hydrolysis of UV-irradiated 5-substituted hydantoins, glycine and alanine were dominantly detected. These experimental results are important for the prebiotic photochemistry of 5-substituted hydantoins in the formation of hydantoin since they have been detected in Solar System materials. (C) 2013 COSPAR. Published by Elsevier Ltd. All rights reserved.
  • Kuhan Chandru, Eiichi Imai, Takeo Kaneko, Yumiko Obayashi, Kensei Kobayashi
    ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES 43 (2) 99 - 108 0169-6149 2013/04 [Peer-reviewed]
     Scientific journal 
    We tested the stability and reaction of several amino acids using hydrothermal system simulators: an autoclave and two kinds of flow reactors at 200-250 A degrees C. This study generally showed that there is a variation in the individual amino acids survivability in the simulators. This is mainly attributed to the following factors; heat time, cold quenching exposure, metal ions and also silica. We observed that, in a rapid heating flow reactor, high aggregation and/or condensation of amino acids could occur even during a heat exposure of 2 min. We also monitored their stability in a reflow-type of simulator for 120 min at 20 min intervals. The non-hydrolyzed and hydrolyzed samples for this system showed a similar degradation only in the absence of metal ions.
  • Formation of amino acid condensates partly having peptide bonds in a simulated submarine hydrothermal environment
    Kuhan Chandru, Yumiko Obayashi, Takeo Kaneko, Kensei Kobayashi
    Viva Origino 41 (3) 24 - 28 2013 [Peer-reviewed]
  • Chui Wei Bong, Yumiko Obayashi, Satoru Suzuki
    AQUATIC MICROBIAL ECOLOGY 69 (1) 33 - 46 0948-3055 2013 [Peer-reviewed]
     Scientific journal 
    Protein biodegradation in the marine environment is caused by proteases derived from various organisms, including bacteria, which are considered to be a major source of these enzymes. We investigated the succession of bacterial proteases in seawater to determine the variation in protease activity over time. The potential activities of proteolytic enzymes in stored seawater and isolated bacteria were studied using 19 different synthetic oligopeptide substrates for aminopeptidase, trypsin, chymotrypsin and elastase. In time-course experiments carried out over 112 d, aminopeptidase activity increased, whereas trypsin activity decreased over time. Amino peptidase activity was mainly found in unfiltered seawater containing bacterial cells, whereas trypsin activity was mainly found in 0.2 mu m seawater filtrates. Individual bacterial isolates showed different proteolytic properties but all exhibited aminopeptidase activity. Members of the Gammaproteobacteria and Bacteroidetes showed high trypsin and chymotrypsin activities. Based on these results, we conclude that protein degradation in seawater occurs via the combined action of various bacterial proteases.
  • Hideharu Kuwahara, Midori Eto, Yukinori Kawamoto, Hironari Kurihara, Takeo Kaneko, Yumiko Obayashi, Kensei Kobayashi
    ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES 42 (6) 533 - 541 0169-6149 2012/12 [Peer-reviewed]
     Scientific journal 
    It is generally thought that the terrestrial atmosphere at the time of the origin of life was CO2-rich and that organic compounds such as amino acids would not have been efficiently formed abiotically under such conditions. It has been pointed out, however, that the previously reported low yields of amino acids may have been partially due to oxidation by nitrite/nitrate during acid hydrolysis. Specifically, the yield of amino acids was found to have increased significantly (by a factor of several hundred) after acid hydrolysis with ascorbic acid as an oxidation inhibitor. However, it has not been shown that CO2 was the carbon source for the formation of the amino acids detected after acid hydrolysis with ascorbic acid. We therefore reinvestigated the prebiotic synthesis of amino acids in a CO2-rich atmosphere using an isotope labeling experiment. Herein, we report that ascorbic acid does not behave as an appropriate oxidation inhibitor, because it contributes amino acid contaminants as a consequence of its reactions with the nitrogen containing species and formic acid produced during the spark discharge experiment. Thus, amino acids are not efficiently formed from a CO2-rich atmosphere under the conditions studied.
  • Hironari Kurihara, Yoshinori Takano, Takeo Kaneko, Yumiko Obayashi, Kensei Kobayashi
    BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 85 (5) 624 - 630 0009-2673 2012/05 [Peer-reviewed]
     Scientific journal 
    Submarine hydrothermal systems (SHSs) have been thought of as a suitable environment for the origin of life subsequent to the abiotic synthesis of organic molecules. However, it has been pointed out that bioorganic molecules, such as amino acids, are easily degraded at a high temperature, and thus not likely to survive for the next step of chemical evolution in a SHS environment. On the other hand, it has been suggested that the main compounds generated abiotically at the first stage of chemical evolution are not "free" amino acid monomers but amino acid precursors with high molecular weights, i.e., complex combined amino acids. In this study, we tested the stability of complex combined amino acids, which were abiotically synthesized from a simulated primitive Earth atmosphere with proton irradiation, in a high-temperature and high-pressure environment compared with that of monomeric amino acids. Complex combined amino acids preserved more amino acids (including amino acid precursors that give amino acids after acid hydrolysis) than free amino acids after heating in simulated SHS environments. Our results suggest the possibility that complex organics prebiotically synthesized by cosmic rays could serve as primitive materials of chemical evolution at hydrothermal systems on primitive Earth.
  • Hironari Kurihara, Hikaru Yabuta, Takeo Kaneko, Yumiko Obayashi, Yoshinori Takano, Kensei Kobayashi
    CHEMISTRY LETTERS 41 (4) 441 - 443 0366-7022 2012/04 [Peer-reviewed]
     Scientific journal 
    We observed formation of organic aggregates from a solution of complex organics which were abiotically synthesized from a simulated primitive earth atmosphere with high-energy protons. The structure of the complex organics was partly altered under hydrothermal conditions to form organic aggregates. The aggregates possessed properties of combined amino acids, which had high tolerance against heating. Formation of this kind of organic aggregates might have been an important step in the chemical evolution leading to the origin of life.
  • Palash K. Sarker, Jun-ichi Takahashi, Yukinori Kawamoto, Yumiko Obayashi, Takeo Kaneko, Kensei Kobayashi
    International Journal of Molecular Sciences 13 (1) 1006 - 1017 1422-0067 2012/01 [Peer-reviewed]
     Scientific journal 
    Aqueous solutions of isovaline and its precursor molecule, 5-ethyl-5-methylhydantoin, were irradiated with ultraviolet and γ-ray photons, to evaluate their structural stability against space radiation. The degree of photolysis was measured and irradiation products were identified using chiral, reversed-phase and ion-exchange high-performance liquid chromatography. The experimental results show that the degree of photolysis of 5-ethyl-5-methylhydantoin is more significant than that of isovaline under ultraviolet light irradiation, while the results under γ-ray irradiation are the opposite. As the products of isovaline photolysis, aspartic acid, serine, glutamic acid and alanine were dominantly detected. © 2012 by the authors licensee MDPI, Basel, Switzerland.
  • Photo-alteration of isovaline and its precursor 5-ethyl-5-methylhydantoin exposed to UV and γ-ray radiation
    Palash K. Sarker, Jun-ichi Takahashi, Yumiko Obayashi, Takeo Kaneko, Kensei Kobayashi
    Viva Origino 40 (2) 4 - 8 2012 [Peer-reviewed]
  • Kensei Kobayashi, Palash K. Sarker, Keisuke Ono, Yukinori Kawamoto, Yumiko Obayashi, Takeo Kaneko, Satoshi Yoshida, Hajime Mita, Hikaru Yabuta, Akihiko Yamagishi
    Transactions of the Japan Society for Aeronautical and Space Sciences 10 (ists28) Tp_7 - 11 2012 [Peer-reviewed]
  • Palash K. Sarker, Jun-ichi Takahashi, Yukinori Kawamoto, Yumiko Obayashi, Takeo Kaneko, Kensei Kobayashi
    INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 13 (1) 1006 - 1017 1661-6596 2012/01 [Peer-reviewed]
     Scientific journal 
    Aqueous solutions of isovaline and its precursor molecule, 5-ethyl-5-methylhydantoin, were irradiated with ultraviolet and gamma-ray photons, to evaluate their structural stability against space radiation. The degree of photolysis was measured and irradiation products were identified using chiral, reversed-phase and ion-exchange high-performance liquid chromatography. The experimental results show that the degree of photolysis of 5-ethyl-5-methylhydantoin is more significant than that of isovaline under ultraviolet light irradiation, while the results under gamma-ray irradiation are the opposite. As the products of isovaline photolysis, aspartic acid, serine, glutamic acid and alanine were dominantly detected.
  • Effect of exposure of zinc at low concentration to bacterial production in seawater
    Chui Wei Bong, Yumiko Obayashi, Satoru Suzuki
    Memoirs of Faculty of Agriculture, Ehime University 56 41 - 45 2011 [Peer-reviewed]
  • Yumiko Obayashi, Nahomi Ueoka, Satoru Suzuki
    JOURNAL OF OCEANOGRAPHY 66 (4) 513 - 521 0916-8370 2010/08 [Peer-reviewed]
     Scientific journal 
    Microbial degradation and utilization of proteins derived from bacterial detritus were investigated in a microcosm experiment using Pseudomonas aeruginosa detritus as a substrate. To assess the effects of natural marine microbial communities on degradation and utilization of protein derived from P. aeruginosa cells, four microcosms were prepared: natural seawater (containing the natural microbial community) with P. aeruginosa detritus (N+Pa), autoclaved seawater with P. aeruginosa detritus (A+Pa), natural seawater (N) and autoclaved seawater (A) without adding anything as a control. The numbers of total and growing bacterial cells, protease activity, and transition of P. aeruginosa proteins were monitored in the four microcosms. Changes in the numbers of total and growing bacterial cells and protease activities indicated that bacterial detritus significantly stimulated the microbial community in the microcosms. Both the surviving P. aeruginosa in A+Pa and natural microbial community in N+Pa microcosms were able to degrade and utilize P. aeruginosa detritus; however, the community in N+Pa including various microbes maintained high activity longer, indicating that diversity is an important factor in keeping the community active. Even under the very high protease activity in N+Pa, 39-kDa and 48-kDa proteins from P. aeruginosa remained in the microcosm during the entire experiment (150 days). Immunoblotting suggested the 48-kDa protein was an intact molecule of OprP, which had been detected from the dissolved fraction of natural seawater in previous studies. This result suggests that the protein molecules that had been detected from natural seawater actually had a high tolerance to microbial degradation.
  • The effect of zinc exposure on the bacteria abundance and proteolytic activity in seawater
    Chui Wei Bong, Francesca Malfatti, Farooq Azam, Yumiko Obayashi, Satoru Suzuki
    Interdisciplinary Studies on Environmental Chemistry, Vol. 3 57 - 63 2010 [Peer-reviewed]
  • Changes in proteolytic activities in stored seawater and bacterial isolates
    Chui Wei Bong, Yumiko Obayashi, Satoru Suzuki
    Interdisciplinary Studies on Environmental Chemistry, Vol. 2 287 - 291 2009 [Peer-reviewed]
  • Kwang-Hyeon Chang, Hideyuki Doi, Yuichiro Nishibe, Yumiko Obayashi, Shin-ichi Nakano
    The Open Marine Biology Journal 3 83 - 88 2009 [Peer-reviewed]
  • Yumiko Obayashi, Satoru Suzuki
    JOURNAL OF OCEANOGRAPHY 64 (3) 367 - 372 0916-8370 2008/06 [Peer-reviewed]
     Scientific journal 
    In aquatic environments extracellular enzymes are bound to microbial cells or exist in a free and adsorbed state. Various filters have been used to fractionate these enzymatic activities, but enzymes may be readily adsorbed onto some materials, and such adsorption can induce errors in the estimation of enzymatic activity. In this study we examined three filters to determine the most suitable filter for fractionation when estimating proteolytic enzyme activity in seawater. We found that the polycarbonate Nuclepore membrane, widely used for size fractionation because of its pore-size accuracy, was the most favorable for this purpose, even though it adsorbed slightly more enzymes than the low-protein-binding polyethersulfone membrane. We also found that trypsin- and chymotrypsin-type enzymes were more easily adsorbed than aminopeptidases.
  • Yumiko Obayashi, Satoru Suzuki
    AQUATIC MICROBIAL ECOLOGY 50 (3) 231 - 237 0948-3055 2008/03 [Peer-reviewed]
     Scientific journal 
    We analyzed potential activities of different proteolytic enzymes in size-fractionated seawater, and estimated the contribution of each size fraction (< 0.2, 0.2-0.8, 0.8-5, and > 5 mu m) to the bulk hydrolytic activity of each enzyme in the seawater. The activity of leucine-aminopeptidase was highly attributed to cell-associated size fractions, while the contribution of the dissolved fraction (< 0.2 mu m) to the bulk activity was only 10 to 30 %. In contrast, the contribution of the dissolved fraction to the activities of the trypsin- and chymotrypsin-type endopeptidases was as high as 40 to 80 % of their bulk activities measured in unfiltered seawater. These results indicated the potential importance of free proteolytic enzymes in seawater, especially for endopeptidases. Significant enzymatic activity in the dissolved fraction was also detected from experiments with isolated bacteria, suggesting that direct secretion of proteases from marine bacteria into surrounding water could be at least one of the sources of the dissolved proteolytic enzymes in seawater. Generally, the natural bacterial community of seawater was able to hydrolyze all of the 16 tested substrates, but at different rates. Selected members of the community (3 bacterial isolates and Synechococcus) hydrolyzed only one or a few of the applied substrates, and the substrate preference varied among the strains. These results suggest that natural bacterial communities are composed of a great variety of bacterial species with different (specific) enzymatic properties, including dissolved endopeptidases and cell-associated aminopeptidase. The combined activities of these enzymes are responsible for an effective degradation and re-use of high molecular weight organic matter at the community level.
  • Hideyuki Doi, Kwang-Hyeon Chang, Yumiko Obayashi, Mizuho Yoshihara, Mary Shime, Takako Yamamoto, Yuichiro Nishibe, Shin-ichi Nakano
    MARINE ECOLOGY PROGRESS SERIES 353 107 - 113 0171-8630 2008 [Peer-reviewed]
     Scientific journal 
    Planktonic food webs are primarily dependent on organic matter derived from phytoplankton. In coastal areas, aquaculture has accelerated in recent decades, and attached algae and invertebrates proliferate on the farming cages. We hypothesized that the organic material on the farm structures is important to planktonic food webs and that the effects of aquaculture differ between fish (fertilized) and pearl oyster farms (not fertilized). To test these hypotheses, we examined the planktonic food webs at fish and pearl oyster farms using stable isotopes in the Uwa Sea, Japan. We collected zooplankton, particulate organic matter (POM, predominantly phytoplankton), attached algae, and macroinvertebrates in July 2005 and February 2006. Based on the isotope mixing model results, the attached microalgae contributed up to approximately 70% of the copepod food sources, and the contribution of attached microalgae to cyclopoid copepods was similar to their contribution to attached macroinvertebrates. Amphipods mainly fed on planktonic detritus from microalgae that had detached from the farm structures. The contribution of attached microalgae to copepod biomass was lower on the pearl oyster farm than on the fish farm. Our results show that attached microalgae from sea farms are important food sources for planktonic food webs in areas with fish farms and that the 2 food webs, attached and pelagic, are coupled through zooplankton grazing.
  • Toshiya Katano, Atsushi Kaneda, Naoto Kanzaki, Yumiko Obayashi, Akihiko Morimoto, Goh Onitsuka, Hideichi Yasuda, Sotaro Mizutani, Yoshihide Kon, Kazuhiro Hata, Hidetaka Takeoka, Shin-ichi Nakan
    AQUATIC MICROBIAL ECOLOGY 46 (2) 191 - 201 0948-3055 2007/02 [Peer-reviewed]
     Scientific journal 
    A 'Kyucho' (an intrusion of warm surface water) occurs in the Bungo Channel, located in southwestern Japan. The abundances of Prochlorococcus and Synechococcus during a Kyucho, together with physical and chemical environmental factors, were investigated from the Kuroshio region to the Seto Inland Sea, via Bungo Channel, from 26 November to 5 December 2003. With the occurrence of the Kyucho, oceanic water intruded from the Kuroshio region into the middle of the Bungo Channel. The abundance of Prochlorococcus was the highest in the Kuroshio region and the southern part of the Bungo Channel (> 25 x 10(3) cells ml(-1)), low in the northern part of the Bungo Channel (< 1 x 10(3) cells ml(-1)), and below detection levels in the Seto Inland Sea. A relatively high abundance of Synechococcus cells (> 15 x 10(3) cells ml(-1)) was detected in the Kuroshio region and in the southern part of the Bungo Channel, but the abundance (< 6 x 10(3) cells ml(-1)) was low in other regions. In the Kuroshio region and the southern part of the Bungo Channel, high-phycourobilin (PUB)-type cells were dominant (> 90%); at this location, most of the available light in the deeper layer (> 25 m depth) was in the 450 to 500 nm range, corresponding to the peak absorbance of PUB. In contrast, the abundance of low-PUB-type cells accounted for > 75% of the total in the northern part of the Bungo Channel and in the Seto Inland Sea, where most of the available light in the deeper layer (> 10 m depth) was in the 480 to 560 nm range, including the peak absorbance of both PUB and phycoerythrobilin (PEB). These results indicate that Synechococcus cells of high-PUB type, which have a higher Ex 495:545 (> 1.5; ratio of orange fluorescence intensity excited at 495 nm to that at 545 nm), as well as Prochlorococcus cells were advected to the Bungo Channel by the Kyucho. The co-occurrence of the 2 pigment types of Synechococcus in coastal waters is highly affected by a physical process, such as the Kyucho.
  • Microbial degradation of organic matter in seawater –Insights from the activity of proteolytic enzymes–
    Yumiko Obayashi, Satoru Suzuki
    Chemical Pollution and Environmental Changes 311 - 313 2007
  • Y Obayashi, S Suzuki
    LIMNOLOGY AND OCEANOGRAPHY 50 (2) 722 - 726 0024-3590 2005/03 [Peer-reviewed]
     Scientific journal 
    We assayed proteolytic enzymes in coastal surface seawater using 16 types of fluorogenic substrates, including those for aminopeptidase, trypsin, elastase, and chymotrypsin. Hydrolysis rates were similar or higher for substrates of trypsin and chymotrypsin than for those of aminopeptidase. Substrates for elastase were hardly hydrolyzed. The results strongly suggest trypsin-type and chymotrypsin-type endopeptidases and aminopeptidases were present in the seawater. In most previous studies of proteolytic enzymes in aquatic environments, leucine-aminopeptidase activity measured using a fluorogenic substrate has been used as a model of proteolytic activity. From the results of this study using various peptide analog fluorogenic substrates, the significance of endopeptidases, which could play a key role in downsizing of dissolved proteins and polypeptides to oligopeptides prior to microbial respiration, was confirmed.
  • Y Obayashi, E Tanoue
    JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY 280 (1-2) 33 - 52 0022-0981 2002/11 [Peer-reviewed]
     Scientific journal 
    Pigment-based growth rates of phytoplankton and mortality rates due to microzooplankton grazing were estimated using a dilution method combined with high-performance liquid chromatography (HPLC) pigment analysis in the northwestern North Pacific in autumn 1998. The dilution experiments were conducted at different hydrographic stations in both colder and warmer water masses. No significant difference was found between the growth rate of the phytoplankton community (0.38-0.70 day(-1); estimated by chlorophyll a) at the colder and warmer water stations, while the mortality rate (0.15-0.88 day(-1); estimated by chlorophyll a) tended to be higher at warmer water stations. The combination of estimates of daily chlorophyll a production and particulate organic carbon (POC) production enabled us to assess the carbon to chlorophyll a ratio (C/chl a) of "new" organic matter produced by living phytoplankton. The method provided an implicit value of the C/chl a of in situ living phytoplankton. The rate estimates from taxon-specific pigments suggested a possibility that chlorophyll b-containing green algae were grazed preferentially by microzooplankton during their active growth, and the standing stock of green algae was more strictly controlled by micrograzer than other algal groups such as diatoms. This result is one possible explanation for the fact that blooms of green algae have not been reported in the open ocean, in contrast with diatoms. (C) 2002 Elsevier Science B.V. All rights reserved.
  • Y Obayashi, E Tanoue, K Suzuki, N Handa, Y Nojiri, CS Wong
    DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS 48 (2) 439 - 469 0967-0637 2001/02 [Peer-reviewed]
     Scientific journal 
    Particulate matter in surface waters of the northern North Pacific and the southern Bering Sea was analyzed for the spatial and temporal distribution of chlorophyll and carotenoid pigment compositions by high-performance liquid chromatography (HPLC). Samples were collected during 11 ship of opportunity cruises between Canada and Japan from April 1995 to June 1996. The cruises each took 13 days and were conducted every six weeks. Seasonal variability of the concentration of chlorophyll a showed different features among the three areas studied: the Alaskan Gyre (eastern part of the subarctic North Pacific), southern Baring Sea, and the area off the Kuril Islands (western part of the subarctic North Pacific). In the Alaskan Gyre, the concentrations of chlorophyll a were around 0.2-0.4 mug/l without any remarkable seasonal variation, consistent with previous studies. In the Bering Sea and the area off the Kuril Islands, a drastic change in chlorophyll a biomass was observed from spring to early summer, with extremely high levels, > 2 mug/l being found. The composition of the phytoplankton community was estimated by multiple regression analysis. A high concentration of chlorophyll a exceeding 1 mug/l was always accompanied by a high contribution of fucoxanthin-containing diatoms constituting up to 90% of the total chlorophyll a biomass, Chlorophyll b-containing green algae were one of the important algal groups in the northern North Pacific throughout the year as were fucoxanthin-containing diatoms and 19'-hexanoyloxyfucoxanthin-containing prymnesiophytes. The results give new insights into the phytoplankton community structure of the subarctic North Pacific, namely, an ubiquitous basic structure made up of rather diverse algal groups, and a flourishing diatom population limited by area and season and superimposed on the basic structure. These two structures are thought to pray their respective roles in the biogeochemical cycle in the surface of the northern North Pacific. (C) 2000 Elsevier Science Ltd. All rights reserved.

Books etc

  • 環境と微生物の辞典
    大林 由美子 (Contributor, 「菌体外酵素」)
    朝倉書店 2014/07

Conference Activities & Talks

  • Responses of bacterial communities and extracellular enzyme activities to addition of protein or free amino acids in the subtropical and subarctic North Pacific  [Not invited]
    PICES-2019 Annual Meeting  2019/10
  • 菌類様原生生物ラビリンチュラ類の細胞外プロテアーゼ  [Not invited]
    大林 由美子, 高尾 祥丈
    2019年日本ベントス学会・日本プランクトン学会合同大会  2019/09
  • Degradation of gelatinous zooplankton carcass by microbial community in seawater  [Not invited]
    PICES-2018 Annual Meeting  2018/10
  • 海水中の微生物群集によるミズクラゲ遺骸とウリクラゲ遺骸の分解  [Not invited]
    大林 由美子, 今中 加奈, 西川 淳
    日本海洋学会 2017年秋季大会  2017/10
  • 真核微生物ラビリンチュラ類の細胞外プロテアーゼプロファイル ~水圏での有機物分解者としてのポテンシャルを探るために~  [Not invited]
    大林 由美子, 高尾 祥丈
    日本微生物生態学会 第31回大会  2016/10
  • Proteolytic enzymes in seawater: contribution of prokaryotes and protists  [Not invited]
    OBAYASHI Yumiko, SUZUKI Satoru
    2016 Ocean Sciences Meeting  2016/02
  • 海洋生態系における微生物と物質循環  [Not invited]
    大林 由美子
    第6回愛媛微生物学ネットワークフォーラム  2015/10
  • 細菌だけではないみたい ―海水中の有機物分解酵素の源―  [Not invited]
    大林 由美子, Ngo Vy Thao, 北村 真一, 横川 太一, 鈴木 聡
    日本海洋学会 2015年春季大会  2015/03
  • 生物活性阻害剤を用いて海水中のタンパク質分解酵素活性の起源を探る  [Not invited]
    大林 由美子, 横川 太一, 鈴木 聡
    環境微生物系学会合同大会2014  2014/10
  • 海水中の有機物分解酵素活性測定:方法論再考  [Not invited]
    大林 由美子, Bong Chui Wei, 鈴木 聡
    日本微生物生態学会 第29回大会  2013/11


  • 『女子中高生夏の学校2015』で海洋学を紹介しました♪
    大林 由美子, 川合 美千代  日本海洋学会ニュースレター  5-  (4)  8  2016/03
  • 海のエッセイ -8-
    大林 由美子  日本海洋学会ニュースレター  5-  (3)  18  -19  2015/11
  • 「女子中高生夏の学校2014 ~科学・技術・人との出会い~」で海洋学を紹介しました♪
    大林 由美子, 川合 美千代, 市川 洋  日本海洋学会ニュースレター  4-  (4)  4  -5  2015/03

Research Grants & Projects

  • 海洋における菌類様原生生物の分布と生態系・有機物動態への寄与
    日本学術振興会:科研費 基盤研究(B)
    Date (from‐to) : 2019/04 -2022/03 
    Author : 大林 由美子
  • 海洋生態系での主要な有機物分解者は従属栄養細菌だけだろうか?
    日本学術振興会:科研費 基盤研究(C)
    Date (from‐to) : 2014/04 -2017/03 
    Author : 大林 由美子
  • 海洋「微生物ループ」への有機物供給メカニズム:名脇役はだれ?
    日本学術振興会:科研費 若手研究(B)
    Date (from‐to) : 2012/04 -2014/03 
    Author : 大林 由美子
  • 海洋細菌群集の共同作業?―水圏の有機物代謝過程での“社会主義”的働き―
    日本学術振興会:科研費 若手研究(B)
    Date (from‐to) : 2009/04 -2012/03 
    Author : 大林 由美子
  • 海洋における高分子溶存有機物の代謝機構に関する研究
    科研費 若手研究(B)
    Date (from‐to) : 2005/04 -2007/03 
    Author : 大林 由美子
  • 水域生態系におけるプロテオーム解析の試み
    Date (from‐to) : 2004/10 -2005/09 
    Author : 大林 由美子




  • 2019, the first semester, under graduate, 環境基礎数学

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