Masayuki USHIO
潮雅之

DSc in Biological Sciences
Kyoto University, 2010

Assistant Professor
Department of Ocean Science


Google Scholar
ResearcherID
Scopus ID

Research Interest


  • Biodiversity
  • Marine ecology
  • Fishing and fisheries science and management
  • Microbial food web dynamics
  • Machine learning

Publications



2024 4

Boosting biodiversity monitoring using smartphone-driven, rapidly accumulating community-sourced data

eLife, v. 13, June 2024, article number RP93694
Atsumi, Keisuke; Nishida, Yuusuke; Ushio, Masayuki; Nishi, Hirotaka; Genroku, Takanori; Fujiki, Shogoro
Article

Changes of bacterial versus fungal community composition along a forest degradation gradient of logged-over tropical rain forests, and their consequences on soil enzyme activities in Malaysian Borneo

Plant and Soil, v. 505, (1-2), September 2024, p. 1-23
Jiang, Linzi; Ushio, Masayuki; Imai, Nobuo; Sugau, John; Kitayama, Kanehiro
Article

Do aquatic fungal environmental DNA assemblages reflect the surrounding terrestrial sporocarp communities?

Fungal Ecology, v. 67, February 2024, article number 101311
Sugiyama, Yoriko; Matsuoka, Shunsuke; Shimono, Yoshito; Ushio, Masayuki; Doi, Hideyuki
Article

Plant and soil microbial community assembly processes across urban vacant lots

Journal of Vegetation Science, v. 35, (3), May 2024, article number e13262
Maehara, Kaho; Iwachido, Yuki; Katsuhara, Himari; Tomitaka, Mahoro; Seto, Kensuke; Ushio, Masayuki; Kagami, Maiko; Sasaki, Takehiro
Article
2023 11

Alternative stable states, nonlinear behavior, and predictability of microbiome dynamics

Microbiome, v. 11, (1), March 2023, article number 63
Fujita, Hiroaki; Ushio, Masayuki; Suzuki, Kenta; Abe, Masato S.; Yamamichi, Masato; Iwayama, Koji; Canarini, Alberto; Hayashi, Ibuki; Fukushima, Keitaro; Fukuda, Shinji; Kiers, E. Toby; Toju, Hirokazu
Article

An ecological network approach for detecting and validating influential organisms for rice growth

eLife, v. 12, September 2023, article number RP87202
Ushio, Masayuki; Saito, Hiroki; Tojo, Motoaki; Nagano, Atsushi J.
Article

Changes of soil chemical properties, microbial biomass and enzymatic activities along a gradient of forest degradation in logged over tropical rain forests, Borneo

Plant and Soil, v. 485, (1-2), April 2023, p. 525-536
Jiang, Linzi; Ushio, Masayuki; Kitayama, Kanehiro
Article

Collection of environmental DNA from stemflow for monitoring arboreal biodiversity: Preliminary validation using lichens

MethodsX, v. 11, December 2023, article number 102448
Sakata, Ayumi; Sado, Tetsuya; Oka, Shin-ichiro; Ushio, Masayuki; Miya, Masaki
Article

Computational capability of ecological dynamics

Royal Society Open Science, v. 10, (4), April 2023, article number 221614
Ushio, Masayuki; Watanabe, Kazufumi; Fukuda, Yasuhiro; Tokudome, Yuji; Nakajima, Kohei
Article

Electrical potentials in the ectomycorrhizal fungus Laccaria bicolor after a rainfall event

Fungal Ecology, v. 63, June 2023, article number 101229
Fukasawa, Yu; Akai, Daisuke; Ushio, Masayuki; Takehi, Takayuki
Article

Facilitative interaction networks in experimental microbial community dynamics

Frontiers in Microbiology, v. 14, 11 April 2023, article number 1153952
Fujita, Hiroaki; Ushio, Masayuki; Suzuki, Kenta; Abe, Masato S.; Yamamichi, Masato; Okazaki, Yusuke; Canarini, Alberto; Hayashi, Ibuki; Fukushima, Keitaro; Fukuda, Shinji; Kiers, E. Toby; Toju, Hirokazu
Article

Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics

Frontiers in Microbiology, v. 14, November 2023, article number 1261137
Fujita, Hiroaki; Ushio, Masayuki; Suzuki, Kenta; Abe, Masato S.; Yamamichi, Masato; Okazaki, Yusuke; Canarini, Alberto; Hayashi, Ibuki; Fukushima, Keitaro; Fukuda, Shinji; Kiers, E. Toby; Toju, Hirokazu
Article

Non-destructive collection and metabarcoding of arthropod environmental DNA remained on a terrestrial plant

Scientific Reports, v. 13, (1), May 2023, article number 7125
Yoneya, Kinuyo; Ushio, Masayuki; Miki, Takeshi
Article

Temperature sensitivity of the interspecific interaction strength of coastal marine fish communities

eLife, v. 12, July 2023, article number RP85795
Ushio, Masayuki; Sado, Testuya; Fukuchi, Takehiko; Sasano, Sachia; Masuda, Reiji; Osada, Yutaka; Miya, Masaki
Article

Variations in the reproductive cycle of Bornean montane tree species along elevational gradients on ultrabasic and non-ultrabasic soils

Biotropica, v. 55, (1), January 2023, p. 210-220
Tsujii, Yuki; Sakai, Shoko; Ushio, Masayuki; Aiba, Shin-ichiro; Kitayama, Kanehiro
Article
2022 5

An efficient early-pooling protocol for environmental DNA metabarcoding

Environmental DNA, July 2022
Ushio, Masayuki; Furukawa, Saori; Murakami, Hiroaki; Masuda, Reiji; Nagano, Atsushi J.
Article

Are microbes growing on flowers evil? Effects of old flower microbes on fruit set in a wild ginger with one-day flowers, Alpinia japonica (Zingiberaceae)

Metabarcoding & Metagenomics, v. 6, July 2022, article number e84331, p. 203-214
Elvira, Nuria Jiménez; Ushio, Masayuki; Sakai, Shoko
Article

Contrasting microbial communities on male and female flowers of a dioecious plant, Mallotus japonicus (Euphorbiaceae)

Environmental DNA, v. 4, (3), May 2022, p. 565-579
Marre, Maxime; Ushio, Masayuki; Sakai, Shoko
Article

Interaction capacity as a potential driver of community diversity

Proceedings of the Royal Society B: Biological Sciences, v. 289, (1969), 23 February 2022, article number 20212690
Ushio, Masayuki
Article

The effects of the floral infection by a bacterial pathogen in a dioecious plant, Mallotus japonicus (Euphorbiaceae)

Population Ecology, February 2022
Marre, Maxime; Ushio, Masayuki; Sakai, Shoko
Article
2021 8

Are networks of trophic interactions sufficient for understanding the dynamics of multi-trophic communities? Analysis of a tri-trophic insect food-web time-series

Ecology Letters, v. 24, (3), March 2021, p. 543-552
Kawatsu, Kazutaka; Ushio, Masayuki; van Veen, F.J.Frank; Kondoh, Michio
Article

Causal analysis of the temperature impact on deep-sea biodiversity

Biology Letters, v. 17, (7), July 2021, article number 0666
Doi, Hideyuki; Yasuhara, Moriaki; Ushio, Masayuki
Article

Evaluation of seasonal dynamics of fungal DNA assemblages in a flow-regulated stream in a restored forest using eDNA metabarcoding

Environmental Microbiology, v. 23, (8), August 2021, p. 4797-4806
Matsuoka, Shunsuke; Sugiyama, Yoriko; Shimono, Yoshito; Ushio, Masayuki; Doi, Hideyuki
Article

Quantitative assessment of multiple fish species around artificial reefs combining environmental DNA metabarcoding and acoustic survey

Scientific Reports, v. 11, (1), September 2021, article number 19477
Sato, Masaaki; Inoue, Nariaki; Nambu, Ryogen; Furuichi, Naoki; Imaizumi, Tomohito; Ushio, Masayuki
Article

Reconstructing large interaction networks from empirical time series data

Ecology Letters, v. 24, (12), December 2021, p. 2763-2774
Chang, Chun-Wei; Miki, Takeshi; Ushio, Masayuki; Ke, Po-Ju; Lu, Hsiao-Pei; Shiah, Fuh-Kwo; Hsieh, Chih-hao
Article

Temperature is a dominant driver of distinct annual seasonality of leaf litter production of equatorial tropical rain forests

Journal of Ecology, v. 109, (2), February 2021, p. 727-736
Kitayama, Kanehiro; Ushio, Masayuki; Aiba, Shin-Ichiro
Article

海洋堆積物に残存する環境DNAを用いた魚類相把握の試み

水環境学会誌, v. 44, (4), July 2021, p. 79-84
白垣友寛; 井上拓; 福田秀樹; 潮雅之; 日下美樹; 岡野孝哉; 高巣裕之
Article

哺乳類の検出

環境DNA: 生態系の真の姿を読み解く / 一般社団法人 環境DNA学会 企画; 土居 秀幸、近藤 倫生 編. 日本東京 : 共立出版, 2021, p. 204-216, Ch. 5.6
潮雅之
Book chapter
2020 11

Complementary molecular methods reveal comprehensive phylogenetic diversity integrating inconspicuous lineages of early-diverged wood-decaying mushrooms

Scientific Reports, v. 10, (1), February 2020, article number 3057
Shirouzu, Takashi; Matsuoka, Shunsuke; Doi, Hideyuki; Nagata, Nobuaki; Ushio, Masayuki; Hosaka, Kentaro
Article

Dynamic and synergistic influences of air temperature and rainfall on general flowering in a Bornean lowland tropical forest

Ecological Research, v. 35, (1), January 2020, p. 17-29
Ushio, Masayuki; Osada, Yutaka; Kumagai, Tomo'omi; Kume, Tomonori; Pungga, Runi anak Sylvester; Nakashizuka, Tohru; Itioka, Takao; Sakai, Shoko
Article

Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population

Molecular Ecology Resources, v. 20, (5), September 2020, p. 1248-1258, Special Issue: Special Feature: Genomics of Natural History Collections for Understanding Evolution in the Wild
Tsuji, Satsuki; Maruyama, Atsuhi; Miya, Masaki; Ushio, Masayuki; Sato, Hirotoshi; Minamoto, Toshifumi; Yamanaka, Hiroki
Article

Environmental DNA metabarcoding reveals the presence of a small, quick-moving, nocturnal water shrew in a forest stream

Conservation Genetics, v. 21, (6), December 2020, p. 1079-1084
Yonezawa, Satoru; Ushio, Masayuki; Yamanaka, Hiroki; Miya, Masaki; Takayanagi, Atsushi; Isagi, Yuji
Article

Evaluating intraspecific genetic diversity using environmental DNA and denoising approach: A case study using tank water

Environmental DNA, v. 2, (1), January 2020, p. 42-52
Tsuji, Satsuki; Miya, Masaki; Ushio, Masayuki; Sato, Hirotoshi; Minamoto, Toshifumi; Yamanaka, Hiroki
Article

Idea paper: Predicting culturability of microbes from population dynamics under field conditions

Ecological Research, v. 35, (4), July 2020, p. 586-590
Ushio, Masayuki
Article

Influence of potential grazers on picocyanobacterial abundance in Lake Biwa revealed with empirical dynamic modeling

Inland Waters, v. 10, (3), February 2020, p. 386-396
Cai, Ji; Hodoki, Yoshikuni; Ushio, Masayuki; Nakano, Shin-ichi
Article

Quantitative evaluation of intraspecific genetic diversity in a natural fish population using environmental DNA analysis

Molecular Ecology Resources, v. 20, (5), September 2020, p. 1323-1332, Special Issue: Special Feature: Genomics of Natural History Collections for Understanding Evolution in the Wild
Tsuji, Satsuki; Shibata, Naoki; Sawada, Hayato; Ushio, Masayuki
Article

Repressive chromatin modification underpins the long-term expression trend of a perennial flowering gene in nature

Nature Communications, v. 11, (1), May 2020, article number 2065
Nishio, Haruki; Buzas, Diana M.; Nagano, Atsushi J.; Iwayama, Koji; Ushio, Masayuki; Kudoh, Hiroshi
Article

A data-driven approach to complex ecological systems

Theoretical Ecology: concepts and applications / edited by Kevin S. McCann, Gabriel Gellner. Oxford, UK : Oxford University Press, 2020, p. 116-133, Ch. 8
Kondoh, Michio; Kawatsu, Kazutaka; Osada, Yutaka; Ushio, Masayuki
Book chapter

Forecasting Ecological Time Series Using Empirical Dynamic Modeling: A Tutorial for Simplex Projection and S-map

Diversity of Functional Traits and Interactions: Perspectives on Community Dynamics / edited by Akihiko Mougi. Singapore : Springer, 2020, p. 193-213, Book series: Theoretical Biology
Ushio, Masayuki; Kawatsu, Kazutaka
Book chapter
2019 2

Seasonal and long-term patterns in litterfall in a Bornean tropical rainforest

Ecological Research, v. 34, (1), January 2019, p. 31-39
Nakagawa, Michiko; Ushio, Masayuki; Kume, Tomonori; Nakashizuka, Tohru
Article

Use of a filter cartridge combined with intra-cartridge bead-beating improves detection of microbial DNA from water samples

Methods in Ecology and Evolution, v. 10, (8), August 2019, p. 1142-1156
Ushio, Masayuki
Article
2018 4

Core microbiomes for sustainable agroecosystems

Nature Plants, v. 4, (5), May 2018, p. 247-257
Toju, Hirokazu; Peay, Kabir G.; Yamamichi, Masato; Narisawa, Kazuhiko; Hiruma, Kei; Naito, Ken; Fukuda, Shinji; Ushio, Masayuki; Nakaoka, Shinji; Onoda, Yusuke; Yoshida, Kentaro; Schlaeppi, Klaus; Bai, Yang; Sugiura, Ryo; Ichihashi, Yasunori; Minamisawa, Kiwamu; Kiers, E. Toby
Article

Demonstration of the potential of environmental DNA as a tool for the detection of avian species

Scientific Reports, v. 8, (1), 14 March 2018, article number 4493
Ushio, Masayuki; Murata, Koichi; Sado, Tetsuya; Nishiumi, Isao; Takeshita, Masamichi; Iwasaki, Wataru; Miya, Masaki
Article

Fluctuating interaction network and time-varying stability of a natural fish community

Nature, v. 554, (7692), 15 February 2018, p. 360-363
Ushio, Masayuki; Hsieh, Chih-Hao; Masuda, Reiji; Deyle, Ethan R.; Ye, Hao; Chang, Chun-Wei; Sugihara, George; Kondoh, Michio
Article

Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing

Metabarcoding and Metagenomics, v. 2, March 2018, article number e23297
Ushio, Masayuki; Murakami, Hiroaki; Masuda, Reiji; Sado, Tetsuya; Miya, Masaki; Sakurai, Sho; Yamanaka, Hiroki; Minamoto, Toshifumi; Kondoh, Michio
Article
2017 8

A lognormal distribution of the lengths of terminal twigs on self-similar branches of elm trees

Proceedings of the Royal Society B: Biological Sciences, v. 284, (1846), January 2017, article number 20162395
Koyama, Kohei; Yamamoto, Ken; Ushio, Masayuki
Article

Empirical dynamic modeling for beginners

Ecological Research, v. 32, (6), November 2017, p. 785-796
Chang, Chun-Wei; Ushio, Masayuki; Hsieh, Chih-hao
Article

Environmental DNA enables detection of terrestrial mammals from forest pond water

Molecular Ecology Resources, v. 17, (6), November 2017, p. e63-e75
Ushio, Masayuki; Fukuda, Hisato; Inoue, Toshiki; Makoto, Kobayashi; Kishida, Osamu; Sato, Keiichi; Murata, Koichi; Nikaido, Masato; Sado, Tetsuya; Sato, Yukuto; Takeshita, Masamichi; Iwasaki, Wataru; Yamanaka, Hiroki; Kondoh, Michio; Miya, Masaki
Article

Plant-soil feedbacks and the dominance of conifers in a tropical montane forest in Borneo

Ecological Monographs, v. 87, (1), February 2017, p. 105-129
Ushio, Masayuki; Aiba, Shin-Ichiro; Takeuchi, Yayoi; Iida, Yoshiko; Matsuoka, Shunsuke; Repin, Rimi; Kitayama, Kanehiro
Article

Tropical-forest mammals as detected by environmental DNA at natural saltlicks in Borneo

Biological Conservation, v. 210, (Part A), June 2017, p. 281-285
Ishige, Taichiro; Miya, Masaki; Ushio, Masayuki; Sado, Tetsuya; Ushioda, Masaharu; Maebashi, Kaori; Yonechi, Risako; Lagan, Peter; Matsubayashi, Hisashi
Article

Water temperature-dependent degradation of environmental DNA and its relation to bacterial abundance

PLoS ONE, v. 12, (4), April 2017, article number e0176608
Tsuji, Satsuki; Ushio, Masayuki; Sakurai, Sho; Minamoto, Toshifumi; Yamanaka, Hiroki
Article

マキ科・ナンヨウスギ科の根の形態・菌根菌・窒素固定活性

日本生態学会誌, v. 67, (3), December 2017, p. 339-345
潮雅之
Article

陸上生態系において球果類の優占度を決定するメカニズム

日本生態学会誌, v. 67, (3), December 2017, p. 355-360
相場慎一郎; 宮本和樹; 潮雅之; 青柳亮太; 澤田佳美
Article
2016 1

Social and ecological factors associated with the use of non-timber forest products by people in rural Borneo

Biological Conservation, v. 204, (Part B), December 2016, p. 340-349
Sakai, Shoko; Choy, Yee Keong; Kishimoto-Yamada, Keiko; Takano, Kohei T.; Ichikawa, Masahiro; Samejima, Hiromitsu; Kato, Yumi; Soda, Ryoji; Ushio, Masayuki; Saizen, Izuru; Nakashizuka, Tohru; Itioka, Takao
Article
2015 4

Effect of water depth on predation frequency by diving beetles on mosquito larvae prey

Entomological Science, v. 18, (4), October 2015, p. 519-522
Ohba, Shin-ya; Ushio, Masayuki
Article

High contribution of Synechococcus to phytoplankton biomass in the aphotic hypolimnion in a deep freshwater lake (Lake Biwa, Japan)

Aquatic Microbial Ecology, v. 75, (1), May 2015, p. 69-79
Takasu, Hiroyuki; Ushio, Masayuki; LeClair, Jessica E.; Nakano, Shin-Ichi
Article

Linkage of root physiology and morphology as an adaptation to soil phosphorus impoverishment in tropical montane forests

Functional Ecology, v. 29, (9), September 2015, p. 1235-1245
Ushio, Masayuki; Fujiki, Yasuto; Hidaka, Armane; Kitayama, Kanehiro
Article

Microbial communities on flower surfaces act as signatures of pollinator visitation

Scientific Reports, v. 5, March 2015, article number 8695
Ushio, Masayuki; Yamasaki, Eri; Takasu, Hiroyuki; Nagano, Atsushi J.; Fujinaga, Shohei; Honjo, Mie N.; Ikemoto, Mito; Sakai, Shoko; Kudoh, Hiroshi
Article
2014 2

Herbivorous insect decreases plant nutrient uptake: The role of soil nutrient availability and association of below-ground symbionts

Ecological Entomology, v. 39, (4), August 2014, p. 511-518
Katayama, Noboru; Silva, Alessandro O.; Kishida, Osamu; Ushio, Masayuki; Kita, Satoshi; Ohgushi, Takayuki
Article

High-throughput sequencing shows inconsistent results with a microscope-based analysis of the soil prokaryotic community

Soil Biology and Biochemistry, v. 76, September 2014, p. 53-56
Ushio, Masayuki; Makoto, Kobayashi; Klaminder, Jonatan; Takasu, Hiroyuki; Nakano, Shin-Ichi
Article
2013 4

A coexisting fungal-bacterial community stabilizes soil decomposition activity in a microcosm experiment

PLoS ONE, v. 8, (11), November 2013, article number e80320
Ushio, Masayuki; Miki, Takeshi; Balser, Teri C.
Article

CARD-FISH analysis of prokaryotic community composition and abundance along small-scale vegetation gradients in a dry arctic tundra ecosystem

Soil Biology and Biochemistry, v. 64, September 2013, p. 147-154
Ushio, Masayuki; Makoto, Kobayashi; Klaminder, Jonatan; Nakano, Shin-Ichi
Article

Effects of condensed tannins in conifer leaves on the composition and activity of the soil microbial community in a tropical montane forest

Plant and Soil, v. 365, (1-2), April 2013, p. 157-170
Ushio, Masayuki; Balser, Teri C.; Kitayama, Kanehiro
Article

Predator-prey body size relationships when predators can consume prey larger than themselves

Biology Letters, v. 9, (3), June 2013, article number 20121193
Nakazawa, Takefumi; Ohba, Shin-ya; Ushio, Masayuki
Article
2012 1

Dynamic Scaling in the Growth of a Non-Branching Plant, Cardiocrinum cordatum

PLoS ONE, v. 7, (9), September 2012, article number e45317
Koyama, Kohei; Hidaka, Yoshiki; Ushio, Masayuki
Article
2011 4

A meta-analysis of the global distribution pattern of condensed tannins in tree leaves

Open Ecology Journal, v. 4, December 2011, p. 18-23
Ushio, Masayuki; Adams, Jonathan M.
Article

In situ enzyme activity in the dissolved and particulate fraction of the fluid from four pitcher plant species of the genus Nepenthes

PLoS ONE, v. 6, (9), September 2011, article number e25144
Takeuchi, Yayoi; Salcher, Michaela M.; Ushio, Masayuki; Shimizu-Inatsugi, Rie; Kobayashi, Masaki J.; Diway, Bibian; von Mering, Christian; Pernthaler, Jakob; Shimizu, Kentaro K.
Article

Scale Dependence of Predator-Prey Mass Ratio. Determinants and Applications

The Role of Body Size in Multispecies Systems / Edited by Andrea Belgrano. Amsterdam, The Netherlands : Academic Press, 2011, p. 269-302, Book series: Advances in Ecological Research, v. 45
Nakazawa, Takefumi; Ushio, Masayuki; Kondoh, Michio
Book chapter

The ecology of podocarps in tropical montane forests of Borneo: distribution, population dynamics, and soil nutrient acquisition

Ecology of the Podocarpaceae in Tropical Forests / edited by Turner, Benjamin L. and Cernusak, Lucas A.. Washington, D.C. : Smithsonian Institution Scholarly Press, 2011, p. 101-117, Ch. 6. Smithsonian Contributions to Botany, number 95
Kitayama, Kanehiro; Aiba, Shin-ichiro; Ushio, Masayuki; Seino, Tatsuyuki; Fujiki, Yasuto
Book chapter
2010 3

Functional diversity of microbial decomposers facilitates plant coexistence in a plant-microbe-soil feedback model

Proceedings of the National Academy of Sciences of the United States of America, v. 107, (32), July 2010, p. 14251-14256
Miki, Takeshi; Ushio, Masayuki; Fukui, Shin; Kondoh, Michio
Article

Tree species effects on soil enzyme activities through effects on soil physicochemical and microbial properties in a tropical montane forest on Mt. Kinabalu, Borneo

Pedobiologia, v. 53, (4), July 2010, p. 227-233
Ushio, Masayuki; Kitayama, Kanehiro; Balser, Teri C.
Article

Tree species-mediated spatial patchiness of the composition of microbial community and physicochemical properties in the topsoils of a tropical montane forest

Soil Biology and Biochemistry, v. 42, (9), September 2010, p. 1588-1595
Ushio, Masayuki; Kitayama, Kanehiro; Balser, Teri C.
Article
2009 1

Phenolic control of plant nitrogen acquisition through the inhibition of soil microbial decomposition processes: A plant-microbe competition model

Microbes and Environments, v. 24, (2), April 2009, p. 180-187
Ushio, Masayuki; Miki, Takeshi; Kitayama, Kanehiro
Article
2008 1

Variations in the soil microbial community composition of a tropical montane forest ecosystem: Does tree species matter?

Soil Biology and Biochemistry, v. 40, (10), October 2008, p. 2699-2702
Ushio, Masayuki; Wagai, Rota; Balser, Teri C.; Kitayama, Kanehiro
Article
2007 1

熱帯降⾬林の⽣態系ー樹⽊と微⽣物の協奏曲

生物の多様性ってなんだろう?: 生命のジグソーパズル / 京都大学総合博物館・京都大学生態学研究センター 編. 日本京都 : 京都大学学術出版会, 2007, p. 250-272, 学術選書 027
北山兼弘; 潮雅之; 和穎朗太
Book chapter
Article 4

Boosting biodiversity monitoring using smartphone-driven, rapidly accumulating community-sourced data

eLife, v. 13, June 2024, article number RP93694
Atsumi, Keisuke; Nishida, Yuusuke; Ushio, Masayuki; Nishi, Hirotaka; Genroku, Takanori; Fujiki, Shogoro

Changes of bacterial versus fungal community composition along a forest degradation gradient of logged-over tropical rain forests, and their consequences on soil enzyme activities in Malaysian Borneo

Plant and Soil, v. 505, (1-2), September 2024, p. 1-23
Jiang, Linzi; Ushio, Masayuki; Imai, Nobuo; Sugau, John; Kitayama, Kanehiro

Do aquatic fungal environmental DNA assemblages reflect the surrounding terrestrial sporocarp communities?

Fungal Ecology, v. 67, February 2024, article number 101311
Sugiyama, Yoriko; Matsuoka, Shunsuke; Shimono, Yoshito; Ushio, Masayuki; Doi, Hideyuki

Plant and soil microbial community assembly processes across urban vacant lots

Journal of Vegetation Science, v. 35, (3), May 2024, article number e13262
Maehara, Kaho; Iwachido, Yuki; Katsuhara, Himari; Tomitaka, Mahoro; Seto, Kensuke; Ushio, Masayuki; Kagami, Maiko; Sasaki, Takehiro
Article 11

Alternative stable states, nonlinear behavior, and predictability of microbiome dynamics

Microbiome, v. 11, (1), March 2023, article number 63
Fujita, Hiroaki; Ushio, Masayuki; Suzuki, Kenta; Abe, Masato S.; Yamamichi, Masato; Iwayama, Koji; Canarini, Alberto; Hayashi, Ibuki; Fukushima, Keitaro; Fukuda, Shinji; Kiers, E. Toby; Toju, Hirokazu

An ecological network approach for detecting and validating influential organisms for rice growth

eLife, v. 12, September 2023, article number RP87202
Ushio, Masayuki; Saito, Hiroki; Tojo, Motoaki; Nagano, Atsushi J.

Changes of soil chemical properties, microbial biomass and enzymatic activities along a gradient of forest degradation in logged over tropical rain forests, Borneo

Plant and Soil, v. 485, (1-2), April 2023, p. 525-536
Jiang, Linzi; Ushio, Masayuki; Kitayama, Kanehiro

Collection of environmental DNA from stemflow for monitoring arboreal biodiversity: Preliminary validation using lichens

MethodsX, v. 11, December 2023, article number 102448
Sakata, Ayumi; Sado, Tetsuya; Oka, Shin-ichiro; Ushio, Masayuki; Miya, Masaki

Computational capability of ecological dynamics

Royal Society Open Science, v. 10, (4), April 2023, article number 221614
Ushio, Masayuki; Watanabe, Kazufumi; Fukuda, Yasuhiro; Tokudome, Yuji; Nakajima, Kohei

Electrical potentials in the ectomycorrhizal fungus Laccaria bicolor after a rainfall event

Fungal Ecology, v. 63, June 2023, article number 101229
Fukasawa, Yu; Akai, Daisuke; Ushio, Masayuki; Takehi, Takayuki

Facilitative interaction networks in experimental microbial community dynamics

Frontiers in Microbiology, v. 14, 11 April 2023, article number 1153952
Fujita, Hiroaki; Ushio, Masayuki; Suzuki, Kenta; Abe, Masato S.; Yamamichi, Masato; Okazaki, Yusuke; Canarini, Alberto; Hayashi, Ibuki; Fukushima, Keitaro; Fukuda, Shinji; Kiers, E. Toby; Toju, Hirokazu

Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics

Frontiers in Microbiology, v. 14, November 2023, article number 1261137
Fujita, Hiroaki; Ushio, Masayuki; Suzuki, Kenta; Abe, Masato S.; Yamamichi, Masato; Okazaki, Yusuke; Canarini, Alberto; Hayashi, Ibuki; Fukushima, Keitaro; Fukuda, Shinji; Kiers, E. Toby; Toju, Hirokazu

Non-destructive collection and metabarcoding of arthropod environmental DNA remained on a terrestrial plant

Scientific Reports, v. 13, (1), May 2023, article number 7125
Yoneya, Kinuyo; Ushio, Masayuki; Miki, Takeshi

Temperature sensitivity of the interspecific interaction strength of coastal marine fish communities

eLife, v. 12, July 2023, article number RP85795
Ushio, Masayuki; Sado, Testuya; Fukuchi, Takehiko; Sasano, Sachia; Masuda, Reiji; Osada, Yutaka; Miya, Masaki

Variations in the reproductive cycle of Bornean montane tree species along elevational gradients on ultrabasic and non-ultrabasic soils

Biotropica, v. 55, (1), January 2023, p. 210-220
Tsujii, Yuki; Sakai, Shoko; Ushio, Masayuki; Aiba, Shin-ichiro; Kitayama, Kanehiro
Article 5

An efficient early-pooling protocol for environmental DNA metabarcoding

Environmental DNA, July 2022
Ushio, Masayuki; Furukawa, Saori; Murakami, Hiroaki; Masuda, Reiji; Nagano, Atsushi J.

Are microbes growing on flowers evil? Effects of old flower microbes on fruit set in a wild ginger with one-day flowers, Alpinia japonica (Zingiberaceae)

Metabarcoding & Metagenomics, v. 6, July 2022, article number e84331, p. 203-214
Elvira, Nuria Jiménez; Ushio, Masayuki; Sakai, Shoko

Contrasting microbial communities on male and female flowers of a dioecious plant, Mallotus japonicus (Euphorbiaceae)

Environmental DNA, v. 4, (3), May 2022, p. 565-579
Marre, Maxime; Ushio, Masayuki; Sakai, Shoko

Interaction capacity as a potential driver of community diversity

Proceedings of the Royal Society B: Biological Sciences, v. 289, (1969), 23 February 2022, article number 20212690
Ushio, Masayuki

The effects of the floral infection by a bacterial pathogen in a dioecious plant, Mallotus japonicus (Euphorbiaceae)

Population Ecology, February 2022
Marre, Maxime; Ushio, Masayuki; Sakai, Shoko
Article 7

Are networks of trophic interactions sufficient for understanding the dynamics of multi-trophic communities? Analysis of a tri-trophic insect food-web time-series

Ecology Letters, v. 24, (3), March 2021, p. 543-552
Kawatsu, Kazutaka; Ushio, Masayuki; van Veen, F.J.Frank; Kondoh, Michio

Causal analysis of the temperature impact on deep-sea biodiversity

Biology Letters, v. 17, (7), July 2021, article number 0666
Doi, Hideyuki; Yasuhara, Moriaki; Ushio, Masayuki

Evaluation of seasonal dynamics of fungal DNA assemblages in a flow-regulated stream in a restored forest using eDNA metabarcoding

Environmental Microbiology, v. 23, (8), August 2021, p. 4797-4806
Matsuoka, Shunsuke; Sugiyama, Yoriko; Shimono, Yoshito; Ushio, Masayuki; Doi, Hideyuki

Quantitative assessment of multiple fish species around artificial reefs combining environmental DNA metabarcoding and acoustic survey

Scientific Reports, v. 11, (1), September 2021, article number 19477
Sato, Masaaki; Inoue, Nariaki; Nambu, Ryogen; Furuichi, Naoki; Imaizumi, Tomohito; Ushio, Masayuki

Reconstructing large interaction networks from empirical time series data

Ecology Letters, v. 24, (12), December 2021, p. 2763-2774
Chang, Chun-Wei; Miki, Takeshi; Ushio, Masayuki; Ke, Po-Ju; Lu, Hsiao-Pei; Shiah, Fuh-Kwo; Hsieh, Chih-hao

Temperature is a dominant driver of distinct annual seasonality of leaf litter production of equatorial tropical rain forests

Journal of Ecology, v. 109, (2), February 2021, p. 727-736
Kitayama, Kanehiro; Ushio, Masayuki; Aiba, Shin-Ichiro

海洋堆積物に残存する環境DNAを用いた魚類相把握の試み

水環境学会誌, v. 44, (4), July 2021, p. 79-84
白垣友寛; 井上拓; 福田秀樹; 潮雅之; 日下美樹; 岡野孝哉; 高巣裕之
Book chapter 1

哺乳類の検出

環境DNA: 生態系の真の姿を読み解く / 一般社団法人 環境DNA学会 企画; 土居 秀幸、近藤 倫生 編. 日本東京 : 共立出版, 2021, p. 204-216, Ch. 5.6
潮雅之
Article 9

Complementary molecular methods reveal comprehensive phylogenetic diversity integrating inconspicuous lineages of early-diverged wood-decaying mushrooms

Scientific Reports, v. 10, (1), February 2020, article number 3057
Shirouzu, Takashi; Matsuoka, Shunsuke; Doi, Hideyuki; Nagata, Nobuaki; Ushio, Masayuki; Hosaka, Kentaro

Dynamic and synergistic influences of air temperature and rainfall on general flowering in a Bornean lowland tropical forest

Ecological Research, v. 35, (1), January 2020, p. 17-29
Ushio, Masayuki; Osada, Yutaka; Kumagai, Tomo'omi; Kume, Tomonori; Pungga, Runi anak Sylvester; Nakashizuka, Tohru; Itioka, Takao; Sakai, Shoko

Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population

Molecular Ecology Resources, v. 20, (5), September 2020, p. 1248-1258, Special Issue: Special Feature: Genomics of Natural History Collections for Understanding Evolution in the Wild
Tsuji, Satsuki; Maruyama, Atsuhi; Miya, Masaki; Ushio, Masayuki; Sato, Hirotoshi; Minamoto, Toshifumi; Yamanaka, Hiroki

Environmental DNA metabarcoding reveals the presence of a small, quick-moving, nocturnal water shrew in a forest stream

Conservation Genetics, v. 21, (6), December 2020, p. 1079-1084
Yonezawa, Satoru; Ushio, Masayuki; Yamanaka, Hiroki; Miya, Masaki; Takayanagi, Atsushi; Isagi, Yuji

Evaluating intraspecific genetic diversity using environmental DNA and denoising approach: A case study using tank water

Environmental DNA, v. 2, (1), January 2020, p. 42-52
Tsuji, Satsuki; Miya, Masaki; Ushio, Masayuki; Sato, Hirotoshi; Minamoto, Toshifumi; Yamanaka, Hiroki

Idea paper: Predicting culturability of microbes from population dynamics under field conditions

Ecological Research, v. 35, (4), July 2020, p. 586-590
Ushio, Masayuki

Influence of potential grazers on picocyanobacterial abundance in Lake Biwa revealed with empirical dynamic modeling

Inland Waters, v. 10, (3), February 2020, p. 386-396
Cai, Ji; Hodoki, Yoshikuni; Ushio, Masayuki; Nakano, Shin-ichi

Quantitative evaluation of intraspecific genetic diversity in a natural fish population using environmental DNA analysis

Molecular Ecology Resources, v. 20, (5), September 2020, p. 1323-1332, Special Issue: Special Feature: Genomics of Natural History Collections for Understanding Evolution in the Wild
Tsuji, Satsuki; Shibata, Naoki; Sawada, Hayato; Ushio, Masayuki

Repressive chromatin modification underpins the long-term expression trend of a perennial flowering gene in nature

Nature Communications, v. 11, (1), May 2020, article number 2065
Nishio, Haruki; Buzas, Diana M.; Nagano, Atsushi J.; Iwayama, Koji; Ushio, Masayuki; Kudoh, Hiroshi
Book chapter 2

A data-driven approach to complex ecological systems

Theoretical Ecology: concepts and applications / edited by Kevin S. McCann, Gabriel Gellner. Oxford, UK : Oxford University Press, 2020, p. 116-133, Ch. 8
Kondoh, Michio; Kawatsu, Kazutaka; Osada, Yutaka; Ushio, Masayuki

Forecasting Ecological Time Series Using Empirical Dynamic Modeling: A Tutorial for Simplex Projection and S-map

Diversity of Functional Traits and Interactions: Perspectives on Community Dynamics / edited by Akihiko Mougi. Singapore : Springer, 2020, p. 193-213, Book series: Theoretical Biology
Ushio, Masayuki; Kawatsu, Kazutaka
Article 2

Seasonal and long-term patterns in litterfall in a Bornean tropical rainforest

Ecological Research, v. 34, (1), January 2019, p. 31-39
Nakagawa, Michiko; Ushio, Masayuki; Kume, Tomonori; Nakashizuka, Tohru

Use of a filter cartridge combined with intra-cartridge bead-beating improves detection of microbial DNA from water samples

Methods in Ecology and Evolution, v. 10, (8), August 2019, p. 1142-1156
Ushio, Masayuki
Article 4

Core microbiomes for sustainable agroecosystems

Nature Plants, v. 4, (5), May 2018, p. 247-257
Toju, Hirokazu; Peay, Kabir G.; Yamamichi, Masato; Narisawa, Kazuhiko; Hiruma, Kei; Naito, Ken; Fukuda, Shinji; Ushio, Masayuki; Nakaoka, Shinji; Onoda, Yusuke; Yoshida, Kentaro; Schlaeppi, Klaus; Bai, Yang; Sugiura, Ryo; Ichihashi, Yasunori; Minamisawa, Kiwamu; Kiers, E. Toby

Demonstration of the potential of environmental DNA as a tool for the detection of avian species

Scientific Reports, v. 8, (1), 14 March 2018, article number 4493
Ushio, Masayuki; Murata, Koichi; Sado, Tetsuya; Nishiumi, Isao; Takeshita, Masamichi; Iwasaki, Wataru; Miya, Masaki

Fluctuating interaction network and time-varying stability of a natural fish community

Nature, v. 554, (7692), 15 February 2018, p. 360-363
Ushio, Masayuki; Hsieh, Chih-Hao; Masuda, Reiji; Deyle, Ethan R.; Ye, Hao; Chang, Chun-Wei; Sugihara, George; Kondoh, Michio

Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing

Metabarcoding and Metagenomics, v. 2, March 2018, article number e23297
Ushio, Masayuki; Murakami, Hiroaki; Masuda, Reiji; Sado, Tetsuya; Miya, Masaki; Sakurai, Sho; Yamanaka, Hiroki; Minamoto, Toshifumi; Kondoh, Michio
Article 8

A lognormal distribution of the lengths of terminal twigs on self-similar branches of elm trees

Proceedings of the Royal Society B: Biological Sciences, v. 284, (1846), January 2017, article number 20162395
Koyama, Kohei; Yamamoto, Ken; Ushio, Masayuki

Empirical dynamic modeling for beginners

Ecological Research, v. 32, (6), November 2017, p. 785-796
Chang, Chun-Wei; Ushio, Masayuki; Hsieh, Chih-hao

Environmental DNA enables detection of terrestrial mammals from forest pond water

Molecular Ecology Resources, v. 17, (6), November 2017, p. e63-e75
Ushio, Masayuki; Fukuda, Hisato; Inoue, Toshiki; Makoto, Kobayashi; Kishida, Osamu; Sato, Keiichi; Murata, Koichi; Nikaido, Masato; Sado, Tetsuya; Sato, Yukuto; Takeshita, Masamichi; Iwasaki, Wataru; Yamanaka, Hiroki; Kondoh, Michio; Miya, Masaki

Plant-soil feedbacks and the dominance of conifers in a tropical montane forest in Borneo

Ecological Monographs, v. 87, (1), February 2017, p. 105-129
Ushio, Masayuki; Aiba, Shin-Ichiro; Takeuchi, Yayoi; Iida, Yoshiko; Matsuoka, Shunsuke; Repin, Rimi; Kitayama, Kanehiro

Tropical-forest mammals as detected by environmental DNA at natural saltlicks in Borneo

Biological Conservation, v. 210, (Part A), June 2017, p. 281-285
Ishige, Taichiro; Miya, Masaki; Ushio, Masayuki; Sado, Tetsuya; Ushioda, Masaharu; Maebashi, Kaori; Yonechi, Risako; Lagan, Peter; Matsubayashi, Hisashi

Water temperature-dependent degradation of environmental DNA and its relation to bacterial abundance

PLoS ONE, v. 12, (4), April 2017, article number e0176608
Tsuji, Satsuki; Ushio, Masayuki; Sakurai, Sho; Minamoto, Toshifumi; Yamanaka, Hiroki

マキ科・ナンヨウスギ科の根の形態・菌根菌・窒素固定活性

日本生態学会誌, v. 67, (3), December 2017, p. 339-345
潮雅之

陸上生態系において球果類の優占度を決定するメカニズム

日本生態学会誌, v. 67, (3), December 2017, p. 355-360
相場慎一郎; 宮本和樹; 潮雅之; 青柳亮太; 澤田佳美
Article 1

Social and ecological factors associated with the use of non-timber forest products by people in rural Borneo

Biological Conservation, v. 204, (Part B), December 2016, p. 340-349
Sakai, Shoko; Choy, Yee Keong; Kishimoto-Yamada, Keiko; Takano, Kohei T.; Ichikawa, Masahiro; Samejima, Hiromitsu; Kato, Yumi; Soda, Ryoji; Ushio, Masayuki; Saizen, Izuru; Nakashizuka, Tohru; Itioka, Takao
Article 4

Effect of water depth on predation frequency by diving beetles on mosquito larvae prey

Entomological Science, v. 18, (4), October 2015, p. 519-522
Ohba, Shin-ya; Ushio, Masayuki

High contribution of Synechococcus to phytoplankton biomass in the aphotic hypolimnion in a deep freshwater lake (Lake Biwa, Japan)

Aquatic Microbial Ecology, v. 75, (1), May 2015, p. 69-79
Takasu, Hiroyuki; Ushio, Masayuki; LeClair, Jessica E.; Nakano, Shin-Ichi

Linkage of root physiology and morphology as an adaptation to soil phosphorus impoverishment in tropical montane forests

Functional Ecology, v. 29, (9), September 2015, p. 1235-1245
Ushio, Masayuki; Fujiki, Yasuto; Hidaka, Armane; Kitayama, Kanehiro

Microbial communities on flower surfaces act as signatures of pollinator visitation

Scientific Reports, v. 5, March 2015, article number 8695
Ushio, Masayuki; Yamasaki, Eri; Takasu, Hiroyuki; Nagano, Atsushi J.; Fujinaga, Shohei; Honjo, Mie N.; Ikemoto, Mito; Sakai, Shoko; Kudoh, Hiroshi
Article 2

Herbivorous insect decreases plant nutrient uptake: The role of soil nutrient availability and association of below-ground symbionts

Ecological Entomology, v. 39, (4), August 2014, p. 511-518
Katayama, Noboru; Silva, Alessandro O.; Kishida, Osamu; Ushio, Masayuki; Kita, Satoshi; Ohgushi, Takayuki

High-throughput sequencing shows inconsistent results with a microscope-based analysis of the soil prokaryotic community

Soil Biology and Biochemistry, v. 76, September 2014, p. 53-56
Ushio, Masayuki; Makoto, Kobayashi; Klaminder, Jonatan; Takasu, Hiroyuki; Nakano, Shin-Ichi
Article 4

A coexisting fungal-bacterial community stabilizes soil decomposition activity in a microcosm experiment

PLoS ONE, v. 8, (11), November 2013, article number e80320
Ushio, Masayuki; Miki, Takeshi; Balser, Teri C.

CARD-FISH analysis of prokaryotic community composition and abundance along small-scale vegetation gradients in a dry arctic tundra ecosystem

Soil Biology and Biochemistry, v. 64, September 2013, p. 147-154
Ushio, Masayuki; Makoto, Kobayashi; Klaminder, Jonatan; Nakano, Shin-Ichi

Effects of condensed tannins in conifer leaves on the composition and activity of the soil microbial community in a tropical montane forest

Plant and Soil, v. 365, (1-2), April 2013, p. 157-170
Ushio, Masayuki; Balser, Teri C.; Kitayama, Kanehiro

Predator-prey body size relationships when predators can consume prey larger than themselves

Biology Letters, v. 9, (3), June 2013, article number 20121193
Nakazawa, Takefumi; Ohba, Shin-ya; Ushio, Masayuki
Article 1

Dynamic Scaling in the Growth of a Non-Branching Plant, Cardiocrinum cordatum

PLoS ONE, v. 7, (9), September 2012, article number e45317
Koyama, Kohei; Hidaka, Yoshiki; Ushio, Masayuki
Article 2

A meta-analysis of the global distribution pattern of condensed tannins in tree leaves

Open Ecology Journal, v. 4, December 2011, p. 18-23
Ushio, Masayuki; Adams, Jonathan M.

In situ enzyme activity in the dissolved and particulate fraction of the fluid from four pitcher plant species of the genus Nepenthes

PLoS ONE, v. 6, (9), September 2011, article number e25144
Takeuchi, Yayoi; Salcher, Michaela M.; Ushio, Masayuki; Shimizu-Inatsugi, Rie; Kobayashi, Masaki J.; Diway, Bibian; von Mering, Christian; Pernthaler, Jakob; Shimizu, Kentaro K.
Book chapter 2

Scale Dependence of Predator-Prey Mass Ratio. Determinants and Applications

The Role of Body Size in Multispecies Systems / Edited by Andrea Belgrano. Amsterdam, The Netherlands : Academic Press, 2011, p. 269-302, Book series: Advances in Ecological Research, v. 45
Nakazawa, Takefumi; Ushio, Masayuki; Kondoh, Michio

The ecology of podocarps in tropical montane forests of Borneo: distribution, population dynamics, and soil nutrient acquisition

Ecology of the Podocarpaceae in Tropical Forests / edited by Turner, Benjamin L. and Cernusak, Lucas A.. Washington, D.C. : Smithsonian Institution Scholarly Press, 2011, p. 101-117, Ch. 6. Smithsonian Contributions to Botany, number 95
Kitayama, Kanehiro; Aiba, Shin-ichiro; Ushio, Masayuki; Seino, Tatsuyuki; Fujiki, Yasuto
Article 3

Functional diversity of microbial decomposers facilitates plant coexistence in a plant-microbe-soil feedback model

Proceedings of the National Academy of Sciences of the United States of America, v. 107, (32), July 2010, p. 14251-14256
Miki, Takeshi; Ushio, Masayuki; Fukui, Shin; Kondoh, Michio

Tree species effects on soil enzyme activities through effects on soil physicochemical and microbial properties in a tropical montane forest on Mt. Kinabalu, Borneo

Pedobiologia, v. 53, (4), July 2010, p. 227-233
Ushio, Masayuki; Kitayama, Kanehiro; Balser, Teri C.

Tree species-mediated spatial patchiness of the composition of microbial community and physicochemical properties in the topsoils of a tropical montane forest

Soil Biology and Biochemistry, v. 42, (9), September 2010, p. 1588-1595
Ushio, Masayuki; Kitayama, Kanehiro; Balser, Teri C.
Article 1

Phenolic control of plant nitrogen acquisition through the inhibition of soil microbial decomposition processes: A plant-microbe competition model

Microbes and Environments, v. 24, (2), April 2009, p. 180-187
Ushio, Masayuki; Miki, Takeshi; Kitayama, Kanehiro
Article 1

Variations in the soil microbial community composition of a tropical montane forest ecosystem: Does tree species matter?

Soil Biology and Biochemistry, v. 40, (10), October 2008, p. 2699-2702
Ushio, Masayuki; Wagai, Rota; Balser, Teri C.; Kitayama, Kanehiro
Book chapter 1

熱帯降⾬林の⽣態系ー樹⽊と微⽣物の協奏曲

生物の多様性ってなんだろう?: 生命のジグソーパズル / 京都大学総合博物館・京都大学生態学研究センター 編. 日本京都 : 京都大学学術出版会, 2007, p. 250-272, 学術選書 027
北山兼弘; 潮雅之; 和穎朗太
2019 2

Seasonal and long-term patterns in litterfall in a Bornean tropical rainforest

Ecological Research, v. 34, (1), January 2019, p. 31-39
Nakagawa, Michiko; Ushio, Masayuki; Kume, Tomonori; Nakashizuka, Tohru
Article

Use of a filter cartridge combined with intra-cartridge bead-beating improves detection of microbial DNA from water samples

Methods in Ecology and Evolution, v. 10, (8), August 2019, p. 1142-1156
Ushio, Masayuki
Article
2018 4

Core microbiomes for sustainable agroecosystems

Nature Plants, v. 4, (5), May 2018, p. 247-257
Toju, Hirokazu; Peay, Kabir G.; Yamamichi, Masato; Narisawa, Kazuhiko; Hiruma, Kei; Naito, Ken; Fukuda, Shinji; Ushio, Masayuki; Nakaoka, Shinji; Onoda, Yusuke; Yoshida, Kentaro; Schlaeppi, Klaus; Bai, Yang; Sugiura, Ryo; Ichihashi, Yasunori; Minamisawa, Kiwamu; Kiers, E. Toby
Article

Demonstration of the potential of environmental DNA as a tool for the detection of avian species

Scientific Reports, v. 8, (1), 14 March 2018, article number 4493
Ushio, Masayuki; Murata, Koichi; Sado, Tetsuya; Nishiumi, Isao; Takeshita, Masamichi; Iwasaki, Wataru; Miya, Masaki
Article

Fluctuating interaction network and time-varying stability of a natural fish community

Nature, v. 554, (7692), 15 February 2018, p. 360-363
Ushio, Masayuki; Hsieh, Chih-Hao; Masuda, Reiji; Deyle, Ethan R.; Ye, Hao; Chang, Chun-Wei; Sugihara, George; Kondoh, Michio
Article

Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing

Metabarcoding and Metagenomics, v. 2, March 2018, article number e23297
Ushio, Masayuki; Murakami, Hiroaki; Masuda, Reiji; Sado, Tetsuya; Miya, Masaki; Sakurai, Sho; Yamanaka, Hiroki; Minamoto, Toshifumi; Kondoh, Michio
Article
2017 8

A lognormal distribution of the lengths of terminal twigs on self-similar branches of elm trees

Proceedings of the Royal Society B: Biological Sciences, v. 284, (1846), January 2017, article number 20162395
Koyama, Kohei; Yamamoto, Ken; Ushio, Masayuki
Article

Empirical dynamic modeling for beginners

Ecological Research, v. 32, (6), November 2017, p. 785-796
Chang, Chun-Wei; Ushio, Masayuki; Hsieh, Chih-hao
Article

Environmental DNA enables detection of terrestrial mammals from forest pond water

Molecular Ecology Resources, v. 17, (6), November 2017, p. e63-e75
Ushio, Masayuki; Fukuda, Hisato; Inoue, Toshiki; Makoto, Kobayashi; Kishida, Osamu; Sato, Keiichi; Murata, Koichi; Nikaido, Masato; Sado, Tetsuya; Sato, Yukuto; Takeshita, Masamichi; Iwasaki, Wataru; Yamanaka, Hiroki; Kondoh, Michio; Miya, Masaki
Article

Plant-soil feedbacks and the dominance of conifers in a tropical montane forest in Borneo

Ecological Monographs, v. 87, (1), February 2017, p. 105-129
Ushio, Masayuki; Aiba, Shin-Ichiro; Takeuchi, Yayoi; Iida, Yoshiko; Matsuoka, Shunsuke; Repin, Rimi; Kitayama, Kanehiro
Article

Tropical-forest mammals as detected by environmental DNA at natural saltlicks in Borneo

Biological Conservation, v. 210, (Part A), June 2017, p. 281-285
Ishige, Taichiro; Miya, Masaki; Ushio, Masayuki; Sado, Tetsuya; Ushioda, Masaharu; Maebashi, Kaori; Yonechi, Risako; Lagan, Peter; Matsubayashi, Hisashi
Article

Water temperature-dependent degradation of environmental DNA and its relation to bacterial abundance

PLoS ONE, v. 12, (4), April 2017, article number e0176608
Tsuji, Satsuki; Ushio, Masayuki; Sakurai, Sho; Minamoto, Toshifumi; Yamanaka, Hiroki
Article

マキ科・ナンヨウスギ科の根の形態・菌根菌・窒素固定活性

日本生態学会誌, v. 67, (3), December 2017, p. 339-345
潮雅之
Article

陸上生態系において球果類の優占度を決定するメカニズム

日本生態学会誌, v. 67, (3), December 2017, p. 355-360
相場慎一郎; 宮本和樹; 潮雅之; 青柳亮太; 澤田佳美
Article
2016 1

Social and ecological factors associated with the use of non-timber forest products by people in rural Borneo

Biological Conservation, v. 204, (Part B), December 2016, p. 340-349
Sakai, Shoko; Choy, Yee Keong; Kishimoto-Yamada, Keiko; Takano, Kohei T.; Ichikawa, Masahiro; Samejima, Hiromitsu; Kato, Yumi; Soda, Ryoji; Ushio, Masayuki; Saizen, Izuru; Nakashizuka, Tohru; Itioka, Takao
Article
2015 4

Effect of water depth on predation frequency by diving beetles on mosquito larvae prey

Entomological Science, v. 18, (4), October 2015, p. 519-522
Ohba, Shin-ya; Ushio, Masayuki
Article

High contribution of Synechococcus to phytoplankton biomass in the aphotic hypolimnion in a deep freshwater lake (Lake Biwa, Japan)

Aquatic Microbial Ecology, v. 75, (1), May 2015, p. 69-79
Takasu, Hiroyuki; Ushio, Masayuki; LeClair, Jessica E.; Nakano, Shin-Ichi
Article

Linkage of root physiology and morphology as an adaptation to soil phosphorus impoverishment in tropical montane forests

Functional Ecology, v. 29, (9), September 2015, p. 1235-1245
Ushio, Masayuki; Fujiki, Yasuto; Hidaka, Armane; Kitayama, Kanehiro
Article

Microbial communities on flower surfaces act as signatures of pollinator visitation

Scientific Reports, v. 5, March 2015, article number 8695
Ushio, Masayuki; Yamasaki, Eri; Takasu, Hiroyuki; Nagano, Atsushi J.; Fujinaga, Shohei; Honjo, Mie N.; Ikemoto, Mito; Sakai, Shoko; Kudoh, Hiroshi
Article
2014 2

Herbivorous insect decreases plant nutrient uptake: The role of soil nutrient availability and association of below-ground symbionts

Ecological Entomology, v. 39, (4), August 2014, p. 511-518
Katayama, Noboru; Silva, Alessandro O.; Kishida, Osamu; Ushio, Masayuki; Kita, Satoshi; Ohgushi, Takayuki
Article

High-throughput sequencing shows inconsistent results with a microscope-based analysis of the soil prokaryotic community

Soil Biology and Biochemistry, v. 76, September 2014, p. 53-56
Ushio, Masayuki; Makoto, Kobayashi; Klaminder, Jonatan; Takasu, Hiroyuki; Nakano, Shin-Ichi
Article
2013 4

A coexisting fungal-bacterial community stabilizes soil decomposition activity in a microcosm experiment

PLoS ONE, v. 8, (11), November 2013, article number e80320
Ushio, Masayuki; Miki, Takeshi; Balser, Teri C.
Article

CARD-FISH analysis of prokaryotic community composition and abundance along small-scale vegetation gradients in a dry arctic tundra ecosystem

Soil Biology and Biochemistry, v. 64, September 2013, p. 147-154
Ushio, Masayuki; Makoto, Kobayashi; Klaminder, Jonatan; Nakano, Shin-Ichi
Article

Effects of condensed tannins in conifer leaves on the composition and activity of the soil microbial community in a tropical montane forest

Plant and Soil, v. 365, (1-2), April 2013, p. 157-170
Ushio, Masayuki; Balser, Teri C.; Kitayama, Kanehiro
Article

Predator-prey body size relationships when predators can consume prey larger than themselves

Biology Letters, v. 9, (3), June 2013, article number 20121193
Nakazawa, Takefumi; Ohba, Shin-ya; Ushio, Masayuki
Article
2012 1

Dynamic Scaling in the Growth of a Non-Branching Plant, Cardiocrinum cordatum

PLoS ONE, v. 7, (9), September 2012, article number e45317
Koyama, Kohei; Hidaka, Yoshiki; Ushio, Masayuki
Article
2011 4

A meta-analysis of the global distribution pattern of condensed tannins in tree leaves

Open Ecology Journal, v. 4, December 2011, p. 18-23
Ushio, Masayuki; Adams, Jonathan M.
Article

In situ enzyme activity in the dissolved and particulate fraction of the fluid from four pitcher plant species of the genus Nepenthes

PLoS ONE, v. 6, (9), September 2011, article number e25144
Takeuchi, Yayoi; Salcher, Michaela M.; Ushio, Masayuki; Shimizu-Inatsugi, Rie; Kobayashi, Masaki J.; Diway, Bibian; von Mering, Christian; Pernthaler, Jakob; Shimizu, Kentaro K.
Article

Scale Dependence of Predator-Prey Mass Ratio. Determinants and Applications

The Role of Body Size in Multispecies Systems / Edited by Andrea Belgrano. Amsterdam, The Netherlands : Academic Press, 2011, p. 269-302, Book series: Advances in Ecological Research, v. 45
Nakazawa, Takefumi; Ushio, Masayuki; Kondoh, Michio
Book chapter

The ecology of podocarps in tropical montane forests of Borneo: distribution, population dynamics, and soil nutrient acquisition

Ecology of the Podocarpaceae in Tropical Forests / edited by Turner, Benjamin L. and Cernusak, Lucas A.. Washington, D.C. : Smithsonian Institution Scholarly Press, 2011, p. 101-117, Ch. 6. Smithsonian Contributions to Botany, number 95
Kitayama, Kanehiro; Aiba, Shin-ichiro; Ushio, Masayuki; Seino, Tatsuyuki; Fujiki, Yasuto
Book chapter
2010 3

Functional diversity of microbial decomposers facilitates plant coexistence in a plant-microbe-soil feedback model

Proceedings of the National Academy of Sciences of the United States of America, v. 107, (32), July 2010, p. 14251-14256
Miki, Takeshi; Ushio, Masayuki; Fukui, Shin; Kondoh, Michio
Article

Tree species effects on soil enzyme activities through effects on soil physicochemical and microbial properties in a tropical montane forest on Mt. Kinabalu, Borneo

Pedobiologia, v. 53, (4), July 2010, p. 227-233
Ushio, Masayuki; Kitayama, Kanehiro; Balser, Teri C.
Article

Tree species-mediated spatial patchiness of the composition of microbial community and physicochemical properties in the topsoils of a tropical montane forest

Soil Biology and Biochemistry, v. 42, (9), September 2010, p. 1588-1595
Ushio, Masayuki; Kitayama, Kanehiro; Balser, Teri C.
Article
2009 1

Phenolic control of plant nitrogen acquisition through the inhibition of soil microbial decomposition processes: A plant-microbe competition model

Microbes and Environments, v. 24, (2), April 2009, p. 180-187
Ushio, Masayuki; Miki, Takeshi; Kitayama, Kanehiro
Article
2008 1

Variations in the soil microbial community composition of a tropical montane forest ecosystem: Does tree species matter?

Soil Biology and Biochemistry, v. 40, (10), October 2008, p. 2699-2702
Ushio, Masayuki; Wagai, Rota; Balser, Teri C.; Kitayama, Kanehiro
Article
2007 1

熱帯降⾬林の⽣態系ー樹⽊と微⽣物の協奏曲

生物の多様性ってなんだろう?: 生命のジグソーパズル / 京都大学総合博物館・京都大学生態学研究センター 編. 日本京都 : 京都大学学術出版会, 2007, p. 250-272, 学術選書 027
北山兼弘; 潮雅之; 和穎朗太
Book chapter
No Publications

Teaching Assignment



DASC3240 Data Visualization in Science
OCES4103 Fisheries and Aquaculture
OCES3160 Ecology
DASC3240 Data Visualization in Science
OCES1001 The Earth as a Blue Planet
OCES4103 Fisheries and Aquaculture
SCIE1500 Guided Study on Research I
No Teaching Assignments
No Teaching Assignments
No Teaching Assignments

Research Postgraduate (RPG) Supervision

From January 2022 to December 2025 (As of 01 April 2025)

Current RPGs


Doctor of Philosophy
  • QIU, Shuting
    Marine Environmental Science

  • LIN, Xiaoqi
    Marine Environmental Science


Master of Philosophy
  • ABBAS, Rauszen Ocean Annika
    Marine Environmental Science

  • HU, Lucia (co-supervision)
    Marine Environmental Science

  • LI, Ming Wai (co-supervision)
    Marine Environmental Science

  • LIU, Chengbin
    Marine Environmental Science

  • HUANG, Suixuan
    Marine Environmental Science

  • KISERO, Robinson Okoth
    Marine Environmental Science

Projects

From January 2023 to December 2025 (As of 01 April 2025)


  • Establishment of an environmental DNA-based cetacean monitoring framework in Hong Kong waters
    在香港水域建立基於環境DNA的鯨目動物監測框架 Leading
    RGC - General Research Fund
    Project Team (HKUST)
    • USHIO Masayuki (Lead)
    2024 -
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