Japanese / English

Masayuki Ushio's Website

(New Caledonia, 2013)

An ecologist working on ecosystem dynamics, nonlinear time-series analysis, environmental DNA, and microbial community

What's New

From 2022.9

I will move to The Department of Ocean Science, The Hong Kong University of Science and Technology (OCES, HKUST) and launch a new lab!

Please contact me (ong8181 [at] gmail.com) if you are interested in performing ocean research using environmental DNA analysis and statistical modeling in Hong Kong.

Also, the personal website has been moved to https://ong8181.github.io (hosted by Github). The website will be upgraded to "a lab website" as soon as possible. This old website will no longer be updated.


Our new paper on eDNA library preparation protocol is out. Open access!

Ushio M*, Furukawa S, Murakami H, Masuda R, Nagano AJ* (2022) An efficient early-pooling protocol for environmental DNA metabarcoding. Environmental DNA (early view)


Paper published in Proceedings of the Royal Society B. Source data and code are available at Github.

Ushio M* (2022) Interaction capacity as a potential driver of community diversity. Proceedings of the Royal Society B 289: 20212690


Posted one preprint and published five original papers.


  • Ushio M*, Watanabe K, Fukuda Y, Tokudome Y, Nakajima K* (2021) Computational capability of ecological dynamics. bioRxiv

  • Published papers
  • Chang CW, Miki T, Ushio M, Ke PJ, Lu HP, Shiah FK, Hsieh CH* (2021) Reconstructing large interaction networks from empirical time series data. Ecology Letters (early view)

  • Fukasawa Y*, Matsukura K, Stephan JG, Makoto K, Suzuki SN, Kominami Y, Takagi M, Tanaka N, Takemoto S, Kinuura H, Okano K, Song Z, Jomura M, Kadowaki K, Yamashita S, Ushio M (2021) Patterns of community composition and diversity in latent fungi of living Quercus serrata trunks across a range of oak wilt prevalence and climate variables in Japan. Fungal Ecology (early view)

  • Sato M*, Inoue N, Nambu R, Furuich N, Imaizumi T, Ushio M (2021) Quantitative assessment of multiple fish species around artificial reefs using environmental DNA metabarcoding. Scientific Reports 11:19477

  • Matsuoka S*, Sugiyama Y, Shimono Y, Ushio M, Doi H (2021) Evaluation of seasonal dynamics of fungal DNA assemblages in a flow-regulated stream in a restored forest using eDNA metabarcoding. Environmental Microbiology 23 (8):4797-4806

  • Doi H*, Yasuhara M*, Ushio M* (2021)
    Causal analysis of the temperature impact on deep-sea biodiversity. Biology Letters 17 (7):20200666

  • 2021.3.1

    Our paper that investigated the potential linkage between trophic interactions and population-level interactions has been out in Ecology Letters!

    Kawatsu K, Ushio M, van Veen F, Kondoh M* (2021) 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 24 (3):543-552


    Two papers out! The eDNA paper reported that eDNA survey discovered a new habitat of a endangered, small, endemic mammalian species in Japan. The other paper reported distinct annual seasonality of equatorial tropical rain forests.

    Yonezawa S, Ushio M*, Yamanaka H, Miya M, Takayanagi A, Isagi Y* (2020) Environmental DNA metabarcoding reveals the presence of a small, quick-moving, nocturnal water shrew in a forest stream. Conservation Genetics (early view)

    Kitayama K*, Ushio M*, Aiba S-I (2020) Temperature is a dominant driver of distinct annual seasonality of leaf litter production of equatorial tropical rain forests. Journal of Ecology (early view)


    Posted my preprint about the interaction capacity hypothesis! The hypothesis enables a mechanistic explanation of how community diversity is determined.

    Ushio M* (2020) Interaction capacity underpins community diversity. bioRxiv


    Two papers published online. One studied potential interactions between grazers and picocyanobacteria in Lake Biwa using intensive plankton time series and empirical dynamic modeling. The other is demonstrating idea to predict "culturability" of microbes using population dynamic under field conditions.

    Cai J, Hodoki Y, Ushio M, Nakano S-I* (2020)
    Influences of potential grazers on picocyanobacteria abundances in Lake Biwa revealed by empirical dynamic modeling. Inland Water (early view)

    Ushio M* (2020)
    Idea paper: Predicting culturability of microbes from population dynamics under field conditions. Ecological Research (early view)


    Papers on environemtal DNA and general flowering have been published. Both are open access . Please check them out!

    Ushio M*, Osada Y, Kumagai T, Kume T, Pungga RS, Nakashizuka T, Itioka T, Sakai S* (2020) Miyadi Award Paper Dynamic and synergistic influences of air temperature and rainfall on general flowering in a Bornean lowland tropical forest. Ecological Research 35 (1):17-29

    Tsuji S*, Miya M, Ushio M, Sato H, Minamoto T, Yamanaka H (2020) Evaluating intraspecific genetic diversity using environmental DNA and denoising approach: A case study using tank water. Environmental DNA 2 (1): 42-52

    2019.9.9 - 9.14

    Visited Scripps Institution of Oceanography in San Diego (Sugihara Lab) and Stanford University (Fukami Lab). I gave a talk on my ongoing research.


    Our paper on mass flowering in Borneo has just been accepted as a publication in Ecological Research (submitted as Miyadi Award Paper).


    My paper on microbial DNA extraction (and prokaryotic internal standard DNA method!) published in Methods in Ecology and Evolution

    Ushio M* (2019) Use of a filter cartridge combined with intra-cartridge bead-beating improved detection of microbial DNA from water samples. Methods in Ecology and Evolution


    Appointed as a project-specific associate professor at Hakubi Center, Kyoto University.


    A collaborative paper on "core microbiomes" in agroecosystems has been publihed in Nature Plants. This perspective paper proposes a framework to understand and utilize complex microbial communities in agroecosystems.

    Toju H*, Peay KG, Yamamichi M, Narisawa K, Hiruma K, Naito K, Fukuda S, Ushio M, Nakaoka S, Onoda Y, Yoshida K, Schlaeppi K, Bai Y, Sugiura R, Ichihashi Y, Minamisawa K, Kiers ET (2018) Core microbiomes for sustainable agroecosystems. Nature Plants 4: 247-257


    Papers on environmental DNA techniques have been accepted.

    Ushio M*, Murata K, Sado T, Nishiumi I, Takeshita M, Iwasaki W, Miya M* (accepted) Demonstration of the potential of environmental DNA as a tool for the detection of avian species. Scientific Reports

    Ushio M*, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (accepted) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding & Metagenomics


    Our new study proposes a method that enables the quantification of time-varying stability of a natural ecological community!

    Ushio M*, Hsieh CH, Masuda R, Deyle RE, Ye H, Chang CW, Sugihara G, Kondoh M* (2018) Fluctuating interaction network and time-varying stability of a natural fish community. Nature (online) doi:10.1038/nature25504


    Papers on plant-soil feedback, environmental DNA and empirical dynamics modeling got published!

    Ushio M*, Fukuda H, Inoue T, Makoto K, Kishida O, Sato K, Murata K, Nikaido M, Sado T, Sato Y, Takeshita M, Iwasaki W, Yamanaka H, Kondoh M, Miya M* (2017)
    Environmental DNA enables detection of terrestiral mammals from forest pond water. Molecular Ecology Resources (online)

    Chang CW*, Ushio M*, Hsieh CH* (2017)
    Emprical dynamic modeling for beginners. Ecological Research (online)

    Ishige T, Miya M, Ushio M,Sado T, Ushioda M, Yonechi R, Lagan P, Matsubayashi H* (2017)
    Tropical-forest mammals as detected by environmental DNA at natural saltlicks. Biological Conservation 210: 281-285

    Tsuji S*, Ushio M, Sakurai S, Minamoto T, Yamanaka H (2017)
    Water temperature-dependent degradation of environmental DNA and its relation to bacterial abundance. PLoS ONE 12 (4): e0176608

    Ushio M*, Aiba S-I, Takeuchi Y, IIda Y, Matsuoka S, Repin R, Kitayama K (2017)
    Plant-soil feedbacks and the dominance of conifers in a tropical montane forest in Borneo. Ecological Monographs 87 (1): 105-129


    Collaborative paper on a log-normal distribution of tree branches has been published.

    Koyama K*, Yamamoto K, Ushio M (2017)
    A lognormal distribution of the lengths of terminal twigs on self-similar branches of elm trees
    Proceedings of the Royal Society B 284: 20162395


    Collaborative paper on the use of non-timber forest products has been accepted.

    Sakai S*, Keong CY, Koizumi M, Kishimoto-Yamada K, Takano KT, Ichikawa M, Samejima H, Kato Y, Soda R, Ushio M, Saizen I, Nakashizuka T, Itioka T (accepted)
    Social and ecological factors associated with the use of non-timber forest products by people in rural Borneo. Biological Conservation


    Moved to Center for Ecological Research, Kyoto University as a PRESTO researcher.


    Our long-term study finally accepted in Ecolgocial Monographs! It took more than 10 years to get it accepted...

    Ushio M*, Aiba S-I, Takeuchi Y, IIda Y, Matsuoka S, Repin R, Kitayama K (accepted)
    Plant-soil feedbacks and the dominance of conifers in a tropical montane forest in Borneo. Ecological Monographs


    Three papers have been accepted!!!

    Ushio M*, Yamasaki E, Takasu H, Nagano AJ, Honjo MN, Fujinaga S, Ikemoto M, Sakai S, Kudoh H (accepted)
    Microbial communities on flower surfaces act as signatures of pollinator visitation. Scientific Reports

    Ushio M*, Fujiki Y, Hidaka A, Kitayama K* (accepted)
    Linkage of root physiology and morphology as an adaptation to soil phosphorus impoverishment in tropical montane forests. Functional Ecology

    Ohba S-Y*, Ushio M (accepted)
    Relationship between predation frequency on mosquito larvae by diving beetles and water depth. Entomological Science


    Website renewal!


    I have moved to Ryukoku University, as a postdoc working on nonlinear time-series analysis. Lab PI is Michio Kondoh, who is working on methematical ecology.


    Our another tundra work has been accepted.

    Ushio M, Makoto K, Klaminder J, Takasu H, Nakano S-I (accepted)
    High-throughput sequencing shows inconsistent results with a microscope-based analysis of the soil prokaryotic community. Soil Biology & Biochemistry


    Collaborative work about the relationship among plant, insect, and microbial symbionts has been accepted.

    Katayama N*, Silva AO, Kishida O, Ushio M, Kita S, Ohgushi T (accepted)
    Herbivorous insect decreases plant nutrient uptake: the role of soil nutrient availability and association of below-ground symbionts. Ecological Entomology


    What I did in University of Wisconsin-Madison has been published in PLoS ONE.

    Ushio M*, Miki T, Balser TC (2013)
    A coexisting fungal-bacterial community stabilizes soil decomposition activity in a microcosm experiment. PLoS ONE 8 (11) e80320


    Our tundra work has been accepted in Soil Biology & Biochemistry.

    Ushio M*, Makoto K, Klaminder J, Nakano S-I. (accepted)
    CARD-FISH analysis of prokaryotic community composition and abundance along small-scale vegetation gradients in a dry arctic tundra ecosystem. Soil Biology & Biochemistry


    Ushio M*, Balser TC, Kitayama K (2013)
    Effects of condensed tannins in conifer leaves on the composition and activity of soil microbial community in a tropical montane forest. Plant and Soil 365 pp.157-170
    The cover photo is our study site in Mt. Kinabalu!


    Nakazawa T*, Ohba S-Y, Ushio M
    Predator-prey body size relationships when predators can consume prey larger than themselves. (TN and SO equally contributed to this work)
    Biology Letters (in press)


    A new paper has been published in PLoS ONE.

    Koyama K, Hidaka Y, Ushio M (2012)
    Dynamic Scaling in the Growth of a Non-Branching Plant, Cardiocrinum cordatum
    PLoS ONE 7 (9) e45317


    Tannin meta-analysis paper has been published.

    Ushio, M., Adams, J. M. (2011)
    A meta-analysis of the global distribution pattern of condensed tannins.
    The Open Ecology Journal 4 pp.18-23


    A new book chapter has been published.

    Kitayama, K., Aiba, S-I., Ushio, M., Seino, T., Fujiki, Y. (2011)
    The ecology of podocarps in tropical montane forests of Borneo: distribution, population dynamics, and soil nutrient acquisition. In Turner, B.L. & Cernusak, L.A. eds. Ecology of the Podocarpaceae in Tropical Forests. Smithsonian Contributions to Botany 95 pp.101-117, Smithsonian Institution Scholarly Press, Washington D.C.


    A new book chapter has been published. Check it out!

    Nakazawa, T.*, Ushio, M.*, Kondoh, M. (2011)
    Scale-dependence of predator-prey body-mass ratio: determinants and applications. In Belgrano, A.and Reiss, J. eds. The Role of Body Size in Multispecies Systems. Advances in Ecological Research 45 pp.269-302, Academic Press, Amsterdam, The Netherlands
    *Both authors equally contributed to this work.