English / Japanese

Masayuki Ushio's Website

Research papers

    Preprints

  • Miki T, Chang CW, Ke PJ, Telschow A, Tsai CH, Ushio M, Hsieh CH (2024) How to quantify interaction strengths? A critical rethinking of the interaction Jacobian and evaluation methods for non-parametric inference in time series analysis.
  • Gao et al. (2024) Diversity and distinctive traits of the global RNA virome in urban environments. Available at SSRN
  • Osada Y*, Ushio M, Kondoh M (2023) Unified understanding of nonparametric causality detection in time series.

    In press/early view

  1. Ushio M*, Nakajima K (in press)
    Reservoir computing: theory and its potential applications in ecology (in Japanese)
    Japanese Journal of Ecology

  2. Jiang L*, Ushio M, Imai N, Sugau J, Kitayama K (2024)
    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

    3. 2024

  3. Atsumi K, Nishida Y, Ushio M, Nishi H, Genroku T, Fujiki S* (2024)
    Boosting biodiversity monitoring using smartphone-driven, rapidly accumulating citizen data
    eLife 13:RP93694

  4. Maehara K, Iwachido Y, Katsuhara H, Tomitaka M, Seto K, Ushio M, Kagami M, Sasaki T* (2024)
    Plant and soil microbial community assembly processes across urban vacant lots
    Journal of Vegetation Science 35:e13262

  5. Sugiyama Y*, Matsuoka S, Shimono Y, Ushio M, Doi H (2024)
    Do aquatic fungal environmental DNA assemblages reflect the surrounding terrestrial sporocarp communities?
    Fungal Ecology 67:101311

    6. 2023

  6. Fujita H*, Ushio M, Suzuki K, Abe MS, Yamamichi M, Okazaki Y, Canarini A, Hayashi I, Fukushima K, Fukuda S, Kiers ET, Toju H* (2023)
    Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics
    Frontiers in Microbiology 14:1261137

  7. Sakata M*, Sado T, Oka S-I, Ushio M, Miya M* (2023)
    Collection of environmental DNA from stemflow for monitoring arboreal biodiversity: preliminary validation using lichens
    MethodsX 11:102448

  8. Maxime M*, Ushio M, Sakai S (2023)
    The effects of the floral infection by a bacterial pathogen in a dioecious plant, Mallotus japonicus (Euphorbiaceae)
    Population Ecology 65:232-239

  9. Ushio M*, Saito H, Tojo M, Nagano AJ (2023)
    An ecological network approach for detecting and validating influential organisms for rice growth
    eLife 12:RP87202

    One of the main outcomes of JST PRESTO project (c) M. Ushio


  10. Ushio M*, Sado T, Fukuchi T, Sasano S, Masuda R, Osada Y, Miya M* (2023)
    Temperature sensitivity of the interspecific interaction strength of coastal marine fish communities
    eLife 12:RP85795

    A water sampling site in Boso Peninsula (c) M. Miya

    ・Featured in EukAlert!, HKUST Press Release, Kyoto University Press Release, Tohoku University Press Release, and Croucher Foundation


  11. Yoneya K*, Ushio M, Miki T (2023)
    Non-destructive collection and metabarcoding of arthropod environmental DNA remained on a terrestrial plant
    Scientific Reports 13:7125

  12. Jiang L*, Ushio M, Kitayama K (2023)
    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 485:525–536

  13. Ushio M*, Watanabe K, Fukuda Y, Tokudome Y, Nakajima K* (2023)
    Computational capability of ecological dynamics
    Royal Society Open Science 10:221614

    Artificial Neural Network was replaced with an ecological network to implement a novel computational method (credit:KyotoU/Jake Tobiyama)

    ・bioRxiv version was featured in New Scientist

    ・bioRxiv version was featured in Focus.pl


  14. Fujita H*, Ushio M, Suzuki K, Abe MS, Yamamichi M, Okazaki Y, Canarini A, Hayashi I, Fukushima K, Fukuda S, Kiers ET, Toju H* (2023)
    Facilitative interaction networks in experimental microbial community dynamics
    Frontiers in Microbiology 14:1153952

  15. Fujita H*, Ushio M, Suzuki K, Abe MS, Yamamichi M, Iwayama K, Canarini A, Hayashi I, Fukushima K, Fukuda S, Kiers ET, Toju H* (2023)
    Alternative stable states, nonlinear behavior, and predictability of microbiome dynamics
    Microbiome 11:63

  16. Fukasawa Y*, Akai D, Ushio M, Takehi T (2023)
    Electrical potentials in the ectomycorrhizal fungus Laccaria bicolor after a rainfall event
    Fungal Ecology 63:101229

  17. Tsujii Y*, Sakai S, Ushio M, Aiba S-I, Kitayama K (2023)
    Variations in the reproductive cycle of Bornean montane tree species along elevational gradients on ultrabasic and non-ultrabasic soils
    Biotropica 55 (1):210–220

    18. 2022

  18. Ushio M*, Furukawa S, Murakami H, Masuda R, Nagano AJ* (2022)
    An efficient early-pooling protocol for environmental DNA metabarcoding
    Environmental DNA 4 (6):1212–1228

  19. Inoue N*, Sato M, Furuichi N, Imaizumi T, Ushio M (2022)
    The relationship between eDNA density distribution and current fields around an artificial reef in the waters of Tateyama Bay, Japan
    Metabarcoding & Metagenomics 6:e87415

  20. 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 (2022)
    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 59:101095

  21. Elvira NJ, Ushio M, Sakai S* (2022)
    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 6:e84331

  22. Maxime M*, Ushio M, Sakai S. (2022)
    Contrasting microbial communities on male and female flowers of a dioecious plant, Mallotus japonicus (Euphorbiaceae)
    Environmental DNA 4 (3):565–579

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

    Interaction networks reconstructed from eDNA monitoring data
    Press release: Kyoto University HP (in Japanese), Detail (PDF; in Japanese),

    24. 2021

  24. 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 24 (12):2763–2774

  25. 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

  26. 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

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

  28. Shiragaki T, Inoue T, Fukuda H, Ushio M, Kusakabe M, Okano T, Takasu H* (2021)
    A pilot study investigating fish species composition using environmental DNA in marine sediment (in Japanese)
    Journal of Japan Society on Water Environment 44 (4):79–84

  29. 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

  30. Kitayama K*, Ushio M*, Aiba S-I (2021)
    Temperature is a dominant driver of distinct annual seasonality of leaf litter production of equatorial tropical rain forests
    Journal of Ecology 109 (2):727–736
    DOI

    Mt. Kinabalu and leaf litter time series
    Press release (in Japanese): Kyoto University HP (in Japanese), Detail (PDF; in Japanese)

    31. 2020

  31. 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 21 (6):1079–1084

  32. Tsuji S*, Shibata N, Sawada H, Ushio M (2020)
    Quantitative evaluation of intraspecific genetic diversity in a natural fish population using environmental DNA analysis
    Molecular Ecology Resources 20 (5):1323–1332

  33. Tsuji, S*, Maruyama A, Miya M, Ushio M, Sato H, Minamoto T, Yamanaka H (2020)
    Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population
    Molecular Ecology Resources 20 (5):1248–1258

  34. 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 10 (3):386–396

  35. Ushio M* (2020) [Special Feature]
    Idea paper: Predicting culturability of microbes from population dynamics under field conditions
    Ecological Research 35 (4):586–590

  36. Nishio H*, Buzas DM, Nagano AJ, Iwayama K, Ushio M, Kudoh H* (2020)
    Repressive chromatin modification underpins the long-term expression trend of a perennial flowering gene in nature
    Nature Communications 11:2065

  37. Shirouzu T*, Matsuoka S, Doi H, Nagata N, Ushio M, Hosaka K (2020)
    Complementary molecular methods reveal a comprehensive phylogenetic diversity with integrating invisible lineages of early-diverged mushrooms
    Scientific Reports 10:3057

  38. 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

  39. 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

    40. 2019

  40. Ushio M* (2019)
    Use of a filter cartridge combined with intra-cartridge bead-beating improves detection of microbial DNA from water samples
    Methods in Ecology and Evolution 10 (8):1142–1156

  41. Nakagawa M, Ushio M, Kume T, Nakashizuka T (2019)
    Seasonal and long-term patterns in litterfall in a Bornean tropical rainforest
    Ecological Research 34 (1): 31–39

    42. 2018

  42. 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

  43. Ushio M*, Murata K, Sado T, Nishiumi I, Takeshita M, Iwasaki W, Miya M* (2018)
    Demonstration of the potential of environmental DNA as a tool for the detection of avian species
    Scientific Reports 8: 4493

  44. Ushio M*, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018)
    Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing
    Metabarcoding & Metagenomics 2: e23297


  45. 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 554 (7692): 360–363
    Interacting fish species © R. Masuda
    Free link to the paper: SharedIt link (read only)
    See also: Nature Ecology & Evolution, Behind the Paper (Blog-post)
    Press Release: Kyoto University, National Taiwan University
    News: EurekAlert!, ScienceDaily, PHYS.ORG

    46. 2017

  46. Aiba S-I*, Miyamoto K, Ushio M, Aoyagi R, Sawada Y (2017)
    Mechanism determining conifer dominance in terrestrial ecosystems: A synthesis (in Japanese)
    Japanese Journal of Ecology 67 (3): 355–360

  47. Ushio M* (2017)
    Root morphology, mycorrhizal fungi and nitrogen fixation capacity of Podocarpaceae and Araucariaceae (in Japanese)
    Japanese Journal of Ecology 67 (3): 339–345

  48. 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 terrestrial mammals from forest pond water
    Molecular Ecology Resources 17 (6): e63–e75
    Tigers drinking water. They may release eDNA to water © M. Ushio

  49. Chang CW*, Ushio M*, Hsieh CH* (2017)
    Empirical dynamic modeling for beginners
    Ecological Research 32 (6): 785–796

  50. 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

  51. 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

  52. 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
    Mt. Kinabalu, Sabah, Malaysia © M. Ushio
    This study integrated multiple evidence and showed that plant-soil feedbacks potentially contributed to the conifer dominance in a lower montane forest in SE Asia.
  53. 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

    54. 2016

  54. 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 (2016)
    Social and ecological factors associated with the use of non-timber forest products by people in rural Borneo
    Biological Conservation 204: 340–349

    55. 2015

  55. Ohba S-Y*, Ushio M (2015)
    Effect of water depth on predation frequency by diving beetles on mosquito larvae prey
    Entomological Science 18 (4): 519–522
  56. Ushio M*, Fujiki Y, Hidaka A, Kitayama K* (2015)
    Linkage of root physiology and morphology as an adaptation to soil phosphorus impoverishment in tropical montane forests
    Functional Ecology 29 (9): 1235–1245
  57. Takasu H, Ushio M, LeClair JE, Nakano S-I* (2015)
    High contribution of Synechococcus to phytoplankton biomass in the aphotic hypolimnion in a deep freshwater lake (Lake Biwa, Japan)
    Aquatic Microbial Ecology 75 (1): 69–79
  58. Ushio M*, Yamasaki E, Takasu H, Nagano AJ, Honjo MN, Fujinaga S, Ikemoto M, Sakai S, Kudoh H (2015)
    Microbial communities on flower surfaces act as signatures of pollinator visitation
    Scientific Reports 5: 8695
    A bumblebee visiting a flower © E. Yamasaki
    Highlighted in Scientific Reports Featured Article (Nature Japan website).

    59. 2014

  59. Katayama N*, Silva AO, Kishida O, Ushio M, Kita S, Ohgushi T (2014)
    Herbivorous insect decreases plant nutrient uptake: the role of soil nutrient availability and association of below-ground symbionts
    Ecological Entomology 39 (4): 511–518
  60. Ushio M*, Makoto K, Klaminder J, Takasu H, Nakano S-I (2014)
    High-throughput sequencing shows inconsistent results with a microscope-based analysis of the soil prokaryotic community
    Soil Biology & Biochemistry 76: 53–56

    61. 2013

  61. 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
  62. Ushio M*, Makoto K, Klaminder J, Nakano S-I (2013)
    CARD-FISH analysis of prokaryotic community composition and abundance along small-scale vegetation gradients in a dry arctic tundra ecosystem
    Soil Biology & Biochemistry 64: 147–154
  63. Nakazawa T*, Ohba S-Y, Ushio M (2013)
    Predator-prey body size relationships when predators can consume prey larger than themselves
    Biology Letters 9 (3) no. 20121193
  64. 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 (1–2): 157–170

    Cover photo is the tropical montane forest in Mt. Kinabalu!

    65. Before 2012

  65. Koyama K*, Hidaka Y, Ushio M (2012)
    Dynamic scaling in the growth of a non-branching plant, Cardiocrinum cordatum
    PLoS ONE 7 (9) e45317
  66. Ushio M, Adams JM* (2011)
    A meta-analysis of the global distribution pattern of condensed tannins in tree leaves
    The Open Ecology Journal 4: 18–23
  67. Takeuchi Y, Salcher MM, Ushio M, Shimizu-Inatsugi R, Kobayashi MJ, Diway B, von Mering C, Pernthaler J, Shimizu KK* (2011)
    In situ enzyme activity in the dissolved and particulate fraction of the fluid from four pitcher plant species of the genus Nepenthes
    PLoS ONE 6 (9) e25144
  68. Ushio M*, Kitayama K, Balser TC (2010)
    Tree species-mediated spatial patchiness of the composition of microbial community and physicochemical properties in the topsoils of a tropical montane forest
    Soil Biology & Biochemistry 42 (9): 1588–1595
  69. Miki T*, Ushio M, Fukui S, Kondoh M (2010)
    Functional diversity of microbial decomposers facilitates plant coexistence in a plant-microbe-soil feedback model
    PNAS 107 (32): 14251–14256
  70. Ushio M*, Kitayama K, Balser TC (2010)
    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 53 (4): 227–233
  71. Ushio M*, Miki T, Kitayama K (2009)
    Phenolic control of plant nitrogen acquisition through the inhibition of soil microbial decomposition processes: A plant-microbe competition model
    Microbes and Environments 24 (2): 180–187
  72. Ushio M*, Wagai R, Balser TC, Kitayama K (2008)
    Variations in the soil microbial community composition of a tropical montane forest ecosystem: Does tree species matter?
    Soil Biology & Biochemistry 40 (10): 2699–2702

    73. : This symbol is downloaded from this website and distributed under Creative Commmons Atribution Liscence (CC BY 2.0) (see also this Wikipedia page).

Book Chapters

  1. Ushio M, Tsuji S (2024) "Ch.3-14 Water sampling, filtration, DNA extraction for aquatic environmental DNA"
    Kashima M, Ito T, Ozaki H (eds)『誰でも再現できるNGS「前」サンプル調製プロトコール』pp.202-215, Yodosha

  2. Ushio M, Tsuji S (2024) "Ch.1-5 Environmental DNA analysis for aquatic ecosystems"
    Kashima M, Ito T, Ozaki H (eds)『誰でも再現できるNGS「前」サンプル調製プロトコール』pp.39-48, Yodosha

  3. Takekata H, Aiba S-I, Nakabayashi M, Nozu R, Furukawa M, Tanaka Y, Ushio M (2022)
    ｢南の生物と時間｣ Journal of Chronobiology vo.28 pp.9–16 (in Japanese)

  4. Ushio M (2021) "5.6 Detection of Mammals" (in Japanese)
    The eDNA Society, Doi H, Kondoh M eds. 『環境DNA – 生態系の真の姿を読み解く –』 pp.204–216 Kyoritsu Shuppan

  5. Ushio M*, Kawatsu K (2020)
    Forecasting ecological time series using empirical dynamic modeling: a tutorial for simplex projection and S-map. DOI:10.1007/978-981-15-7953-0_9. In Mougi A ed. "Diversity of Functional Traits and Interactions". pp.193–213 Springer, Singapore.

  6. Kondoh M*, Kawatsu K, Osada Y, Ushio M (2020)
    A data-driven approach to complex ecological systems. DOI:10.1093/oso/9780198824282.003.0008. In McCann K.S. & Gellner G eds. "Theoretical Ecology: concepts and applications". pp. 117–122. Oxford University Press, Oxford, UK.

  7. 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. Smithsonian Contributions to Botany 95 pp.101–117. In Turner, B.L. & Cernusak, L.A. eds. "Ecology of the Podocarpaceae in Tropical Forests". Smithsonian Institution Scholarly Press, Washington D.C.

  8. Nakazawa T, Ushio M, Kondoh M* (2011)
    Scale-dependence of predator-prey body-mass ratio: determinants and applications. Advances in Ecological Research 45 pp.269–302. In Belgrano, A. and Reiss, J. eds. "The Role of Body Size in Multispecies Systems". Academic Press, Amsterdam, The Netherlands
    TN and MU equally contributed to this work.
  9. Kitayama K, Ushio M, Wagai R (2007) (in Japanese)
    "熱帯降雨林の生態系－樹木と微生物の協奏曲" 京都大学総合博物館・生態学研究センター（編）『生物の多様性ってなんだろう？－生命のジグソーパズル－』 pp.250-272 Kyoto University Press

Awards

  1. 2021.4. The Young Scientists' Award, The Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology
  2. 2018.3. 22nd Miyadi Award, ESJ
  3. 2014.3. 61st ESJ, English Presentation Award, Best Award (Microbial and Ecosystem Ecology section)
  4. 2009.3. 56th ESJ, Poster Award (Nutrient Cycling and Production section)
  5. 2008.3. 55th ESJ, Poster Award (Nutrient Cycling section)
  6. 2007.2. 3rd ESJ Kinki Chapter, Young Researcher Award

Presentations

Referee service for scientific journals and research fundings

African Journal of Agricultural Research, African Journal of Biotechnology, African Journal of Microbiology Research, Agricultural Science, Applied Soil Ecology, Australian Journal of Botany, Communications Biology, Ecological Entomology, Ecological Indicators, Ecological Research, Ecology, Ecology Letters, Ecosystems, Ecosphere, Environmental DNA, European Journal of Soil Science, Fisheries Science, Forest Ecology and Management, Geoderma, Genes & Genetic Systems, Journal of Animal Ecology, Journal of Applied Microbiology, Journal of Arid Land, Journal of Forest Research, Metabarcoding & Metagenomics,, Microbial Ecology, Molecular Ecology Resources, Nature Climate Change, Nature Communications, Plant and Soil, PLoS ONE, Population Ecology, Proceedings of the Royal Society B, The Research Foundation Flanders (FWO), Review of Palaeobotany and Palynology, Science of the Total Environment, Scientific Reports, National Scientific Research Fund (F.R.S.-FNRS) (Belgium), Soil Biology & Biochemistry, Soil Research, Soil Science and Plant Nutrition