Publications

See Google Scholar for the citation information.

Representative papers

  • 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
  • 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
  • Ushio M*, Watanabe K, Fukuda Y, Tokudome Y, Nakajima K* (2023) Computational capability of ecological dynamics. Royal Society Open Science 10:221614
  • Ushio M* (2022) Interaction capacity as a potential driver of community diversity. Proceedings of the Royal Society B 289: 20212690
  • 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
  • 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: e63–e75
  • 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


Published / Preprints

Preprints

  • Atsumi K, Nishida Y, Ushio M, Nishi H, Genroku T, Fujiki S* (2023) Boosting biodiversity monitoring using smartphone-driven, rapidly accumulating citizen data. bioRxiv eLife (Reviewed Preprint)
  • Osada Y*, Ushio M, Kondoh M (2023) A unified framework for nonparametric causality detection. bioRxiv

In press / early view

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

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

2024

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

2023

  1. 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
  2. Sakata A*, 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. Ushio M*, Watanabe K, Fukuda Y, Tokudome Y, Nakajima K* (2023)
    Computational capability of ecological dynamics. Royal Society Open Science 10:221614
  9. 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
  10. 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
  11. 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
  12. 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

Before joining HKUST

2022

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. Ushio M* (2022) Interaction capacity as a potential driver of community diversity. Proceedings of the Royal Society B 289: 20212690

2021

  1. 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
  2. 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
  3. 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
  4. Doi H*, Yasuhara M*, Ushio M* (2021)
    Causal analysis of the temperature impact on deep-sea biodiversity. Biology Letters 17 (7):20200666
  5. 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
  6. 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
  7. 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

2020

  1. 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
  2. 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
  3. 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
  4. 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
  5. Ushio M* (2020) [Special Feature]
    Idea paper: Predicting culturability of microbes from population dynamics under field conditions. Ecological Research 35 (4):586–590
  6. 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
  7. 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
  8. Ushio M*, Osada Y, Kumagai T, Kume T, Pungga RS, Nakashizuka T, Itioka T, Sakai S* (2020) Dynamic and synergistic influences of air temperature and rainfall on general flowering in a Bornean lowland tropical forest. Ecological Research 35 (1):17–29
  9. 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

  1. 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
  2. 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

2018

  1. 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
  2. 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
  3. 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
  4. 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

2017

  1. 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
  2. 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
  3. 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
  4. Chang CW*, Ushio M*, Hsieh CH* (2017)
    Empirical dynamic modeling for beginners. Ecological Research 32 (6): 785–796
  5. 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
  6. 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
  7. 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
  8. 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

2016

  1. 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

2015

  1. 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
  2. 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
  3. 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
  4. 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

2014

  1. 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
  2. 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

2013

  1. 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
  2. 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
  3. 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
  4. 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

Before 2012

  1. Koyama K*, Hidaka Y, Ushio M (2012)
    Dynamic scaling in the growth of a non-branching plant, Cardiocrinum cordatum. PLoS ONE 7 (9) e45317
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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