Research papers
- Atsumi K, Nishida Y, Ushio M, Nishi H, Genroku T, Fujiki S* (2023) Boosting biodiversity monitoring using smartphone-driven, rapidly accumulating citizen data.
- Osada Y*, Ushio M, Kondoh M (2023)
Unified understanding of nonparametric causality detection in time series.
Preprints
- 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 - Ushio M*, Nakajima K (in press)
Reservoir computing: theory and its potential applications in ecology (in Japanese)
Japanese Journal of Ecology - 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 - 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 - 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 - 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 - 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 - 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
- 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
- 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 - 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
- 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
- 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
- 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
- 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 - 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
- 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 - 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 - 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
- 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 - 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),
- 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
- 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 - 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 - 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 - 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
Mt. Kinabalu and leaf litter time series Press release (in Japanese): Kyoto University HP (in Japanese), Detail (PDF; in Japanese)
- 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 - 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 - 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
- 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 - Ushio M* (2020) [Special Feature]
Idea paper: Predicting culturability of microbes from population dynamics under field conditions
Ecological Research 35 (4):586–590
- 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 - 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 - 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
- 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
- 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 - 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 - 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
- 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
- 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 - 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 - 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 - 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
- Chang CW*, Ushio M*, Hsieh CH* (2017)
Empirical dynamic modeling for beginners
Ecological Research 32 (6): 785–796 - 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
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.
- 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 - 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 - 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 - 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 - 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 - 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).
- 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 - 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 - 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
- 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
- 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
- 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! - Koyama K*, Hidaka Y, Ushio M (2012)
Dynamic scaling in the growth of a non-branching plant, Cardiocrinum cordatum
PLoS ONE 7 (9) e45317
- 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
- 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
- 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
- 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
- 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
- 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
- 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
In press/early view
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Before 2012
: 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
- 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) - 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 - 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. - 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. - 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. - 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. - 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
- 2021.4. The Young Scientists' Award, The Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology
- 2018.3. 22nd Miyadi Award, ESJ
- 2014.3. 61st ESJ, English Presentation Award, Best Award (Microbial and Ecosystem Ecology section)
- 2009.3. 56th ESJ, Poster Award (Nutrient Cycling and Production section)
- 2008.3. 55th ESJ, Poster Award (Nutrient Cycling section)
- 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