Japanese / English
(New Caledonia, 2013)
An ecologist working on ecosystem dynamics, nonlinear time-series analysis, environmental DNA, and microbial community
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.
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)
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
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.
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!
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
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.