Research topics
1. Nonlinear time-series analysis (2014-)
In recent decades, nonlinear methods that acknowledge state dependence have been developed based on state space reconstruction (SSR). These methods do not assume any set of equations governing the system but recover the dynamics from time series data, thus called Empirical Dynamic Modeling (EDM). I am curerntly analyzing ecological time series using EDM to forecast and understand state-dependent behaviour of complex ecological dynamics.
Related papers
Ushio 2022 Proceedings of the Royal Society B 289:20212690
Kitayama et al. 2021 Journal of Ecology 109 (2):727-736
Ushio et al. 2020 Ecological Research 35 (1):17-29
Ushio et al. 2018 Nature 554 (7692): 360-363
Chang et al. 2017 Ecological Research 32 (6): 785-796
2. Developments and applications of environmental DNA techniques (2015-)
I have been developing methods to monitor ecosystem dynamics using DNAs derived from environmental samples (e.g., soil and water) (i.e., environmantel DNA; eDNA).
Related papers
Ushio 2022 Proceedings of the Royal Society B 289:20212690
Yonezawa et al. 2020 Consevation Genetics 21 (6): 1078-1084
Ushio 2019 Methods in Ecology and Evolution 10 (8):142-1156
Ushio et al. 2018 Metabarcoding & Metagenomics 2: e23297
Ushio et al. 2017 Molecular Ecology Resouces 17: e63-e75
Ishige et al. 2017 Biological Consevation 210: 281-285
3. Plant-soil feedbacks in a forest ecosystem (2005-)
I have been working on plant-soil feedbacks in a forest ecosystem, mainly in a forest in Malaysian Borneo. I am focusing on the relationship among plant secondary metabolites, soil microbial community, decomposition process and ecosystem dynamics. These works are still ongoing.
Related papers
Ushio et al. 2017 Ecological Monographs 87 (1): 105-129
Ushio et al. 2013 Plant and Soil 365 (1-2): 157-170
Ushio et al. 2010 Soil Biology & Biochemistry 42 (9): 1588-1595
Ushio et al. 2008 Soil Biology & Biochemistry 40 (10): 2699-2702
4. Lab experiments on soil microbial ecology (2010-2014)
I did mesocosm experiments to study the relationship between diversity and function of soil microbial community. I also tested the performance of several methodologies commonly used in soil microbial ecology. Lipid biomarker method, CARD-FISH and high-throughput sequencer were used in these studies.
Related papers
Ushio et al. 2014 Soil Biology & Biochemistry 76: 53-56
Ushio et al. 2013 Soil Biology & Biochemistry 64: 147-154
Ushio et al. 2013 PLos ONE 8 (11) e80320
5. Theoretical analysis of plant-soil feedbacks (2008-2011)
The consequences of plant-soil feedbacks for nutrient cycling and plant species coexistence were studied using mathematical models.
Related papers
Miki et al. 2010 PNAS 107 (32): 14251-14256
Ushio et al. 2009 Microbes and Environment 24 (2): 180-187
6. Others (collaborative works etc.)
I am also working on several different topics; e.g., environmental DNA, microbial fingerprint, theoretical formulations of prey-predator relationships etc...
Related papers
Takeuchi et al. 2011 PLoS ONE 6 (9) e25144
Nakazawa et al. 2013 Biology Letters 9 (3) no.20121193
Ushio et al. 2015 Scientific Reports 8: 8695
Ushio et al. 2017 Molecular Ecology Resources 17 (6): e63-e75
Ushio et al. 2018 Metabarcoding & Metagenomics 2: e23297
Field work experience
Mt. Kinabalu, Borneo, Malaysia (2005-2016)
UW-Madison Arboretum, Wisconsin, USA (2010)
Abisko, Sweden (2011)
South province in New Caledonia (2013)
Rice paddy field in Japan (2016-2019)
Research funds
*Research projects as a principal investigator only
2020.4 - 2024.3, JSPS Grand-in-aid for Scientific Research (B) "Development of a framework for controlling aquatic ecosystem dynamics using host-parasite systems as a model system" JPY 13,300,000 (approx. USD 122,000)
2018.10 - 2023.9, Kyoto University Hakubi Project "Automated ecosystem monitoring system for forecasting ecological dynamics" JPY 13,000,000 (approx. USD 120,000)
(Completed) 2016.10 - 2020.3, Japan Science and Technology Agency, PRESTO "Forecasting agricultural ecosystem dynamics using ecological networks" JPY 40,000,000 (approx. USD 360,000)
(Completed) 2014.4 - 2017.3, JSPS Grand-in-aid for Young Scientists (B) "Identification and quantification of microbial pathogens that drive plant-soil feedbacks in a forest ecosystem" JPY 3,100,000 (approx. USD 31,000)
(Completed) 2012.4 - 2014.3, Grand-in-aid from Institution for Fermentation, Osaka "Microbes on a pollen: their detection and its application" JPY 3,000,000 (approx. USD 38,000)
(Completed) 2011.4 - 2014.3, JSPS Research Fellowship for Young Scientist PD (23-586) "A new terrestrial ecosystem model incorporating microbial functional diversity and dispersal process" JPY 2,400,000 (approx. USD 30,000)
(Completed) 2010.4 - 2010.9, JSPS Excellent Young Researcher Oversea Visit Program. JPY 1,060,840 (approx. USD 13,000)
(Completed) 2009.4 - 2011.3, JSPS Research Fellowship for Young Scientist DC2 (21-1526) "Elucidation of the mechanism of forest ecosystem dynamics regulated by soil microbial communities: a model study in a tropical montane forest" JPY 1,400,000 (approx. USD 17,000)
Research skills
- Soil pH, moisture, C and N content
- Soil nutrient quantification (P, N)
- Phenolic quantification (total phenolics and condensed tannins)
- Soil respiration rate (LI6400, INNOVA)
- Soil enzyme activity (p-nitrophenol substrate, MUB substrate)
- Analysis of soil microbial community (lipid biomarker analysis, CARD-FISH)
- Extraction and purification of condensed tannins from plant leaves
- Nitrogen fixation activity (acethylene reduction assay)
- Utilization ability of organic nitrogen by plant roots (stable isotope tracer)
- Measurements of sapling growth rates in field
- Evaluation of rice performance in field
- Rice RNA extraction
- Environmental DNA sampling (GF/F filter, Sterivex)
- Extraction and PCR of eDNA (Fish, mammal, bird, invertebrate etc...)
- Quantitative and multispecis monitoring of eDNA (Quantitative MiSeq)
- Environmental DNA sequencing (IonPGM, MiSeq, iSeq, MinION)
- Construction and analysis of mathematical model
- Statistics by R and Python
- C/C++ (beginner-level)
- Sequence data analysis (Claident, QIIME, UPARSE, DADA2, phyloseq)
- Nonlinear time-series analysis (Empirical Dynamic Modeling)