Embedded Files
2025
78. Wan-Hsuan Cheng, Takeshi Miki, Chao-Chen Lai, Fuh-Kwo Shiah, Chia-Ying Ko, Chih-hao Hsieh, Chun-Wei Chang* (2025). Biodiversity consistently promotes ecosystem multifunctionality across multiple temporal scales in an aquatic microbial community. Ecology Letters https://onlinelibrary.wiley.com/doi/10.1111/ele.70185
77. Wan-Hsuan Cheng**, Takeshi Miki**, Motohiro Ido, Kinuyo Yoneya, Kazuaki Matsui, Taichi Yokokawa, Hiroki Yamanaka, Shin-ichi Nakano (2025). Advancing marker-gene-based methods for prokaryote-mediated multifunctional redundancy: exploring random and nonrandom extinctions in a catchment. Freshwater Biology, http://dx.doi.org/10.1111/fwb.70020 (** Equaly contributed)
Read-only free link: https://onlinelibrary.wiley.com/share/author/NS4DG7WKX3PBAHRECEMG?target=10.1111/fwb.70020
76. Takeshi Miki*, Chun-Wei Chang, Po-Ju Ke, Arndt Telschow, Cheng-Han Tsai, Masayuki Ushio, Chih-hao Hsieh (2025) How to quantify interaction strengths? A critical rethinking of the interaction Jacobian and evaluation methods for non-parametric inference in time series analysis. Physica D. https://doi.org/10.1016/j.physd.2025.134613
(50 days free access link before May 04) https://authors.elsevier.com/a/1kmVbc2Eevp3Q
2024
(preprint) Takeshi Miki*, Chun-Wei Chang, Po-Ju Ke, Arndt Telschow, Cheng-Han Tsai, Masayuki Ushio, Chih-hao Hsieh (2024) How to quantify interaction strengths? A critical rethinking of the interaction Jacobian and evaluation methods for non-parametric inference in time series analysis. https://arxiv.org/abs/2411.09030
75. Akiko Ebihara, Hideki Fukuda, Yosuke Yamada, Taichi Yokokawa, Takeshi Miki and Toshi Nagata (2024) Structuring of particle-associated bacterial communities along the extracellular polymeric substance gradient of sinking and suspended particles in an oligotrophic, subtropical region of the western North Pacific Ocean. Frontiers in Marine Science, https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2024.1462522/full
74. Takeshi Miki*, Po-Ju Ke (2024) Macroscale vertical power-law distribution of bacteria in dark oceans can emerge from microscale bacteria-particle interactions. Journal of Theoretical Biology https://doi.org/10.1016/j.jtbi.2024.111956
73. Masahiro Nakamura et al. (2024) (Data Paper) Physiological profiling of the soil microbe community using the EcoPlate and assessment of soil properties at 74 planted forest sites across Japan. Ecological Research
https://esj-journals.onlinelibrary.wiley.com/doi/full/10.1111/1440-1703.12506
(Preprint) Takeshi Miki, Po-Ju Ke Macroscale vertical power-law distribution of bacteria in dark oceans can emerge from microscale bacteria-particle interactions. https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4884247#
(Preprint) Wan-Hsuan Cheng, Takeshi Miki, Motohiro Ido, Kinuyo Yoneya, Kazuaki Matsui, Taichi Yokokawa, Hiroki Yamanaka, Shin-ichi Nakano. Advancing marker-gene-based methods for prokaryote-mediated multifunctional redundancy: exploring random and nonrandom extinctions in a watershed. https://www.biorxiv.org/content/10.1101/2024.03.14.584931v1
2023
72. Kinuyo Yoneya*, Takeshi Miki, Noboru Katayama (2023) Plant volatiles and priority effects interactively determined initial community assembly of arthropods on multiple willow species. Ecology and Evolution https://onlinelibrary.wiley.com/doi/10.1002/ece3.10270
71. Takanori Kawase, Daisuke Kyogoku, Kazutaka Kawatsu, Noboru Katayama, Takeshi Miki*, Michio Kondoh (2023) Time series analysis showing how different environmental conditions affect the interspecific interactions of Callosobruchus maculatus and Callosobruchus chinensis. Population Ecology https://doi.org/10.1002/1438-390X.12160
70. Takeshi Miki*, Hiroki Yamanaka*, Atsushi Sogabe, Koji Omori, Yasuhisa Saito, Toshifumi Minamoto, Kimiko Uchii, Mie N.Honjo, Alata A. Suzuki, Yukihiro Kohmatsu, Zen’ichiro Kawabata (2023) Spatial epidemiology model can explain the seasonal dynamics of infectious disease Cyprinid herpesvirus 3 (CyHV-3) by thermoregulation behavior of the host, common carp (Cyprinus carpio). Theoretical Ecology https://rdcu.be/deUw4
69. Kinuyo Yoneya, Masayuki Ushio, Takeshi Miki (2023) Non-destructive collection and metabarcoding of arthropod environmental DNA remained on a terrestrial plant. https://www.nature.com/articles/s41598-023-32862-4
68. Kazuaki Matsui, Takeshi Miki (2023) Microbial community composition and function in an urban waterway with combined sewer overflows before and after implementation of a stormwater storage pipe. PeerJ https://doi.org/10.7717/peerj.14684
67. Kinuyo Yoneya, Takeshi Miki, Junji Takabayashi (2023) Initial herbivory and exposure to herbivory-induced volatiles enhance arthropod species richness by diversifying community assemblages. Front. Ecol. Evo. https://doi.org/10.3389/fevo.2022.1031664
2022
66. Chuan-Ya Lin, Takeshi Miki, Tomonori Kume* (2022) Potential Factors Canceling Interannual Cycles of Shoot Production in a Moso Bamboo (Phyllostachys pubescens) Stand. Front. For. Glob. Change, 07 July 2022 Sec. Tropical Forests https://doi.org/10.3389/ffgc.2022.913426
65. Takeshi Miki*, Masahiro Nakamura, Hiroko Kurokawa, Kazuaki Matsui (2022) Preface: “Idea Paper” for sharing diverse research ideas. Ecological Research 37: 450-454 https://doi.org/10.1111/1440-1703.12338
64. Wan-Hsuan Cheng, Chih-hao Hsieh, Chun-Wei Chang, Fuh-Kwo Shiah, Takeshi Miki* (2022) New index of functional specificity to predict the redundancy of ecosystem functions in microbial communities. FEMS Microbiology Ecology 98:1-9 (here)
63. Chun-Wei Chang, Takeshi Miki, Hao Ye, Sami Souissi, Rita Adrian, Orlane Anneville, Helen Agasild, Syuhei Ban, Yaron Be’eri-Shlevin, Yin-Ru Chiang, Heidrun Feuchtmayr, Gideon Gal, Satoshi Ichise, Maiko Kagami, Michio Kumagai, Xin Liu, Shin-Ichiro S. Matsuzaki, Marina M. Manca, Peeter Nõges, Roberta Piscia, Michela Rogora, Fuh-Kwo Shiah, Stephen J. Thackeray, Claire E. Widdicombe, Jiunn-Tzong Wu, Tamar Zohary & Chih-hao Hsieh* (2022) Causal networks of phytoplankton diversity and biomass are modulated by environmental context. Nature Communications https://doi.org/10.1038/s41467-022-28761-3
62. Luca Zoccarato*, Daniel Sher*, Takeshi Miki , Daniel Segrè, Hans-Peter Grossart* (2022) A comparative whole-genome approach identifies bacterial traits for marine microbial interactions. Communications Biology 5, Article number: 276 (2022)
2021
61. Chun-Wei Chang, Takeshi Miki, Masayuki Ushio, Po-Ju Ke, Hsiao-Pei Lu, Fuh-Kwo Shiah, Chih-hao Hsieh* . Reconstructing large interaction networks from empirical time series data. Ecology Letters https://doi.org/10.1111/ele.13897
60. Kinuyo Yoneya, Takeshi Miki*, Silke Van den Wyngaert, Hans-Peter Grossart, Maiko Kagami (2021) Non-random patterns of chytrid infections on phytoplankton host cells: mathematical and chemical ecology approaches. Aquatic Microbial Ecology 87: 1-15 https://doi.org/10.3354/ame01966
59. Pak-Yin CHEUNG, Yoko NOZAWA, Takeshi MIKI* (2021) Ecosystem engineering structures facilitate ecological resilience: a coral reef model. Ecological Research. http://doi.org/10.1111/1440-1703.12230 Ecological Research Paper Award (Open Access!)
(Preprint) Chun-Wei Chang, Takeshi Miki, Masayuki Ushio, Hsiao-Pei Lu, Fuh-Kwo Shiah, Chih-hao Hsieh (2021) Reconstructing large networks with time-varying interactions. arXiv:2102.04069 https://arxiv.org/abs/2102.04069
58. Yuji Tomaru, Haruo Yamaguchi, and Takeshi Miki (2021) Growth Rate-dependent Cell Death of Diatoms due to Viral Infection and Their Subsequent Coexistence in a Semi-continuous Culture System. https://www.jstage.jst.go.jp/browse/jsme2 doi:10.1264/jsme2.ME20116
2020
57. (Peer reviewed book chapter) Takeshi Miki (2020) Mathematical Modeling on Microbes and Their Roles in Community and Ecosystem: How to Handle Microbial Diversity in Modeling. In Diversity of Functional Traits and Interactions: Perspectives on Community Dynamics (Akihiko Mougi, ed), Springer, pp.109-157.
56. Chun‐Wei Chang, Hao Ye, Takeshi Miki, Ethan R. Deyle, Sami Souissi, Orlane Anneville, Rita Adrian, Yin‐Ru Chiang, Satoshi Ichise, Michio Kumagai, Shin‐ichiro S. Matsuzaki, Fuh‐Kwo Shiah, Jiunn‐Tzong Wu, Chih‐hao Hsieh, George Sugihara (2020) Long‐term warming destabilizes aquatic ecosystems through weakening biodiversity‐mediated causal networks. Global Change Biology 26(11): https://doi.org/10.1111/gcb.15323
55. Takeshi Miki, Masahiro Nakamura , Kazuaki Matsui, Hazime Mizoguchi, Emi Tamaki (2020) Promoting the sharing of ideas via “Idea Papers”. Ecological Research 35(4): https://doi.org/10.1111/1440-1703.12156 詳しくはこちら
(Preprint of [57]) Chun-Wei Chang, Hao Ye, Takeshi Miki, Ethan R. Deyle, Sami Souissi, Orlane Anneville, Rita Adrian, Yin-Ru Chiang, Satoshi Ichise, Michio Kumagai, Shin-ichiro S. Matsuzaki, Fuh-Kwo Shiah, Jiunn-Tzong Wu, Chih-hao Hsieh, George Sugihara (2020) Long-term warming weakens stabilizing effects of biodiversity in aquatic ecosystems. bioRxiv doi: https://doi.org/10.1101/2020.01.06.896746
2019
54. Wye‐Lup Kong, Takeshi Miki, Ya‐Ying Lin, Wataru Makino, Jotaro Urabe, Shi‐Hong Gu, Ryuji J. Machida* (2019) Nuclear and mitochondrial ribosomal ratio as an index of animal growth rate. Limnology and Oceanography Methods https://aslopubs.onlinelibrary.wiley.com/doi/10.1002/lom3.10334
(Preprint). Chun-Wei Chang, Chih-hao Hsieh, Takeshi Miki (2019) Ecosystem-level stabilizing effects of biodiversity via nutrient-diversity feedbacks in multitrophic systems. arXiv:1909.0557
53. Thijs Frenken, Takeshi Miki, Maiko Kagami, Dedmer B. Van de Waal, Ellen Van Donk, Thomas Rohrlack, Alena S. Gsell * (2019) The potential of zooplankton in constraining chytrid epidemics in phytoplankton hosts. Ecology https://doi.org/10.1002/ecy.2900 (open access)
2018
52. Maria Arias-Andres, Marie Therese Kettner, Takeshi Miki, Hans-Peter Grossart* (2018) Microplastics: New substrates for heterotrophic activity contribute to altering organic matter cycles in aquatic ecosystems. Science of The Total Environment 635: 1152-1159
51. Yoshikazu Kato*, Michio Kondoh, Naoto F. Ishikawa, Hiroyuki Togashi, Yukihiro Kohmatsu, Mayumi Yoshimura, Chikage Yoshimizu, Takashi F. Haraguchi, Yutaka Osada, Nobuhito Ohte, Naoko Tokuchi, Noboru Okuda, Takeshi Miki, Ichiro Tayasu (2018) Using food network unfolding to evaluate food-web complexity in terms of biodiversity: theory and applications. Ecology Letters 21: 1065-1074
50. T Miki**, T Yokokawa**, P-J Ke, I-F Hsieh, C-h Hsieh, T Kume, K Yoneya, K Matsui* (2018) Statistical recipe for quantifying microbial functional diversity from EcoPlate metabolic profiling. Ecological Research 33: 249-260. **Equally contributed, *Corresponding.
The related R tutorial is available in English and Japanese.
https://sites.google.com/view/cer-ecoplate/lecture-materials-ecoplate-analysis
2017
49. I-Ching Chen, Chih-hao Hsieh, Michio Kondoh, Hsing-Juh Lin, Takeshi Miki*, Masahiro Nakamura*, Takayuki Ohgushi, Jotaro Urabe, Takehito Yoshida (2017) Filling the gaps in ecological studies of socioecological systems. Ecological Research 32: 873-885. OPEN ACCESS
48. Thijs Frenken et al. (2017) Integrating chytrid fungal parasites into plankton ecology: research gaps and needs. Environmental Microbiology, DOI: 10.1111/1462-2920.13827
47. Masayuki Itoh, Hisaya Kojima, Pei-Chi Ho, Chun-Wei Chang, Tzong-Yueh Chen, Silver Sung-Yun Hsiao, Yuki Kobayashi, Megumi Fujibayashi, Shih-Ji Kao, Chih-hao Hsieh, Manabu Fukui, Noboru Okuda, Takeshi Miki*, Fuh-Kwo Shiah* . Integrating isotopic, microbial, and modeling approaches to understand methane dynamics in a frequently disturbed deep reservoir in Taiwan. Ecological Research 32: 861-871. Ecological Research Paper Award Open Access
46. Arndt Telschow*, Florian Grziwotz, Philip Crain, Takeshi Miki, James W. Mains, George Sugihara, Stephen L Dobson*, Chih-hao Hsieh* (2017) Infections of Wolbachia may destabilize mosquito population dynamics. Journal of Theoretical Biology 428:98-105
2016
45. P-C Ho*, N Okuda, Takeshi Miki, M Itoh, F-K Shiah, C-W Chang, SSY Hsiao, S-J Kao, M Fujibayashi, C-H Hsieh (2016) Summer profundal hypoxia determines the coupling of methanotrophic production and the pelagic food web in a subtropical reservoir. Freshwater Biology 61: 1694-1706
44. I-F. Hsieh, T. Kume*, M-Y Lin, C-H Cheng, Takeshi Miki. Characteristics of soil CO2 efflux under an invasive species, Moso bamboo, in forests of central Taiwan. Tree: Structure and Function 30: 1749-1759
43. Takeshi Miki, Hideyuki Doi* (2016) Leaf phenological shifts and plant-microbe-soil interactions can determine forest productivity and nutrient cycling under climate change in an ecosystem model. Ecological Research 31: 263-
42. Kota Ikeda*, Takeshi Miki (2016) Regime shift in a phytoplankton-phosphorus model with vertical structure and seasonality. Tamkang Journal of Mathematics 47
41. Koji Hamasaki, Akito Taniguchi, Yuya Tada, Ryo Kaneko, and Takeshi Miki (2016) Active populations of rare microbes in oceanic environments as revealed by bromodeoxyuridine incorporation and 454 tag sequencing.Gene 576: 650-656
2015
40. Po-Ju Ke*, Takeshi Miki (2015) Incorporating the soil environment and microbial community into plant competition theory. frontiers in Microbiology 10.3389/fmicb.2015.01066
39. Masayuki Itoh*, Yuki Kobayashi, Tzong-Yueh Chen, Takeshi Tokida, Manabu Fukui, Hisaya Kojima, Takeshi Miki, Ichiro Tayasu, Fuh-Kwo Shiah and Noboru Okuda (2015) Effect of inter-annual variation in winter vertical mixing on CH4 dynamics in a subtropical reservoir. Journal of Geophysical Research Biogeosciences DOI: 10.1002/2015JG002972
38. Kinuyo Yoneya, Takeshi Miki* (2015) Coevolution of foraging behaviour in herbivores and their natural enemies predicts multifunctionality of herbivore-induced plant volatiles. Functional Ecology (Open Access) DOI: 10.1111/1365-2435.12398
37. Po-Ju Ke, Takeshi Miki*, Tzung-Su Ding (2015) The soil microbial community predicts the importance of plant traits in plant-soil feedback. New Phytologist DOI: 10.1111/nph.13215
2014
36. Cheng-Han Tsai, Takeshi Miki, Chun-Wei Chang, Kanako Ishikawa, Satoshi Ichise, Michio Kumagai, Chih-hao Hsieh* (2014) Phytoplankton functional group dynamics explain species abundance distribution in a directionally changing environment. Ecology 95:3335–3343
35. Maiko Kagami*, Takeshi Miki, Gaku Takimoto (2014) Mycoloop: chytrids in aquatic food webs. frontiers in Microbiology (OPEN ACCESS!!)
34. Tsutomu Enoki, Tohru Nakashizuka, Shin-ichi Nakano, Takeshi Miki, Yu-Pin Lin, Masahiro Nakaoka, Eri Mizumachi, Hideaki Shibata (2014) Progress in the 21st century: a roadmap for the Ecological Society of Japan.Ecological Research 29: 357-368 (OPEN ACCESS!!)
33. Chun-Wei Chang, Fuh-Kwo Shiah, Jiunn-Tzong Wu, Takeshi Miki, Chih-hao Hsieh*(2014) The role of food availability and phytoplankton community dynamics in the seasonal succession of zooplankton community in a subtropical reservoir. Limnologica - Ecology and Management of Inland Waters 46:131-138
32. Takeshi Miki, Taichi Yokokawa, Kazuaki Matsui* (2014) Biodiversity and multifunctionality in a microbial community: a novel theoretical approach to quantify functional redundancy. Proceedings of The Royal Society B(OPEN ACCESS!!) vol.281 no.1776 20132498
31. Chun-Wei Chang, Takeshi Miki, Fuh-Kwo Shiah, Shuh-ji Kao, Jiuun_Tzong Wu, Akash R. Sastri, and Chih-hao Hsieh* (2014) Linking secondary structure of individual size distributions with nonlinear size-trophic level relationship in food web. Ecology 95:897-909
2013
30. M. Ushio*, T. Miki, TC Balser (2013) A coexisting fungal-bacterial community stabilizes soil decomposition activity in a microcosm experiment. PLOS ONE (LINK).
29. Chiaki Motegi*, Toshi Nagata, Takeshi Miki, Markus G. Weinbauer, Louis Legendre, Fereidoun Rassoulzadegan. (2013) Interactive effects of viral and bacterial proudction on marine bacterial diversity. PLOS ONE (Link)
28. Pei-Chi Ho, Chun-Wei Chang, Chih-hao Hsieh, Fuh-Kwo Shiah, T. Miki* (2013) Effects of increasing nutrient supply and omnivorous feeding on the size spectrum slope: a size-based nutrient-phytoplankton-zooplankton model. Population Ecology 55: 247-259
27. Wei-Ting Lin, Chih-hao Hsieh, T. Miki* (2013) Difference in adaptive dispersal ability can promote species coexistence in fluctuating environments. PLOS ONE (Link)
2012
26. T. Miki (2012) Microbe-mediated plant-soil feedback and its roles in a changing world. Ecological Research27: 509-520 ESJ Miyadi Award Paper
25. Shin Fukui*, T. Miki, Masakazu Shimada (2012) Consumers can enhance ecosystem productivity and stability in changing environments. Population Ecology 54: 177-186
2011
24. Yuya Tada, Akito Taniguchi, Ippei Nagao, T. Miki, Mitsuo Uematsu, Atsushi Tsuda, Koji Hamasaki (2011) Differing growth Responses of major phylogenetic groups of marine bacteria to natural phytoplankton blooms in the western North Pacific Ocean. Applied and Environmental Microbiology 77: 4055-4065
23. Joe Yuichiro Wakano, Kota Ikeda, T. Miki*, Masayasu Mimura (2011) Effective dispersal rate is a function of habitat size and corridor shape: mechanistic formulation of a two-patch compartment model for spatially continuous systems. Oikos 120: 1712-1720
22. T. Miki*, Gaku Takimoto, Maiko Kagami (2011) Roles of parasitic fungi in aquatic food webs: a theoretical approach. Freshwater Biology 56:1173-1183
2010
21. Yasuhisa Saito, T. Miki* (2010) Species coexistence under resource competition and intra- and interspecific direct competition in the chemostat. Theoretical Population Biology 78: 173-182
20. T. Miki*, Masayuki Ushio, Shin Fukui, Michio Kondoh. (2010) Functional diversity of microbial decomposers facilitates plant coexistence in a plant-microbe-soil feedback model. Proceedings of the National Academy of Sciences, USA 107:14251-14256, doi:10.1073/pnas.0914281107
19. Shunsuke Utsumi*, Yoshino Ando, T. Miki (2010) Linkages among trait-mediated indirect effects: a new framework for the indirect interaction web. Population Ecology 52:485-497
18. T. Miki*, Stephan Jacquet (2010) Indirect interactions in the microbial world: specificities and similarities to plant-insect systems. Population Ecology 52:475-483
17. Stephan Jacquet*, T. Miki, Rachel Noble, Peter Pedduzi, Steven Wilhelm (2010) Viruses in aquatic ecosystems: important advancements of the last 20 years and prospects for the future in the field of microbial oceanography and limnology. Advances in Oceanography and Limnology 1: 71-101
16. Takefumi Nakazawa*, T. Miki, Toshiyuki Namba (2010) Influence of predator-specific defense adaptation on intraguild predation. Oikos 119:418-427
2009
15. Chiaki Motegi, Toshi Nagata*, T. Miki, Markus G. Weinbauer, Louis Legendre, Fereidoun Rassoulzadegan (2009) Viral control of bacterial growth efficiency in marine pelagic environments. Limnology and Oceanography54: 1901-1910
14. Masayuki Ushio*, T. Miki, Kanehiro Kitayama (2009) Phenolic control of plant nitrogen acquisition through the inhibition of soil microbial decomposition processes: a plant-microbe competition model. Microbes and Environments 24: 180-187
13. T. Miki*, Luca Giuggioli, Yutaka Kobayashi, Toshi Nagata, Simon A. Levin (2009) Vertically-structured prokaryotic community can control the efficiency of the biological pump in the oceans. Theoretical Ecology 2: 199-216
12. T. Miki* (2009) A new graphical model for untangling complex relationships among environment, biodiversity, and ecosystem functioning. Ecological Research 24: 937-941
11. Atsushi Yamauchi*, T. Miki (2009) Intraspecific niche flexibility facilitates species coexistence in a competitive community with a fluctuating environment.Oikos 118:55-66
2008
10. T. Miki*, Taichi Yokokawa, Toshi Nagata, Norio Yamamura (2008) Immigration of prokaryotes to local environments enhances remineralization efficiency of sinking particles: a metacommunity model. Marine Ecology Progress Series 366:1-14 (free access!)
9. T. Miki, Stephan Jacquet* (2008) Complex interactions in the microbial world: under-explored key links between viruses, bacteria and protozoan grazers in aquatic environments. Aquatic Microbial Ecology 51:195-208
8. T. Miki*, Takefumi Nakazawa, Taichi Yokokawa & Toshi Nagata (2008) Functional consequences of viral impacts on bacterial communities: a food-web model analysis. Freshwater Biology 53:1142-1153
-2007
7. T. Miki*, M. Ueki, Z. Kawabata, & N. Yamamura (2007) Long-term dynamics of catabolic plasmids introduced to a microbial community in a polluted environment: mathematical model. FEMS Microbiology Ecology 62:211-221
6. Gaku Takimoto*, T. Miki, & Maiko Kagami (2007) Intraguild predation promotes complex alternative states along a productivity gradient . Theoretical Population Biology 72:264-273
5. M. Nakamura* , S. Utsumi, T. Miki & T. Ohgushi (2005) Flood initiates bottom-up cascades in a tri-trophic systems: host plant regrowth increases densities of a leaf beetle and its predators. Journal of Animal Ecology 74: 683-691
4. T. Miki* & N. Yamamura (2005) Intraguild predation reduces bacterial richness and loosens the viral loop in aquatic systems: 'kill the killer of the winner' hypothesis. Aquatic Microbial Ecology 40: 1-12
3. T. Miki* & N. Yamamura (2005) Theoretical model for interactions between particle-associated and free-living bacteria to predict functional composition and succession in the bacterial communities. Aquatic Microbial Ecology39: 35-46
2. T. Miki* & N. Yamamura (2005) Effects of asynchronous fluctuations in DOC supply and bacterial growth on biodegradation efficiency. Ecological Modelling 183: 281-299
1. T. Miki* & M. Kondoh (2002) Feedbacks between nutrient cycling and vegetation predict plant species coexistence and invasion. Ecology Letters 5: 624-633
*Corresponding author
Proceedings and Books
1. T. Miki (2012) Bacterial community should be considered in ecosystem model in the ocean? - Comparison between community-based model, black box model, and exponential decay model. Interdisciplinary Studies on Environmental Chemistry 6 pp407-418
2. T. Miki (2020) Mathematical modeling on microbes and their roles in community and ecosystem: how to handle microbial diversity in modeling? Diversity of Functional Traits and Interactions (Akihiko Mougi eds) Springer
3. Akira. S. Mori, Takehiro Sasaki, Maiko Kagami, Takeshi Miki, and Moriaki Yasuhara (2022) Feedbacks between biodiversity and climate change. in The Ecological and Societal Consequences of Biodiversity Loss ISBN 9781789450729
日本語総説
1. 三木 健 (2006) 生物多様性と生物間相互作用からの物質循環研究: 新しい方法論の芽生え. 日本生態学会誌５６巻：240-252
2. 三木 健 (2007) 細菌群集の時空間分布と物質循環をつなぐ：細菌とメタ群集理論. 日本生態学会誌５７巻：398-406
3. 三木 健・松井一彰・横川太一・西田貴明・小林由紀・内井喜美子 (2007) マイクロビアル・プールと生物多様性. 日本生態学会誌５７巻:424-431
4. 三木 健 (2008) 細菌の系統的多様性が可能にする集団レベルの可塑的応答. 日本微生物生態学会誌２３巻:51-57
5. 松井一彰・横川太一・上田匡邦・道越祐一・水口亜樹・松田裕之・三木健 (2016) カルタヘナ議定書にある「生物の多様性の保全及び持続可能な利用への影響」はどのように評価できるか？：まとめと今後の展望．日本生態学会誌６６巻：325-335
日本語書籍
1. 三木 健 (2008) 群集―環境間のフィードバック―生物多様性と生態系機能のつながりを再考する. 京都大学学術出版会（「生態系と群集をむすぶ」第５章（大串隆之・近藤倫生・仲岡雅裕 編））
2. 三木 健 (2011) 微生物の集団生物学．共立出版（「微生物の生態学」第14章 (大園享司・鏡味麻衣子 編)）
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