英文論文（査読付き）


Submitted manuscripts:

Toju H, Suzuki S, Sánchez-Pinillos, M, Shima G, Kageyama T, Hayashi I, Noguchi M, Fujita H, Goto Y, Nakaoka S, Ushio M, Ichihashi Y, Fricke WF, Mizumoto K, Takayasu L, Suda W, Takayasu M, Yamamichi M, Weckwerth W. (submitted) Microbiome stability: statistics for controlling and forecasting ecosystem-scale phenomena. 

Hayashi I, Sánchez-Pinillos M, Toju H (submitted) Stochastic Forces in Microbial Community Assembly: Founding Community Size Governs Divergent Ecological Trajectories. https://doi.org/10.1101/2025.08.09.669462


In preparation:

Fujita et al.,  Exploring candidate species driving successional changes in microbiome dynamics.

Hayashi et al., Colonization conditions and microbiome alternative states.

Kageyama et al., Dynamics of soybean-associated biomes in soil ecosystems.



2025

Fujita H, Yoshida S, Suzuki K, Toju H (2025) Alternative stable states of microbiome structure and soil ecosystem functions. Environmental Microbiome 20:28 [Link]


Shimizu H, Miyamoto J, Hisa K, Ohue-Kitano R, Takada H, Yamano M, Nishida A, Sasahara D, Masujima Y, Watanabe K, Nishikawa S, Takahashi S, Ikeda T, Nakajima Y, Yoshida N, Matsuzaki C, Kageyama T, Hayashi I, Matsuki A, Akashi R, Kitahama S, Ueyama M, Murakami T, Inuki S, Irie J, Satoh-Asahara N, Toju H, Mori H, Nakaoka S, Yamashita T, Toyoda A, Yamamoto K, Ohno H, Katayama T, Itoh H, Kimura I. (2025). Sucrose-preferring gut microbes prevent host obesity by producing exopolysaccharides. Nature Communications 16:1145 [Link]


2024

Noguchi M, Toju H (2024) Mycorrhizal and endophytic fungi structure contrasting but interdependent assembly processes. Environmental Microbiome 19:84 [Link]

Abrego N et al. (2024) Airborne DNA reveals predictable spatial and seasonal dynamics of fungi. Nature 631:835-842 [Link]

Ovaskainen O et al. (2024) Global Spore Sampling Project: a global, standardized dataset of airborne fungal DNA. Scientific Data 11:561 [Link]

Fujita H, Yoshida S, Suzuki S, Toju H (2024) Soil prokaryotic and fungal biome structures associated with crop disease status across the Japan Archipelago. mSphere 9: e00803-23 [Link]

Toju H, Suzuki SS, Baba YG. (2024) Dynamics of interaction networks and species’ contributions to community-scale flexibility. PNAS Nexus 3:page047 [Link]

Hayashi, Fujita H, Toju H (2024) Deterministic and stochastic processes generating alternative states of microbiomes. ISME Communications 4: ycae007 [Link]


2023

Nakamura N, Toju H, Kitajima K  (2023) Leaf, root and rhizosphere microbiomes of an invasive plant, Ardisia crenata, differ between its native and exotic ranges. Frontiers in Microbiology 14:1302167 [Link]

Fujita H, Ushio M, Suzuki K, Abe MS, Yamamichi Y, Yusuke Okazaki, 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 [Link]

Suzuki SS, Baba YG, Toju H (2023) Dynamics of species-rich predator–prey networks and seasonal alternations of core species. Nature Ecology & Evolution 7:1432-1443 [Link] [Online-only full text]

Fujita H, Ushio M, Suzuki K, Abe MS, Yamamichi Y, Yusuke Okazaki, 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.  [Link]

Fujita H, Ushio M, Suzuki K, Abe MS, Yamamichi Y, 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. [Link]

Yajima D, Fujita H, Hayashi I, Shima G, Suzuki K, Toju H (2023) Core species and interactions prominent in fish-associated microbiome dynamics. Microbiome. 11:53. [Link]


2022

Kageyama T, Toju H (2022) Effects of source sample amount on biodiversity surveys of bacteria, fungi, and nematodes in soil ecosystems. Frontiers in Ecology and Evolution  10:959945. https://doi.org/10.3389/fevo.2022.959945


2021

Hori, Y., Fujita, H., Himura, K., Narisawa, K. and Toju, H. (2021), Synergistic and Offset Effects of Fungal Species Combinations on Plant Performance. Frontiers in Microbiology 12:713180. https://doi.org/10.3389/fmicb.2021.713180

Kadowaki K, Yamamoto S, Sato H, Tanabe AS, Toju H (2021) Aboveground herbivores drive stronger plant species-specific feedback than belowground fungi to regulate tree community assembly. Oecologia 195:773-784 [Link]


2020

Toju H, Abe MS, Ishii C, Hori Y, Fujita H, Fukuda S (2020) Scoring species for synthetic community design: network analyses of functional core microbiomes. Frontiers in Microbiology 11:1361 [Link] [PDF]

Suetsugu K, Taketomi S, Tanabe AS, Haraguchi T, Tayasu I, Toju H (2020) Isotopic and molecular data support mixotrophy in Ophioglossum at the sporophytic stage. New Phytologist 228:415-419 [Link]


2019

Toju H, Tanaka Y (2019) Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes. Royal Society Open Science 6:181693 [Link] [PDF]

Toju H, Kurokawa H, Kenta T (2019) Factors influencing leaf- and root-associated communities of bacteria and fungi across 33 plant orders in a grassland. Frontiers in Microbiology 10:241 [Link] [PDF]

Sato H, Toju H (2019) Timing of evolutionary innovation: scenarios of evolutionary diversification in a species-rich fungal clade, Boletales. New Phytologist 222: 1670–1672. [Link] [PDF]

Toju H, Okayasu K, Notaguchi M (2019) Leaf-associated microbiomes of grafted tomato plants. Scientific Reports  9:1787 [Link] [PDF]


2018

Toju H, Sato H, Yamamoto, S, Tanabe AS (2018) Structural diversity across arbuscular mycorrhizal, ectomycorrhizal, and endophytic plant-fungus networks. BMC Plant Biology 18:292 [Link] [PDF]

Kadowaki K, Yamamoto S, Sato H, Tanabe AS, Hidaka A, Toju H(2018) Mycorrhizal fungi mediate the direction and strength of plant–soil feedbacks differently between arbuscular mycorrhizal and ectomycorrhizal communities. Communications Biology1:196 [Link] [PDF]

Toju H, Tanabe AS, Sato H (2018) Network hubs in root-associated fungal metacommunities. Microbiome 6:116 [Link] [PDF]

Kitada Y, Muramatsu K, Toju H, Kibe R, Benno Y, Kurihara S, Matsumoto M (2018) Bioactive polyamine production by a novel hybrid system comprising multiple indigenous gut bacterial strategies. Science Advances 4:eaat0062 [Link] [PDF]

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. [Link] [PDF]

Hiruma K, Kobae Y, Toju H (2018) Beneficial associations between Brassicaceae plants and fungal endophytes under nutrient-limiting conditions: evolutionary origins and host–symbiont molecular mechanisms. Current Opinion in Plant Biology 44:145-154. [Link]

Toju H, Sato H (2018) Root-associated fungi shared between arbuscular mycorrhizal and ectomycorrhizal conifers in a temperate forest. Frontiers in Microbiology 9:433 [Link] [PDF]

Amma S, Toju H, Wachrinrat C, Sato H, Tanabe AS, Artchawakom T, Kanzaki M (2018) Composition and diversity of soil fungi in Dipterocarpaceae-dominated seasonal tropical forests in Thailand. Microbes and Environments 33:135-143.

Toju H, Baba YG (2018) DNA metabarcoding of spiders, insects, and springtails for exploring potential linkage between above- and below-ground food webs. Zoological Letters 4:4 [Link] [PDF]

Toju H, Vannette RL, Gauthier MPL, Dhami MK, Fukami T (2018) Priority effects can persist across floral generations in nectar microbial metacommunities. Oikos 127:345-352 [Link]


2017

Peay KG, von Sperber C, Cardarelli E, Toju H, Francis CA, Chadwick OA, Vitousek PM (2017) Convergence and contrast in the community structure of Bacteria, Fungi and Archaea along a tropical elevation-climate gradient. FEMS Microbiology Ecology 93:fix045. [Link]

Toju H, Yamamichi M, Guimarães PR Jr, Olesen JM, Mougi A, Yoshida T, Thompson JN (2017) Species-rich networks and eco-evolutionary synthesis at the metacommunity level. Nature Ecology & Evolution 1:0024. [Link]

Kouduka M, Tanabe AS, Yamamoto S, Yanagawa K, Nakamura Y, Akiba F, Tomaru H, Toju H, Suzuki Y. (2017) Eukaryotic diversity in late Pleistocene marine sediments around a shallow methane hydrate deposit in the Japan Sea. Geobiology 15: 715-727.

Sato H, Tanabe AS, Toju H. (2017) Host shifts enhance diversification of ectomycorrhizal fungi: diversification rate analysis of the ectomycorrhizal fungal genera Strobilomyces and Afroboletus with a 80-gene phylogeny. New Phytologist 214: 443-454. [Link].


2016

Toju H, Kishida O, Katayama N, Takagi K (accepted) Networks depicting the fine-scale co-occurrences of fungi in soil horizons. PLOS ONE 11:e0165987 [Link] [PDF].

Toju H, Tanabe AS, Ishii HS (2016) Ericaceous plant–fungus network in a harsh alpine–subalpine environment. Molecular Ecology 25:3242–3257. [Link]

Toju H, Yamamoto S, Tanabe AS, Hayakawa T, Ishii HS (2016) Network modules and hubs in plant–root fungal biomes. Journal of the Royal Society Interface 13:20151097. [Link] [Archived.PDF]

Izuno A, Tanabe AS, Toju H, Yamasaki M, Indrioko S, Isagi Y (2016) Structure of phyllosphere fungal communities in a tropical dipterocarp plantation: a massively parallel next-generation sequencing analysis. Mycoscience 57:171-180. [Link]


2015

Toju H, Guimarães PR Jr, Olesen JM, and Thompson JN (2015) Below-ground plant–fungus network topology is not congruent with above-ground plant–animal network topology. Science Advances 1:e1500291. [Link] [PDF]

Sato H, Tanabe AS, Toju H. (2015) Contrasting diversity and host association of ectomycorrhizal basidiomycetes versus root-associated ascomycetes in a dipterocarp rainforest. PLOS ONE 10:e0125550. [Link]

Toju H (2015) High-throughput DNA barcoding for ecological network studies. Population Ecology 57:37-51. [Invited review in Special Feature] [Link] [Archived.PDF]


2014

Toju H, Guimarães PR Jr, Olesen JM, and Thompson JN (2014) Assembly of complex plant–fungus networks. Nature Communications 5:5273. [Link] [PDF]

Hata H, Tanabe AS, Yamamoto S, Toju H, Kohda M and Hori M (2014) Diet disparity among sympatric herbivorous cichlids in the same ecomorphs in Lake Tanganyika: amplicon pyrosequences on algal farms and stomach contents. BMC Biology 12:90. [Link] [PDF]

Yamamoto S, Sato H, Tanabe AS, Hidaka A, Kadowaki, K, and Toju H. (2014) Spatial segregation and aggregation of ectomycorrhizal and root-endophytic fungi in the seedlings of two Quercus species. PLoS ONE 9:e96363. [Link] [PDF]

Toju H, Sato H, and Tanabe AS. (2014) Diversity and spatial structure of belowground plant–fungal symbiosis in a mixed subtropical forest of ectomycorrhizal and arbuscular mycorrhizal plants. PLoS ONE 9: e86566. [Link] [PDF]

Kadowaki K, Sato H, Yamamoto S, Tanabe AS, Hidaka A and Toju H. (2014) Detection of the horizontal spatial structure of soil fungal communities in a natural forest. Population Ecology 56:301-310. [Link] [PDF]


2013

Toju H, Yamamoto S, Sato H, and Tanabe AS. (2013) Sharing of diverse mycorrhizal and root-endophytic fungi among plant species in an oak-dominated cool–temperate forest. PLoS ONE 8:  e78248. [Link] [PDF]

Tanabe AS and Toju H. (2013) Two new computational methods for universal DNA barcoding: A benchmark using barcode sequences of bacteria, archaea, animals, fungi, and land plants. PLoS ONE 8: e76910. [Link] [PDF]

Toju H, Sato H, Yamamoto S, Kadowaki K, Tanabe AS, Yazawa S, Nishimura O, and Agata K. (2013) How are plant and fungal communities linked to each other in below-ground ecosystems? A massively-parallel pyrosequencing analysis of the association specificity of root-associated fungi and their host plants. Ecology and Evolution 3: 3112-3124. [Link] [PDF].

Toju H, Yamamoto S, Sato H, Tanabe AS, Gilbert GS, and Kadowaki K. (2013) Community composition of root-associated fungi in a Quercus-dominated temperate forest: “co-dominance” of mycorrhizal and root-endophytic fungi. Ecology and Evolution 3: 1281-1293. [Link][PDF]

Toju H,Tanabe AS, Notsu Y, Sota T, and Fukatsu T. (2013) Diversification of endosymbiosis: replacements, co-speciation and promiscuity of bacteriocyte symbionts in weevils. The ISME Journal 7: 1378-1390. [Link]


2012

Toju H, Tanabe AS,Yamamoto S, and Sato H. High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples. (2012) PLoS ONE 7: e40863. [Link] [PDF]


2011

Iseki N, Sasaki A, and Toju H. (2011) Arms race between weevil rostrum length and camellia pericarp thickness: Geographical cline and theory. Journal of Theoretical Biology 285: 1-9. [Link]

Toju H, Ueno S, Taniguchi F, and Sota T. (2011) Metapopulation structure of a seed-predatory weevil and its host plant in arms race coevolution. Evolution 65: 1707-1722. [Link]

Toju H, Abe H, Ueno S, Miyazawa Y, Taniguchi F, Sota T, and Yahara T. (2011) Climatic gradients of arms race coevolution. The American Naturalist 177: 562-573. [Link]

Toju H. (2011) Weevils and camellias in a Darwin’s race: model system for the study of eco-evolutionary interactions between species. Ecological Research 26: 239-251. [Miyadi Award Review] [Link].

Toju H and Fukatsu T. (2011) Diversity and infection prevalence of endosymbionts in natural populations of the chestnut weevil: relevance of local climate and host plants. Molecular Ecology 20: 853-868. [Link]


2010

Toju H, Hosokawa T, Koga R, Nikoh, N, Meng X-Y, Kimura N, and Fukatsu T. (2010) “Candidatus Curculioniphilus buchneri”, a novel clade of bacterial endocellular symbionts from weevils of the genus Curculio. Applied and Environmental Microbiology 76: 275-282. [Link].


2009

Toju H (2009) Natural selection drives the fine-scale divergence of a coevolutionary arms race involving a long-mouthed weevil and its obligate host plant. BMC Evolutionary Biology 9: 273. [PDF]

Toju H and Sota T. (2009) Do arms races punctuate evolutionary stasis? Unified insights from phylogeny, phylogeography and microevolutionary processes. Molecular Ecology 18: 3940-3954. [Link]


2008

Toju H (2008) Fine-scale local adaptation of weevil mouthpart length and camellia pericarp thickness: altitudinal gradient of a putative arms race. Evolution 62: 1086–1102. [Link]


2007

Toju H (2007) Interpopulation variation in predator foraging behaviour promotes the evolutionary divergence of prey. Journal of Evolutionary Biology 20: 1544-1553. [Link]


2006

Toju H and Sota T. (2006) Phylogeography and the geographic cline in the armament of a seed-predatory weevil: effects of historical events vs.natural selection from the host plant. Molecular Ecology 15: 4161-4173. [Link]

Toju H and Sota T. (2006) Adaptive divergence of scaling relationships mediates the arms race between a weevil and its host plant. Biology Letters 2: 539-542. [PDF]

Toju H and Sota T. (2006) Imbalance of predator and prey armament: geographic clines in phenotypic interface and natural selection. The American Naturalist 167: 105-117. [Link]


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