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Sakata A, Sado T, Oka SI, Ushio M, Miya M. Collection of environmental DNA from stemflow for monitoring arboreal biodiversity: Preliminary validation using lichens. MethodsX 2023; 11:102448. [PMID: 38023308 PMCID: PMC10630645 DOI: 10.1016/j.mex.2023.102448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
The forest canopy harbors a diverse array of organisms. However, monitoring their biodiversity poses challenges due to limited accessibility and the vast taxonomic diversity. To address these challenges, we present a novel method for capturing arboreal biodiversity by harnessing stemflow as a source of DNA from organisms inhabiting trees. Our method involves encircling the tree trunk with gauze, directing the stemflow along the gauze into a funnel, and collecting it in a plastic bag. We employed dual collection systems to retrieve environmental DNA (eDNA) from the stemflow: the gauze trap, designed to capture macroscopic biological fragments, and the plastic bag trap, which collected the stemflow itself. The trapped fragments and stemflow were separately filtered, and eDNA was subsequently extracted from the filter membranes. To validate our method, we focused on foliose lichens, which are easily observable on tree surfaces. We performed eDNA metabarcoding and successfully detected a majority of the observed foliose lichen species, including those not identified through visual observation alone.•We have developed a non-invasive and straightforward method for monitoring arboreal biodiversity by collecting eDNA from stemflow, which has been validated using lichens for its efficacy.•This cost-effective approach minimizes disruptions to tree ecosystems and is expected to provide an efficient means of sampling and monitoring arboreal organisms.
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Affiliation(s)
- Ayumi Sakata
- Natural History Museum and Institute, Chiba, Japan
| | - Tetsuya Sado
- Natural History Museum and Institute, Chiba, Japan
| | | | - Masayuki Ushio
- Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Masaki Miya
- Natural History Museum and Institute, Chiba, Japan
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Fujita H, Ushio M, Suzuki K, Abe MS, Yamamichi M, Okazaki Y, Canarini A, Hayashi I, Fukushima K, Fukuda S, Kiers ET, Toju H. Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics. Front Microbiol 2023; 14:1261137. [PMID: 38033594 PMCID: PMC10684785 DOI: 10.3389/fmicb.2023.1261137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Species utilizing the same resources often fail to coexist for extended periods of time. Such competitive exclusion mechanisms potentially underly microbiome dynamics, causing breakdowns of communities composed of species with similar genetic backgrounds of resource utilization. Although genes responsible for competitive exclusion among a small number of species have been investigated in pioneering studies, it remains a major challenge to integrate genomics and ecology for understanding stable coexistence in species-rich communities. Here, we examine whether community-scale analyses of functional gene redundancy can provide a useful platform for interpreting and predicting collapse of bacterial communities. Through 110-day time-series of experimental microbiome dynamics, we analyzed the metagenome-assembled genomes of co-occurring bacterial species. We then inferred ecological niche space based on the multivariate analysis of the genome compositions. The analysis allowed us to evaluate potential shifts in the level of niche overlap between species through time. We hypothesized that community-scale pressure of competitive exclusion could be evaluated by quantifying overlap of genetically determined resource-use profiles (metabolic pathway profiles) among coexisting species. We found that the degree of community compositional changes observed in the experimental microbiome was correlated with the magnitude of gene-repertoire overlaps among bacterial species, although the causation between the two variables deserves future extensive research. The metagenome-based analysis of genetic potential for competitive exclusion will help us forecast major events in microbiome dynamics such as sudden community collapse (i.e., dysbiosis).
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Affiliation(s)
- Hiroaki Fujita
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Masayuki Ushio
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
- Department of Ocean Science (OCES), The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
| | - Kenta Suzuki
- Integrated Bioresource Information Division, BioResource Research Center, RIKEN, Tsukuba, Ibaraki, Japan
| | - Masato S. Abe
- Faculty of Culture and Information Science, Doshisha University, Kyotanabe, Kyoto, Japan
| | - Masato Yamamichi
- Center for Frontier Research, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Yusuke Okazaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Alberto Canarini
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Ibuki Hayashi
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Keitaro Fukushima
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima, Japan
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Laboratory for Regenerative Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - E. Toby Kiers
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
- Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, Japan
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Ushio M, Saito H, Tojo M, Nagano AJ. An ecological network approach for detecting and validating influential organisms for rice growth. eLife 2023; 12:RP87202. [PMID: 37702717 PMCID: PMC10499375 DOI: 10.7554/elife.87202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023] Open
Abstract
How to achieve sustainable food production while reducing environmental impacts is a major concern in agricultural science, and advanced breeding techniques are promising for achieving such goals. However, rice is usually grown under field conditions and influenced by surrounding ecological community members. How ecological communities influence the rice performance in the field has been underexplored despite the potential of ecological communities to establish an environment-friendly agricultural system. In the present study, we demonstrate an ecological-network-based approach to detect potentially influential, previously overlooked organisms for rice (Oryza sativa). First, we established small experimental rice plots, and measured rice growth and monitored ecological community dynamics intensively and extensively using quantitative environmental DNA metabarcoding in 2017 in Japan. We detected more than 1000 species (including microbes and macrobes such as insects) in the rice plots, and nonlinear time series analysis detected 52 potentially influential organisms with lower-level taxonomic information. The results of the time series analysis were validated under field conditions in 2019 by field manipulation experiments. In 2019, we focused on two species, Globisporangium nunn and Chironomus kiiensis, whose abundance was manipulated in artificial rice plots. The responses of rice, namely, the growth rate and gene expression patterns, were measured before and after the manipulation. We confirmed that, especially in the G. nunn-added treatment, rice growth rate and gene expression pattern were changed. In the present study, we demonstrated that intensive monitoring of an agricultural system and the application of nonlinear time series analysis were helpful to identify influential organisms under field conditions. Although the effects of the manipulations were relatively small, the research framework presented here has future potential to harness the ecological complexity and utilize it in agriculture. Our proof-of-concept study would be an important basis for the further development of field-basis system management.
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Affiliation(s)
- Masayuki Ushio
- Hakubi Center, Kyoto UniversityKyotoJapan
- Center for Ecological Research, Kyoto UniversityOtsuJapan
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, KowloonHong Kong SARChina
| | - Hiroki Saito
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural SciencesOkinawaJapan
| | - Motoaki Tojo
- Graduate School of Agriculture, Osaka Metropolitan UniversityOsakaJapan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku UniversityOtsuJapan
- Institute for Advanced Biosciences, Keio UniversityTsuruokaJapan
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Ushio M, Sado T, Fukuchi T, Sasano S, Masuda R, Osada Y, Miya M. Temperature sensitivity of the interspecific interaction strength of coastal marine fish communities. eLife 2023; 12:RP85795. [PMID: 37431235 PMCID: PMC10393047 DOI: 10.7554/elife.85795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023] Open
Abstract
The effects of temperature on interaction strengths are important for understanding and forecasting how global climate change impacts marine ecosystems; however, tracking and quantifying interactions of marine fish species are practically difficult especially under field conditions, and thus, how temperature influences their interaction strengths under field conditions remains poorly understood. We herein performed quantitative fish environmental DNA (eDNA) metabarcoding on 550 seawater samples that were collected twice a month from 11 coastal sites for 2 years in the Boso Peninsula, Japan, and analyzed eDNA monitoring data using nonlinear time series analytical tools. We detected fish-fish interactions as information flow between eDNA time series, reconstructed interaction networks for the top 50 frequently detected species, and quantified pairwise, fluctuating interaction strengths. Although there was a large variation, water temperature influenced fish-fish interaction strengths. The impact of water temperature on interspecific interaction strengths varied among fish species, suggesting that fish species identity influences the temperature effects on interactions. For example, interaction strengths that Halichoeres tenuispinis and Microcanthus strigatus received strongly increased with water temperature, while those of Engraulis japonicus and Girella punctata decreased with water temperature. An increase in water temperature induced by global climate change may change fish interactions in a complex way, which consequently influences marine community dynamics and stability. Our research demonstrates a practical research framework to study the effects of environmental variables on interaction strengths of marine communities in nature, which would contribute to understanding and predicting natural marine ecosystem dynamics.
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Affiliation(s)
- Masayuki Ushio
- Hakubi Center, Kyoto University, Kyoto, Hong Kong
- Center for Ecological Research, Kyoto University, Otsu, Japan
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, China
| | - Testuya Sado
- Natural History Museum and Institute, Chiba, Japan
| | | | - Sachia Sasano
- Maizuru Fisheries Research Station, Kyoto University, Maizuru, Japan
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Japan
| | - Reiji Masuda
- Maizuru Fisheries Research Station, Kyoto University, Maizuru, Japan
| | - Yutaka Osada
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Masaki Miya
- Natural History Museum and Institute, Chiba, Japan
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Fukasawa Y, Akai D, Ushio M, Takehi T. Electrical potentials in the ectomycorrhizal fungus Laccaria bicolor after a rainfall event. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2023.101229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
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Yoneya K, Ushio M, Miki T. Non-destructive collection and metabarcoding of arthropod environmental DNA remained on a terrestrial plant. Sci Rep 2023; 13:7125. [PMID: 37173307 PMCID: PMC10182007 DOI: 10.1038/s41598-023-32862-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 04/04/2023] [Indexed: 05/15/2023] Open
Abstract
Reliable survey of arthropods is a crucial for their conservation, community ecology, and pest control on terrestrial plants. However, efficient and comprehensive surveys are hindered by challenges in collecting arthropods and identifying especially small species. To address this issue, we developed a non-destructive environmental DNA (eDNA) collection method termed "plant flow collection" to apply eDNA metabarcoding to terrestrial arthropods. This involves spraying distilled or tap water, or using rainfall, which eventually flows over the surface of the plant, and is collected in a container that is set at the plant base. DNA is extracted from collected water and a DNA barcode region of cytochrome c oxidase subunit I (COI) gene is amplified and sequenced using a high-throughput Illumina Miseq platform. We identified more than 64 taxonomic groups of arthropods at the family level, of which 7 were visually observed or artificially introduced species, whereas the other 57 groups of arthropods, including 22 species, were not observed in the visual survey. These results show that the developed method is possible to detect the arthropod eDNA remained on plants although our sample size was small and the sequence size was unevenly distributed among the three water types tested.
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Affiliation(s)
- Kinuyo Yoneya
- Faculty of Agriculture, Kindai University, 3327-204, Nakamachi, Nara, 631-8505, Japan.
- Center for Biodiversity Science, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan.
| | - Masayuki Ushio
- Hakubi Center, Kyoto University, Kyoto, 606-8501, Japan
- Center for Ecological Research, Kyoto University, Otsu, 520-2113, Japan
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Takeshi Miki
- Center for Biodiversity Science, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
- Faculty of Advanced Science and Technology, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
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Ushio M, Watanabe K, Fukuda Y, Tokudome Y, Nakajima K. Computational capability of ecological dynamics. R Soc Open Sci 2023; 10:221614. [PMID: 37090968 PMCID: PMC10113807 DOI: 10.1098/rsos.221614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
Ecological dynamics is driven by complex ecological networks. Computational capabilities of artificial networks have been exploited for machine learning purposes, yet whether an ecological network possesses a computational capability and whether/how we can use it remain unclear. Here, we developed two new computational/empirical frameworks based on reservoir computing and show that ecological dynamics can be used as a computational resource. In silico ecological reservoir computing (ERC) reconstructs ecological dynamics from empirical time series and uses simulated system responses for information processing, which can predict near future of chaotic dynamics and emulate nonlinear dynamics. The real-time ERC uses real population dynamics of a unicellular organism, Tetrahymena thermophila. The temperature of the medium is an input signal and population dynamics is used as a computational resource. Intriguingly, the real-time ecological reservoir has necessary conditions for computing (e.g. synchronized dynamics in response to the same input sequences) and can make near-future predictions of empirical time series, showing the first empirical evidence that population-level phenomenon is capable of real-time computations. Our finding that ecological dynamics possess computational capability poses new research questions for computational science and ecology: how can we efficiently use it and how is it actually used, evolved and maintained in an ecosystem?
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Affiliation(s)
- Masayuki Ushio
- Hakubi Center, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, People's Republic of China
| | | | - Yasuhiro Fukuda
- Graduate School of Agricultural Science, Tohoku University, Yomogida Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | - Yuji Tokudome
- Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kohei Nakajima
- Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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Fujita H, Ushio M, Suzuki K, Abe MS, Yamamichi M, Iwayama K, Canarini A, Hayashi I, Fukushima K, Fukuda S, Kiers ET, Toju H. Alternative stable states, nonlinear behavior, and predictability of microbiome dynamics. Microbiome 2023; 11:63. [PMID: 36978146 PMCID: PMC10052866 DOI: 10.1186/s40168-023-01474-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Microbiome dynamics are both crucial indicators and potential drivers of human health, agricultural output, and industrial bio-applications. However, predicting microbiome dynamics is notoriously difficult because communities often show abrupt structural changes, such as "dysbiosis" in human microbiomes. METHODS We integrated theoretical frameworks and empirical analyses with the aim of anticipating drastic shifts of microbial communities. We monitored 48 experimental microbiomes for 110 days and observed that various community-level events, including collapse and gradual compositional changes, occurred according to a defined set of environmental conditions. We analyzed the time-series data based on statistical physics and non-linear mechanics to describe the characteristics of the microbiome dynamics and to examine the predictability of major shifts in microbial community structure. RESULTS We confirmed that the abrupt community changes observed through the time-series could be described as shifts between "alternative stable states" or dynamics around complex attractors. Furthermore, collapses of microbiome structure were successfully anticipated by means of the diagnostic threshold defined with the "energy landscape" analysis of statistical physics or that of a stability index of nonlinear mechanics. CONCLUSIONS The results indicate that abrupt microbiome events in complex microbial communities can be forecasted by extending classic ecological concepts to the scale of species-rich microbial systems. Video Abstract.
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Affiliation(s)
- Hiroaki Fujita
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2133, Japan.
| | - Masayuki Ushio
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2133, Japan
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Kenta Suzuki
- Integrated Bioresource Information Division, BioResource Research Center, RIKEN, Tsukuba, Ibaraki, 305-0074, Japan
| | - Masato S Abe
- Faculty of Culture and Information Science, Doshisha University, Kyotanabe, Kyoto, 610-0321, Japan
| | - Masato Yamamichi
- School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Koji Iwayama
- Faculty of Data Science, Shiga University, Hikone, 522-8522, Japan
| | - Alberto Canarini
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2133, Japan
| | - Ibuki Hayashi
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2133, Japan
| | - Keitaro Fukushima
- Faculty of Food and Agricultural Sciences, Fukushima University, Kanayagawa 1, Fukushima, Fukushima, 960-1296, Japan
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, 210-0821, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - E Toby Kiers
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2133, Japan.
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Fujita H, Ushio M, Suzuki K, Abe MS, Yamamichi M, Okazaki Y, Canarini A, Hayashi I, Fukushima K, Fukuda S, Kiers ET, Toju H. Facilitative interaction networks in experimental microbial community dynamics. Front Microbiol 2023; 14:1153952. [PMID: 37113242 PMCID: PMC10126487 DOI: 10.3389/fmicb.2023.1153952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/09/2023] [Indexed: 04/29/2023] Open
Abstract
Facilitative interactions between microbial species are ubiquitous in various types of ecosystems on the Earth. Therefore, inferring how entangled webs of interspecific interactions shift through time in microbial ecosystems is an essential step for understanding ecological processes driving microbiome dynamics. By compiling shotgun metagenomic sequencing data of an experimental microbial community, we examined how the architectural features of facilitative interaction networks could change through time. A metabolic modeling approach for estimating dependence between microbial genomes (species) allowed us to infer the network structure of potential facilitative interactions at 13 time points through the 110-day monitoring of experimental microbiomes. We then found that positive feedback loops, which were theoretically predicted to promote cascade breakdown of ecological communities, existed within the inferred networks of metabolic interactions prior to the drastic community-compositional shift observed in the microbiome time-series. We further applied "directed-graph" analyses to pinpoint potential keystone species located at the "upper stream" positions of such feedback loops. These analyses on facilitative interactions will help us understand key mechanisms causing catastrophic shifts in microbial community structure.
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Affiliation(s)
- Hiroaki Fujita
- Center for Ecological Research, Kyoto University, Kyoto, Japan
- *Correspondence: Hiroaki Fujita,
| | - Masayuki Ushio
- Department of Ocean Science (OCES), The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
| | - Kenta Suzuki
- Integrated Bioresource Information Division, BioResource Research Center, RIKEN, Tsukuba, Japan
| | - Masato S. Abe
- Faculty of Culture and Information Science, Doshisha University, Kyoto, Japan
| | - Masato Yamamichi
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Yusuke Okazaki
- Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | | | - Ibuki Hayashi
- Center for Ecological Research, Kyoto University, Kyoto, Japan
| | - Keitaro Fukushima
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima, Japan
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan
- Laboratory for Regenerative Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - E. Toby Kiers
- Amsterdam Institute for Life and Environment, Vrije Universiteit, Amsterdam, Netherlands
| | - Hirokazu Toju
- Center for Ecological Research, Kyoto University, Kyoto, Japan
- Hirokazu Toju,
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Tsujii Y, Sakai S, Ushio M, Aiba S, Kitayama K. Variations in the reproductive cycle of Bornean montane tree species along elevational gradients on ultrabasic and non‐ultrabasic soils. Biotropica 2022. [DOI: 10.1111/btp.13177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Yuki Tsujii
- Center for Ecological Research Kyoto University Otsu Japan
- Faculty of Science Kyushu University Fukuoka Japan
- School of Natural Sciences Macquarie University Sydney New South Wales Australia
- Hawkesbury Institute for the Environment Western Sydney University Penrith New South Wales Australia
| | - Shoko Sakai
- Center for Ecological Research Kyoto University Otsu Japan
| | - Masayuki Ushio
- Center for Ecological Research Kyoto University Otsu Japan
- Hakubi Center Kyoto University Kyoto Japan
- Department of Ocean Science The Hong Kong University of Science and Technology Kowloon Hong Kong SAR
| | - Shin‐ichiro Aiba
- Faculty of Environmental Earth Science Hokkaido University Sapporo Japan
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Inoue N, Sato M, Furuichi N, Imaizumi T, Ushio M. The relationship between eDNA density distribution and current fields around an artificial reef in the waters of Tateyama Bay, Japan. MBMG 2022. [DOI: 10.3897/mbmg.6.87415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Monitoring of artificial reefs (ARs) has been conducted through such methods as visual censuses, surveys using fishing gear, and echo sounder. These methods have disadvantages: visual census is not possible at ARs in deeper waters, fishing gear surveys are invasive to fish individuals, and echo sounders have difficulty in species identification. A new AR monitoring method is required to compensate for these disadvantages. While eDNA has become a valid monitoring tool for marine biodiversities, it is influenced by degradation and transport of the molecules that affect information about the spatio-temporal distribution of fish. An understanding of the relationship between current fields and eDNA distribution, particularly in open waters, is critical when using eDNA as an index for fish aggregation at ARs. We investigated the relationship between eDNA distribution and current fields around an AR for four dominant species (Engraulis japonicus, Parapristipoma trilineatum, Scomber spp and Trachurus japonicus) in Tateyama Bay, Japan. The highest density of fish schools is formed directly above or at the upstream side of ARs. If we assume that the center of eDNA originates at these locations at an AR and eDNA is simply transported by currents, a higher density of eDNA would distribute downstream from the AR. However, our results indicate that eDNA distribution is in accord with actual fish distribution, namely eDNA densities are more abundant in the upstream side of ARs. We thus consider that eDNA distribution is more influenced by actual distribution patterns than by the transport processes.
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Jiménez Elvira N, Ushio M, Sakai S. 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). MBMG 2022. [DOI: 10.3897/mbmg.6.84331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Flowers are colonized and inhabited by diverse microbes. Flowers have various mechanisms to suppress microbial growth, such as flower volatiles, reactive oxygen and secondary compounds. Besides, plants rapidly replace flowers that have a short lifespan, and old flowers senesce. They may contribute to avoiding adverse effects of the microbes. In this study, we investigate if the flower microbial community on old flowers impedes fruit and seed production in a wild ginger with one-day flowers. We focus on microbes on old flowers because they may be composed of microbes that would grow during flowering if the flowers did not have mechanisms to suppress microbial growth. We inoculated newly opened flowers with old flower microbes, and monitored the effects on fruit and seed set. We also assessed prokaryotic communities on the flowers using 16S rRNA amplicon sequencing. We found six bacterial amplicon sequence variants (ASVs) whose proportions were increased on the inoculated flowers. These ASVs were also found on flower buds and flowers that were bagged by net or paper during anthesis, suggesting that they had been present in small numbers prior to flowering. Fruit set was negatively associated with the proportions of these ASVs, while seed set was not. The results suggest that old flowers harbor microbial communities different from those at anthesis, and that the microbes abundant on old flowers negatively affect plant reproduction. Although it has received little attention, antagonistic microbes that rapidly proliferate on the flowers may have affected the evolution of various flower characteristics such as flower volatiles and life span.
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Abstract
How patterns in community diversity emerge is a long-standing question in ecology. Studies suggested that community diversity and interspecific interactions are interdependent. However, evidence from high-diversity ecological communities is lacking because of practical challenges in characterizing speciose communities and their interactions. Here, I analysed time-varying interaction networks that were reconstructed using 1197 species, DNA-based ecological time series taken from experimental rice plots and empirical dynamic modelling, and introduced 'interaction capacity', namely, the sum of interaction strength that a single species gives and receives, as a potential driver of community diversity. As community diversity increases, the number of interactions increases exponentially but the mean interaction capacity of a community becomes saturated, weakening interspecific interactions. These patterns are modelled with simple mathematical equations, based on which I propose the 'interaction capacity hypothesis': that interaction capacity and network connectance can be two fundamental properties that influence community diversity. Furthermore, I show that total DNA abundance and temperature influence interaction capacity and connectance nonlinearly, explaining a large proportion of diversity patterns observed in various systems. The interaction capacity hypothesis enables mechanistic explanations of community diversity. Therefore, analysing ecological community data from the viewpoint of interaction capacity would provide new insight into community diversity.
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Affiliation(s)
- Masayuki Ushio
- Hakubi Center, Kyoto University, Kyoto 606-8501, Japan,Center for Ecological Research, Kyoto University, Otsu 520-2113, Japan
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14
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Marre M, Ushio M, Sakai S. The effects of the floral infection by a bacterial pathogen in a dioecious plant,
Mallotus japonicus
(Euphorbiaceae). POPUL ECOL 2022. [DOI: 10.1002/1438-390x.12110] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Maxime Marre
- Center for Ecological Research Kyoto University Otsu Japan
| | - Masayuki Ushio
- Center for Ecological Research Kyoto University Otsu Japan
- Hakubi Center Kyoto University Kyoto Japan
| | - Shoko Sakai
- Center for Ecological Research Kyoto University Otsu Japan
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15
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Chang CW, Miki T, Ushio M, Ke PJ, Lu HP, Shiah FK, Hsieh CH. Reconstructing large interaction networks from empirical time series data. Ecol Lett 2021; 24:2763-2774. [PMID: 34601794 DOI: 10.1111/ele.13897] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/03/2021] [Indexed: 01/03/2023]
Abstract
Reconstructing interactions from observational data is a critical need for investigating natural biological networks, wherein network dimensionality is usually high. However, these pose a challenge to existing methods that can quantify only small interaction networks. Here, we proposed a novel approach to reconstruct high-dimensional interaction Jacobian networks using empirical time series without specific model assumptions. This method, named "multiview distance regularised S-map," generalised the state space reconstruction to accommodate high dimensionality and overcome difficulties in quantifying massive interactions with limited data. When evaluating this method using time series generated from theoretical models involving hundreds of interacting species, estimated strengths of interaction Jacobians were in good agreement with theoretical expectations. Applying this method to a natural bacterial community helped identify important species from the interaction network and revealed mechanisms governing the dynamical stability of a bacterial community. The proposed method overcame the challenge of high dimensionality in large natural dynamical systems.
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Affiliation(s)
- Chun-Wei Chang
- National Center for Theoretical Sciences, Taipei, Taiwan.,Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan
| | - Takeshi Miki
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.,Faculty of Advanced Science and Technology, Ryukoku University, Otsu, Japan.,Center for Biodiversity Science, Ryukoku University, Otsu, Japan
| | - Masayuki Ushio
- Hakubi Center, Kyoto University, Kyoto, Japan.,Center for Ecological Research, Kyoto University, Otsu, Japan
| | - Po-Ju Ke
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA.,Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Hsiao-Pei Lu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Fuh-Kwo Shiah
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan.,Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Chih-Hao Hsieh
- National Center for Theoretical Sciences, Taipei, Taiwan.,Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan.,Institute of Oceanography, National Taiwan University, Taipei, Taiwan.,Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
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16
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Matsuoka S, Sugiyama Y, Shimono Y, Ushio M, Doi H. Evaluation of seasonal dynamics of fungal DNA assemblages in a flow-regulated stream in a restored forest using eDNA metabarcoding. Environ Microbiol 2021; 23:4797-4806. [PMID: 34258854 DOI: 10.1111/1462-2920.15669] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 11/27/2022]
Abstract
Investigation of seasonal variation in fungal communities is essential for understanding biodiversity and ecosystem functions. However, the conventional sampling method, with substrate removal and high spatial heterogeneity of community composition, makes surveying the seasonality of fungal communities challenging. Recently, water environmental DNA (eDNA) analysis has been explored for its utility in biodiversity surveys. In this study, we assessed whether the seasonality of fungal communities can be detected by monitoring eDNA in a forest stream. We conducted monthly water sampling in a forest stream over 2 years and used DNA metabarcoding to identify fungal eDNA. The stream water contained DNA from functionally diverse aquatic and terrestrial fungi, such as plant decomposers, parasites and mutualists. The variation in the fungal assemblage showed a regular annual periodicity, meaning that the assemblages in a given season were similar, irrespective of the year or sampling. Furthermore, the strength of the annual periodicity varied among functional groups. Our results suggest that forest streams may act as a 'trap' for terrestrial fungal DNA derived from different habitats, allowing the analysis of fungal DNA in stream water to provide information about the temporal variation in fungal communities in both the aquatic and the surrounding terrestrial ecosystems.
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Affiliation(s)
- Shunsuke Matsuoka
- Graduate School of Information Science, University of Hyogo, Kobe, Japan
| | - Yoriko Sugiyama
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Yoshito Shimono
- Graduate School of Bioresources, Mie University, Tsu, Japan.,Osaka Museum of Nature History, Osaka, Japan
| | - Masayuki Ushio
- Hakubi Center, Kyoto University, Kyoto, Japan.,Center for Ecological Research, Kyoto University, Kyoto, Japan
| | - Hideyuki Doi
- Graduate School of Information Science, University of Hyogo, Kobe, Japan
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17
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Abstract
The deep sea comprises more than 90% of the ocean; therefore, understanding the controlling factors of biodiversity in the deep sea is of great importance for predicting future changes in the functioning of the ocean system. Consensus has recently been increasing on two plausible factors that have often been discussed as the drivers of deep-sea species richness in the contexts of the species-energy and physiological tolerance hypotheses: (i) seafloor particulate organic carbon (POC) derived from primary production in the euphotic zone and (ii) temperature. Nonetheless, factors that drive deep-sea biodiversity are still actively debated potentially owing to a mirage of correlations (sign and magnitude are generally time dependent), which are often found in nonlinear, complex ecological systems, making the characterization of causalities difficult. Here, we tested the causal influences of POC flux and temperature on species richness using long-term palaeoecological datasets derived from sediment core samples and convergent cross mapping, a numerical method for characterizing causal relationships in complex systems. The results showed that temperature, but not POC flux, influenced species richness over 103-104-year time scales. The temperature-richness relationship in the deep sea suggests that human-induced future climate change may, under some conditions, affect deep-sea ecosystems through deep-water circulation changes rather than surface productivity changes.
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Affiliation(s)
- Hideyuki Doi
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Moriaki Yasuhara
- Division of Ecology and Biodiversity, School of Biological Sciences, Swire Institute of Marine Science, and State Key Laboratory of Marine Pollution, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Masayuki Ushio
- Hakubi Center, Kyoto University, Kyoto 606-8501, Japan.,Center for Ecological Research, Kyoto University, Otsu 520-2113, Japan
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18
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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. 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 ECOL 2021. [DOI: 10.1016/j.funeco.2021.101095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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19
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Kawatsu K, Ushio M, van Veen FJF, Kondoh M. Are networks of trophic interactions sufficient for understanding the dynamics of multi-trophic communities? Analysis of a tri-trophic insect food-web time-series. Ecol Lett 2021; 24:543-552. [PMID: 33439500 DOI: 10.1111/ele.13672] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/24/2020] [Accepted: 12/04/2020] [Indexed: 01/24/2023]
Abstract
Resource-consumer interactions are considered a major driving force of population and community dynamics. However, species also interact in many non-trophic and indirect ways and it is currently not known to what extent the dynamic coupling of species corresponds to the distribution of trophic links. Here, using a 10-year data set of monthly observations of a 40-species tri-trophic insect community and nonlinear time series analysis, we compare the occurrence and strengths of both the trophic and dynamic interactions in the insect community. The matching between observed trophic and dynamic interactions provides evidence that population dynamic interactions reflect resource-consumer interactions in the many-species community. However, the presence of a trophic interaction does not always correspond to a detectable dynamic interaction especially for top-down effects. Moreover a considerable proportion of dynamic interactions are not attributable to direct trophic interactions, suggesting the unignorable role of non-trophic and indirect interactions as co-drivers of community dynamics.
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Affiliation(s)
- Kazutaka Kawatsu
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Masayuki Ushio
- Hakubi Center, Kyoto University, Kyoto, Japan.,Center for Ecological Research, Kyoto University, Otsu, Japan
| | - F J Frank van Veen
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Michio Kondoh
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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20
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Yonezawa S, Ushio M, Yamanaka H, Miya M, Takayanagi A, Isagi Y. Environmental DNA metabarcoding reveals the presence of a small, quick-moving, nocturnal water shrew in a forest stream. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01310-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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21
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Tsuji S, Shibata N, Sawada H, Ushio M. Quantitative evaluation of intraspecific genetic diversity in a natural fish population using environmental DNA analysis. Mol Ecol Resour 2020; 20:1323-1332. [PMID: 32452621 DOI: 10.1111/1755-0998.13200] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/01/2020] [Accepted: 05/18/2020] [Indexed: 01/04/2023]
Abstract
Recent advances in environmental DNA (eDNA) analysis using high-throughput sequencing (HTS) enable evaluation of intraspecific genetic diversity in a population. As the intraspecific genetic diversity provides invaluable information for wildlife conservation and management, there is an increasing demand to apply eDNA analysis to population genetics and the phylogeography by quantitative evaluation of intraspecific diversity. However, quantitative evaluations of intraspecific genetic diversity using eDNA is not straightforward because the number of eDNA sequence reads obtained by HTS may not be an index of the quantity of eDNA. In this study, to quantitatively evaluate genetic diversity using eDNA analysis, we applied a quantitative eDNA metabarcoding method using the internal standard DNAs. We targeted Ayu (Plecoglossus altivelis altivelis) and added internal standard DNAs with known copy numbers to each eDNA sample obtained from three rivers during the library preparation process. The sequence reads of each Ayu haplotype were successfully converted to DNA copy numbers based on the relationship between the copy numbers and sequence reads of the internal standard DNAs. In all rivers, the calculated copy number of each haplotype showed a significant positive correlation with the haplotype frequency estimated by a capture-based survey. Furthermore, estimates of genetic indicators such as nucleotide diversity based on the eDNA copy numbers were comparable with those estimated based on a capture-based study. Our results demonstrate that eDNA analysis with internal standard DNAs enables reasonable quantification of intraspecific genetic diversity, and this method could thus be a promising tool in the field of population genetics and phylogeography.
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Affiliation(s)
- Satsuki Tsuji
- Graduate School of Science, Kyoto University, Kyoto, Japan.,Faculty of Science and Technology/Graduate School of Science and Technology, Ryukoku University, Otsu, Japan
| | - Naoki Shibata
- Faculty of Science and Technology/Graduate School of Science and Technology, Ryukoku University, Otsu, Japan
| | - Hayato Sawada
- Faculty of Science and Technology/Graduate School of Science and Technology, Ryukoku University, Otsu, Japan
| | - Masayuki Ushio
- Hakubi Center, Kyoto, Japan.,Center for Ecological Research, Kyoto University, Otsu, Japan.,Japan Science and Technology Agency, PRESTO, Kawaguchi, Japan
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22
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Tsuji S, Maruyama A, Miya M, Ushio M, Sato H, Minamoto T, Yamanaka H. Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population. Mol Ecol Resour 2020; 20:1248-1258. [PMID: 32293104 DOI: 10.1111/1755-0998.13165] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 04/06/2020] [Indexed: 11/28/2022]
Abstract
Environmental DNA (eDNA) analysis has recently been used as a new tool for estimating intraspecific diversity. However, whether known haplotypes contained in a sample can be detected correctly using eDNA-based methods has been examined only by an aquarium experiment. Here, we tested whether the haplotypes of Ayu fish (Plecoglossus altivelis altivelis) detected in a capture survey could also be detected from an eDNA sample derived from the field that contained various haplotypes with low concentrations and foreign substances. A water sample and Ayu specimens collected from a river on the same day were analysed by eDNA analysis and Sanger sequencing, respectively. The 10 L water sample was divided into 20 filters for each of which 15 PCR replications were performed. After high-throughput sequencing, denoising was performed using two of the most widely used denoising packages, unoise3 and dada2. Of the 42 haplotypes obtained from the Sanger sequencing of 96 specimens, 38 (unoise3) and 41 (dada2) haplotypes were detected by eDNA analysis. When dada2 was used, except for one haplotype, haplotypes owned by at least two specimens were detected from all the filter replications. Accordingly, although it is important to note that eDNA-based method has some limitations and some risk of false positive and false negative, this study showed that the eDNA analysis for evaluating intraspecific genetic diversity provides comparable results for large-scale capture-based conventional methods. Our results suggest that eDNA-based methods could become a more efficient survey method for investigating intraspecific genetic diversity in the field.
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Affiliation(s)
- Satsuki Tsuji
- Graduate School of Science, Kyoto University, Kyoto, Japan.,Faculty of Science and Technology, Graduate School of Science and Technology, Ryukoku University, Otsu, Japan
| | - Atsushi Maruyama
- Faculty of Science and Technology, Graduate School of Science and Technology, Ryukoku University, Otsu, Japan
| | - Masaki Miya
- Department Ecology and Environmental Sciences, Natural History Museum and Institute, Chiba, Japan
| | - Masayuki Ushio
- Hakubi Center, Kyoto University, Kyoto, Japan.,Center for Ecological Research, Kyoto University, Otsu, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Hirotoshi Sato
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
| | - Hiroki Yamanaka
- Faculty of Science and Technology, Graduate School of Science and Technology, Ryukoku University, Otsu, Japan.,Center for Biodiversity Science, Ryukoku University, Otsu, Japan
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23
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Abstract
Interspecific interaction has been a key concept in ecology to understand the structure and dynamics of ecological communities. Important, yet often overlooked, is that an interspecific interaction is a product of multiple biological processes at various temporal and spatial scales, including changes in demographic parameters such as birth and death rates, behavioral responses such as inter-habitat movements, and hiding and evolutionary responses in a longer temporal scale. Each of those mechanisms, according to ecological theory, potentially affects population dynamics and modifies the community-level properties such as community complexity and stability in different manners. Here, a question arises: how does the net interspecific interaction, which is made up with those multiple processes, look like in the real nature? How do changes depend on the temporal or spatial scale? In this chapter we show that a data-driven approach using demographic time series is a powerful tool to answer those questions. According to nonlinear dynamics theory, a time series of a variable contains information about the dynamic system that the variable belongs to. We can use this fact to identify interspecific interactions, quantify their signs and strengths and evaluate its effect to community-level dynamic properties. Some results we got by applying the time-series analysis based on nonlinear dynamics theory (called Empirical Dynamic Modeling) to empirical demographic data, experimental or observational, will be presented, which will demonstrate how fluctuating and condition-dependent the real interactions are and reveal how those interactions give rise to the dynamic properties at higher organization levels.
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24
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Nishio H, Buzas DM, Nagano AJ, Iwayama K, Ushio M, Kudoh H. Repressive chromatin modification underpins the long-term expression trend of a perennial flowering gene in nature. Nat Commun 2020; 11:2065. [PMID: 32358518 PMCID: PMC7195410 DOI: 10.1038/s41467-020-15896-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 04/01/2020] [Indexed: 11/17/2022] Open
Abstract
Natural environments require organisms to possess robust mechanisms allowing responses to seasonal trends. In Arabidopsis halleri, the flowering regulator AhgFLC shows upregulation and downregulation phases along with long-term past temperature, but the underlying machinery remains elusive. Here, we investigate the seasonal dynamics of histone modifications, H3K27me3 and H3K4me3, at AhgFLC in a natural population. Our advanced modelling and transplant experiments reveal that H3K27me3-mediated chromatin regulation at AhgFLC provides two essential properties. One is the ability to respond to the long-term temperature trends via bidirectional interactions between H3K27me3 and H3K4me3; the other is the ratchet-like character of the AhgFLC system, i.e. reversible in the entire perennial life cycle but irreversible during the upregulation phase. Furthermore, we show that the long-term temperature trends are locally indexed at AhgFLC in the form of histone modifications. Our study provides a more comprehensive understanding of H3K27me3 function at AhgFLC in a complex natural environment. The flowering regulator FLC shows upregulation and downregulation phases along with long-term past temperature in Arabidopsishalleri. Here, the authors reveal that H3K27me3-mediated chromatin regulation at AhgFLC provides the ability to respond to both the seasonal temperature trends and the perennial life cycle.
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Affiliation(s)
- Haruki Nishio
- Center for Ecological Research, Kyoto University, Otsu, 520-2113, Japan.
| | - Diana M Buzas
- Tsukuba-Plant Innovation Research Center and Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Atsushi J Nagano
- Center for Ecological Research, Kyoto University, Otsu, 520-2113, Japan.,Faculty of Agriculture, Ryukoku University, Seta Oe-cho, Otsu, 520-2194, Japan
| | - Koji Iwayama
- Faculty of Data Science, Shiga University, Hikone, 522-8522, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, 332-0012, Japan
| | - Masayuki Ushio
- Center for Ecological Research, Kyoto University, Otsu, 520-2113, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, 332-0012, Japan.,Hakubi Center, Kyoto University, Yoshida-honmachi, Kyoto, 606-8501, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, 520-2113, Japan.
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25
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Affiliation(s)
- Masayuki Ushio
- Hakubi Center Kyoto University Kyoto Japan
- Center for Ecological Research Kyoto University Otsu Shiga Japan
- PRESTO Japan Science and Technology Agency Kawaguchi Saitama Japan
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26
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Shirouzu T, Matsuoka S, Doi H, Nagata N, Ushio M, Hosaka K. Complementary molecular methods reveal comprehensive phylogenetic diversity integrating inconspicuous lineages of early-diverged wood-decaying mushrooms. Sci Rep 2020; 10:3057. [PMID: 32080243 PMCID: PMC7033186 DOI: 10.1038/s41598-020-59620-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/03/2020] [Indexed: 11/28/2022] Open
Abstract
Among terrestrial microorganisms, mushroom-forming fungi have been relatively well investigated, however the inconspicuous strains may be overlooked by conventional visual investigations causing underestimation of their phylogenetic diversity. Herein, we sought to obtain a comprehensive phylogenetic diversity profile for the early-diverging wood-decaying mushrooms Dacrymycetes, using an approach that combines fruiting-body collection, culture isolation, and environmental DNA (eDNA) metabarcoding of decaying branches. Among the 28 operational taxonomic units (OTUs) detected during a three-year investigation, 10 each were from fruiting bodies and cultured mycelia and 27 were detected as eDNA sequences. eDNA metabarcoding revealed various lineages across the Dacrymycetes phylogeny. Alternatively, fruiting-body and culture surveys uncovered only ~50% of the OTUs detected through eDNA metabarcoding, suggesting that several inconspicuous or difficult-to-isolate strains are latent in the environment. Further, eDNA and culture surveys revealed early-diverging clades that were not identified in the fruiting-body survey. Thus, eDNA and culture-based techniques can uncover inconspicuous yet phylogenetically important mushroom lineages that may otherwise be overlooked via typical visual investigations.
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Affiliation(s)
- Takashi Shirouzu
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie, 514-8507, Japan.
| | - Shunsuke Matsuoka
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Hideyuki Doi
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Nobuaki Nagata
- Collection Center, National Museum of Nature and Science, 4-1-1 Amakubo, Ibaraki, 305-0005, Japan
| | - Masayuki Ushio
- Hakubi Center, Kyoto University, Kyoto, 606-8501, Japan
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga, 520-2113, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, 332-0012, Japan
| | - Kentaro Hosaka
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan
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27
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Ushio M, Osada Y, Kumagai T, Kume T, Pungga RAS, Nakashizuka T, Itioka T, Sakai S. Dynamic and synergistic influences of air temperature and rainfall on general flowering in a Bornean lowland tropical forest. Ecol Res 2019. [DOI: 10.1111/1440-1703.12057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Masayuki Ushio
- Hakubi Center Kyoto University Kyoto Japan
- Center for Ecological Research Kyoto University Otsu Japan
- PRESTO Japan Science and Technology Agency Kawaguchi Japan
| | - Yutaka Osada
- Graduate School of Life Science Tohoku University Sendai Japan
| | - Tomo'omi Kumagai
- Graduate School of Agricultural and Life Sciences The University of Tokyo Tokyo Japan
| | - Tomonori Kume
- Kasuya Research Forest Kyushu University Fukuoka Japan
| | | | - Tohru Nakashizuka
- Research Department Research Institute for Humanity and Nature Kyoto Japan
| | - Takao Itioka
- Graduate School of Human and Environmental Studies Kyoto University Kyoto Japan
| | - Shoko Sakai
- Center for Ecological Research Kyoto University Otsu Japan
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28
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Affiliation(s)
- Masayuki Ushio
- Hakubi Center, Kyoto University Kyoto Japan
- Center for Ecological Research Kyoto University Otsu Japan
- PRESTO Japan Science and Technology Agency Kawaguchi Japan
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29
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Affiliation(s)
- Michiko Nakagawa
- Graduate School of Bioagricultural Sciences Nagoya University Nagoya Japan
| | - Masayuki Ushio
- Center for Ecological Research Kyoto University Otsu Japan
- PRESTO, Japan Science and Technology Agency Kawaguchi Japan
| | - Tomonori Kume
- Kasuya Research Forest Kyushu University, Sasaguri Fukuoka Japan
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30
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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. Publisher Correction: Core microbiomes for sustainable agroecosystems. Nat Plants 2018; 4:733. [PMID: 30108297 DOI: 10.1038/s41477-018-0245-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Owing to a technical error, this Perspective was originally published without its received and accepted dates; the dates "Received: 31 December 2017; Accepted: 23 March 2018" have now been included in all versions.
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Affiliation(s)
- Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan.
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
| | - Kabir G Peay
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Masato Yamamichi
- Department of General Systems Studies, University of Tokyo, Meguro, Tokyo, Japan
| | - Kazuhiko Narisawa
- Department of Bioresource Science, College of Agriculture, Ibaraki University, Ami, Ibaraki, Japan
| | - Kei Hiruma
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Department of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Ken Naito
- Genetic Resource Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Shinji Fukuda
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Masayuki Ushio
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Shinji Nakaoka
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Institute of Industrial Sciences, The University of Tokyo, Tokyo, Japan
| | - Yusuke Onoda
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kentaro Yoshida
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe, Japan
| | - Klaus Schlaeppi
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing, China
- Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Science & John Innes Centre, Beijing, China
| | - Ryo Sugiura
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Hokkaido Agricultural Research Center, NARO (National Agriculture and Food Research Organization), Memuro, Hokkaido, Japan
| | - Yasunori Ichihashi
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, Katahira, Sendai, Japan
| | - E Toby Kiers
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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31
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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. Core microbiomes for sustainable agroecosystems. Nat Plants 2018; 4:247-257. [PMID: 29725101 DOI: 10.1038/s41477-018-0139-4] [Citation(s) in RCA: 356] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 03/23/2018] [Indexed: 05/18/2023]
Abstract
In an era of ecosystem degradation and climate change, maximizing microbial functions in agroecosystems has become a prerequisite for the future of global agriculture. However, managing species-rich communities of plant-associated microbiomes remains a major challenge. Here, we propose interdisciplinary research strategies to optimize microbiome functions in agroecosystems. Informatics now allows us to identify members and characteristics of 'core microbiomes', which may be deployed to organize otherwise uncontrollable dynamics of resident microbiomes. Integration of microfluidics, robotics and machine learning provides novel ways to capitalize on core microbiomes for increasing resource-efficiency and stress-resistance of agroecosystems.
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Affiliation(s)
- Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan.
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
| | - Kabir G Peay
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Masato Yamamichi
- Department of General Systems Studies, University of Tokyo, Meguro, Tokyo, Japan
| | - Kazuhiko Narisawa
- Department of Bioresource Science, College of Agriculture, Ibaraki University, Ami, Ibaraki, Japan
| | - Kei Hiruma
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Department of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Ken Naito
- Genetic Resource Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Shinji Fukuda
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Masayuki Ushio
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Shinji Nakaoka
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Institute of Industrial Sciences, The University of Tokyo, Tokyo, Japan
| | - Yusuke Onoda
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kentaro Yoshida
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe, Japan
| | - Klaus Schlaeppi
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing, China
- Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Science & John Innes Centre, Beijing, China
| | - Ryo Sugiura
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Hokkaido Agricultural Research Center, NARO (National Agriculture and Food Research Organization), Memuro, Hokkaido, Japan
| | - Yasunori Ichihashi
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, Katahira, Sendai, Japan
| | - E Toby Kiers
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
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32
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Ushio M, Hsieh CH, Masuda R, Deyle ER, Ye H, Chang CW, Sugihara G, Kondoh M. Fluctuating interaction network and time-varying stability of a natural fish community. Nature 2018; 554:360-363. [PMID: 29414940 DOI: 10.1038/nature25504] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 01/09/2018] [Indexed: 11/09/2022]
Abstract
Ecological theory suggests that large-scale patterns such as community stability can be influenced by changes in interspecific interactions that arise from the behavioural and/or physiological responses of individual species varying over time. Although this theory has experimental support, evidence from natural ecosystems is lacking owing to the challenges of tracking rapid changes in interspecific interactions (known to occur on timescales much shorter than a generation time) and then identifying the effect of such changes on large-scale community dynamics. Here, using tools for analysing nonlinear time series and a 12-year-long dataset of fortnightly collected observations on a natural marine fish community in Maizuru Bay, Japan, we show that short-term changes in interaction networks influence overall community dynamics. Among the 15 dominant species, we identify 14 interspecific interactions to construct a dynamic interaction network. We show that the strengths, and even types, of interactions change with time; we also develop a time-varying stability measure based on local Lyapunov stability for attractor dynamics in non-equilibrium nonlinear systems. We use this dynamic stability measure to examine the link between the time-varying interaction network and community stability. We find seasonal patterns in dynamic stability for this fish community that broadly support expectations of current ecological theory. Specifically, the dominance of weak interactions and higher species diversity during summer months are associated with higher dynamic stability and smaller population fluctuations. We suggest that interspecific interactions, community network structure and community stability are dynamic properties, and that linking fluctuating interaction networks to community-level dynamic properties is key to understanding the maintenance of ecological communities in nature.
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Affiliation(s)
- Masayuki Ushio
- Department of Environmental Solution Technology, Faculty of Science and Technology, Ryukoku University, Otsu 520-2194, Japan.,Joint Research Center for Science and Technology, Ryukoku University, Otsu 520-2194, Japan.,Center for Ecological Research, Kyoto University, Otsu 520-2113, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
| | - Chih-Hao Hsieh
- Institute of Oceanography, Institute of Ecology and Evolutionary Biology, and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.,Taiwan International Graduate Program (TIGP)-Earth System Science Program, Academia Sinica and National Central University, Taipei 11529, Taiwan.,National Center for Theoretical Science, Taipei 10617, Taiwan
| | - Reiji Masuda
- Maizuru Fisheries Research Station, Field Science Education and Research Center, Kyoto University, Maizuru, Kyoto 625-0086, Japan
| | - Ethan R Deyle
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093, USA
| | - Hao Ye
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093, USA.,Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida 32611, USA
| | - Chun-Wei Chang
- Taiwan International Graduate Program (TIGP)-Earth System Science Program, Academia Sinica and National Central University, Taipei 11529, Taiwan
| | - George Sugihara
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093, USA
| | - Michio Kondoh
- Department of Environmental Solution Technology, Faculty of Science and Technology, Ryukoku University, Otsu 520-2194, Japan
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33
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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. Environmental DNA enables detection of terrestrial mammals from forest pond water. Mol Ecol Resour 2017; 17:e63-e75. [PMID: 28603873 DOI: 10.1111/1755-0998.12690] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 04/25/2017] [Accepted: 05/02/2017] [Indexed: 11/27/2022]
Abstract
Terrestrial animals must have frequent contact with water to survive, implying that environmental DNA (eDNA) originating from those animals should be detectable from places containing water in terrestrial ecosystems. Aiming to detect the presence of terrestrial mammals using forest water samples, we applied a set of universal PCR primers (MiMammal, a modified version of fish universal primers) for metabarcoding mammalian eDNA. The versatility of MiMammal primers was tested in silico and by amplifying DNAs extracted from tissues. The results suggested that MiMammal primers are capable of amplifying and distinguishing a diverse group of mammalian species. In addition, analyses of water samples from zoo cages of mammals with known species composition suggested that MiMammal primers could successfully detect mammalian species from water samples in the field. Then, we performed an experiment to detect mammals from natural ecosystems by collecting five 500-ml water samples from ponds in two cool-temperate forests in Hokkaido, northern Japan. MiMammal amplicon libraries were constructed using eDNA extracted from water samples, and sequences generated by Illumina MiSeq were subjected to data processing and taxonomic assignment. We thereby detected multiple species of mammals common to the sampling areas, including deer (Cervus nippon), mouse (Mus musculus), vole (Myodes rufocanus), raccoon (Procyon lotor), rat (Rattus norvegicus) and shrew (Sorex unguiculatus). Many previous applications of the eDNA metabarcoding approach have been limited to aquatic/semiaquatic systems, but the results presented here show that the approach is also promising even for forest mammal biodiversity surveys.
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Affiliation(s)
- Masayuki Ushio
- Center for Ecological Research, Kyoto University, Otsu, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan.,Joint Research Center for Science and Technology, Ryukoku University, Otsu, Japan
| | - Hisato Fukuda
- Department of Environmental Solution Technology, Ryukoku University, Otsu, Japan
| | - Toshiki Inoue
- Department of Environmental Solution Technology, Ryukoku University, Otsu, Japan
| | - Kobayashi Makoto
- Teshio Experimental Forest, Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan
| | - Osamu Kishida
- Teshio Experimental Forest, Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan.,Tomakomai Experimental Forest, Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan
| | - Keiichi Sato
- Okinawa Churashima Research Center, Okinawa, Japan
| | - Koichi Murata
- College of Bioresource Sciences, Nihon University, Kanagawa, Japan.,Yokohama Zoological Gardens ZOORASIA, Kanagawa, Japan
| | - Masato Nikaido
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Tetsuya Sado
- Natural History Museum and Institute, Chiba, Japan
| | - Yukuto Sato
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | | | - Wataru Iwasaki
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroki Yamanaka
- Department of Environmental Solution Technology, Ryukoku University, Otsu, Japan.,The Research Center for Satoyama Studies, Ryukoku University, Shiga, Japan
| | - Michio Kondoh
- Department of Environmental Solution Technology, Ryukoku University, Otsu, Japan
| | - Masaki Miya
- Natural History Museum and Institute, Chiba, Japan
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34
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Tsuji S, Ushio M, Sakurai S, Minamoto T, Yamanaka H. Water temperature-dependent degradation of environmental DNA and its relation to bacterial abundance. PLoS One 2017; 12:e0176608. [PMID: 28448613 PMCID: PMC5407774 DOI: 10.1371/journal.pone.0176608] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/13/2017] [Indexed: 01/14/2023] Open
Abstract
Environmental DNA (eDNA) is DNA shed by organisms into surrounding environments such as soil and water. The new methods using eDNA as a marker for species detection are being rapidly developed. Here we explore basic knowledge regarding the dependence of the eDNA degradation rate on time and water temperature, and the relationship between eDNA degradation and bacterial abundance. This subject has not been well clarified, even though it is essential for improving the reliability of eDNA analysis. To determine the time- and water temperature-dependent degradation of eDNA, river water was sampled and eDNA concentrations were determined for ayu sweetfish (Plecoglossus altivelis altivelis) and common carp (Cyprinus carpio) at seven time points, over a 48-h period, and at three different water temperatures. The degradation of eDNA was modeled for each species using an existing exponential decay model with an extension to include water temperature effects. The degradation models were constructed for ayu sweetfish as Nt = 229,901.2 × exp [− (0.01062 × k − 0.07081) × t] and for common carp as Nt = 2,558.0 × exp [− (0.01075 × k − 0.07372) × t]. Nt is the DNA concentration at time t (elapsed time in hours) and k is the water temperature (°C). We also measured the concentration of eDNA derived from purified genomic DNA of the common carp, which was spiked into aquarium water without the target species, and we measured the bacterial abundance in the sample water after 12 and 24 h of incubation. Environmental DNA degradation was accelerated at higher water temperatures (generalized linear model, GLM; p < 0.001), but bacterial abundance did not have a significant effect on eDNA degradation (GLM, p = 0.097). These results suggest that the proper treatment of this temperature effect in data interpretations and adjustments would increase the reliability of eDNA analysis in future studies.
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Affiliation(s)
- Satsuki Tsuji
- Graduate School of Science and Technology, Ryukoku University, 1–5 Yokotani, Seta Oe-cho, Otsu, Japan
- * E-mail:
| | - Masayuki Ushio
- Joint Research Center for Science and Technology, Ryukoku University, Otsu, Japan
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Sho Sakurai
- Graduate School of Science and Technology, Ryukoku University, 1–5 Yokotani, Seta Oe-cho, Otsu, Japan
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, Tsurukabuto, Nada-ku, Kobe, Japan
| | - Hiroki Yamanaka
- Faculty of Science and Technology, Ryukoku University, Yokotani, Seta Oe-cho, Otsu, Japan
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35
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Ushio M, Aiba SI, Takeuchi Y, Iida Y, Matsuoka S, Repin R, Kitayama K. Plant-soil feedbacks and the dominance of conifers in a tropical montane forest in Borneo. ECOL MONOGR 2017. [DOI: 10.1002/ecm.1236] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Masayuki Ushio
- Center for Ecological Research; Kyoto University; 2-509-3, Hirano Otsu 520-2113 Japan
- Department of Environmental Solution Technology; Faculty of Science and Technology; Ryukoku University; 1-5 Yokotani, Seta Oe-cho Otsu 520-2194 Japan
- Joint Research Center for Science and Technology; Ryukoku University; Otsu 520-2194 Japan
| | - Shin-ichiro Aiba
- Graduate School of Science and Engineering; Kagoshima University; Kagoshima 890-0065 Japan
| | - Yayoi Takeuchi
- Center for Environmental Biology and Ecosystem Studies; National Institute for Environmental Studies; Onogawa 16-2 Tsukuba 305-8506 Japan
| | - Yoshiko Iida
- Kyushu Research Center; Forestry and Forest Products Research Institute; 4-11-16 Kurokami, Chuo-ku Kumamoto 860-0862 Japan
- Graduate School of Agriculture; Kyoto University; Oiwake-cho, Kitashirakawa, Sakyo-ku Kyoto 606-8502 Japan
| | - Shunsuke Matsuoka
- Center for Ecological Research; Kyoto University; 2-509-3, Hirano Otsu 520-2113 Japan
| | - Rimi Repin
- Sabah Parks; Lot 45 & 46, Level 1-5, Blok H, KK Times Square 88806 Kota Kinabalu Sabah Malaysia
| | - Kanehiro Kitayama
- Center for Ecological Research; Kyoto University; 2-509-3, Hirano Otsu 520-2113 Japan
- Graduate School of Agriculture; Kyoto University; Oiwake-cho, Kitashirakawa, Sakyo-ku Kyoto 606-8502 Japan
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36
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Koyama K, Yamamoto K, Ushio M. A lognormal distribution of the lengths of terminal twigs on self-similar branches of elm trees. Proc Biol Sci 2017; 284:20162395. [PMID: 28053062 PMCID: PMC5247503 DOI: 10.1098/rspb.2016.2395] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/05/2016] [Indexed: 11/12/2022] Open
Abstract
Lognormal distributions and self-similarity are characteristics associated with a wide range of biological systems. The sequential breakage model has established a link between lognormal distributions and self-similarity and has been used to explain species abundance distributions. To date, however, there has been no similar evidence in studies of multicellular organismal forms. We tested the hypotheses that the distribution of the lengths of terminal stems of Japanese elm trees (Ulmus davidiana), the end products of a self-similar branching process, approaches a lognormal distribution. We measured the length of the stem segments of three elm branches and obtained the following results: (i) each occurrence of branching caused variations or errors in the lengths of the child stems relative to their parent stems; (ii) the branches showed statistical self-similarity; the observed error distributions were similar at all scales within each branch and (iii) the multiplicative effect of these errors generated variations of the lengths of terminal twigs that were well approximated by a lognormal distribution, although some statistically significant deviations from strict lognormality were observed for one branch. Our results provide the first empirical evidence that statistical self-similarity of an organismal form generates a lognormal distribution of organ sizes.
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Affiliation(s)
- Kohei Koyama
- Department of Life Science and Agriculture, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro 080-8555, Japan
| | - Ken Yamamoto
- Department of Physics, Faculty of Science and Engineering, Chuo University, Bunkyo, Tokyo 112-8551, Japan
| | - Masayuki Ushio
- Department of Environmental Solution Technology, Faculty of Science and Technology, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu 520-2194, Japan
- Joint Research Center for Science and Technology, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu 520-2194, Japan
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37
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Ushio M, Sumitani M, Abe H, Mietani K, Hozumi J, Inoue R, Shinokawa M, Ushida T, Yamada Y. Abstract PR339. Anesth Analg 2016. [DOI: 10.1213/01.ane.0000492734.32162.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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38
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Ushio M, Yamasaki E, Takasu H, Nagano AJ, Fujinaga S, Honjo MN, Ikemoto M, Sakai S, Kudoh H. Microbial communities on flower surfaces act as signatures of pollinator visitation. Sci Rep 2015; 5:8695. [PMID: 25733079 PMCID: PMC4346974 DOI: 10.1038/srep08695] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 02/02/2015] [Indexed: 11/30/2022] Open
Abstract
Microbes are easily dispersed from one place to another, and immigrant microbes might contain information about the environments from which they came. We hypothesized that part of the microbial community on a flower's surface is transferred there from insect body surfaces and that this community can provide information to identify potential pollinator insects of that plant. We collected insect samples from the field, and found that an insect individual harbored an average of 12.2 × 105 microbial cells on its surface. A laboratory experiment showed that the microbial community composition on a flower surface changed after contact with an insect, suggesting that microbes are transferred from the insect to the flower. Comparison of the microbial fingerprint approach and direct visual observation under field condition suggested that the microbial community on a flower surface could to some extent indicate the structure of plant–pollinator interactions. In conclusion, species-specific insect microbial communities specific to insect species can be transferred from an insect body to a flower surface, and these microbes can serve as a “fingerprint” of the insect species, especially for large-bodied insects. Dispersal of microbes is a ubiquitous phenomenon that has unexpected and novel applications in many fields and disciplines.
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Affiliation(s)
- Masayuki Ushio
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan
| | - Eri Yamasaki
- 1] Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan [2] Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Hiroyuki Takasu
- 1] Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan [2] Atmosphere and Ocean Research Institute (AORI), The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Atsushi J Nagano
- 1] Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan [2] PRESTO, Japan Science and Technology Agency, Japan
| | - Shohei Fujinaga
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan
| | - Mito Ikemoto
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan
| | - Shoko Sakai
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan
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39
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Ushio M, Fujiki Y, Hidaka A, Kitayama K. Linkage of root physiology and morphology as an adaptation to soil phosphorus impoverishment in tropical montane forests. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12424] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Masayuki Ushio
- Center for Ecological Research Kyoto University 2‐509‐3 Hirano Otsu Shiga 520‐2113 Japan
| | - Yasuto Fujiki
- Center for Ecological Research Kyoto University 2‐509‐3 Hirano Otsu Shiga 520‐2113 Japan
- Mitsubishi UFJ Research and Consulting, Co., Ltd. 2‐5‐25 Umeda Kita‐ku Osaka 530‐8213 Japan
| | - Amane Hidaka
- Center for Ecological Research Kyoto University 2‐509‐3 Hirano Otsu Shiga 520‐2113 Japan
- Graduate School of Agriculture Kyoto University Oiwake‐cho Kitashirakawa Sakyo‐ku Kyoto 606‐8502 Japan
- Network Center of Forest and Grassland Survey in Monitoring Sites 1000 Project Japan Wildlife Research Center c/o Tomakomai Research Station Field Science Center for Northern Biosphere Hokkaido University Takaoka Tomakomai Hokkaido 053‐0035 Japan
| | - Kanehiro Kitayama
- Center for Ecological Research Kyoto University 2‐509‐3 Hirano Otsu Shiga 520‐2113 Japan
- Graduate School of Agriculture Kyoto University Oiwake‐cho Kitashirakawa Sakyo‐ku Kyoto 606‐8502 Japan
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40
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Baba S, Kondo K, Toma-Hirano M, Kanaya K, Suzukawa K, Ushio M, Suzukawa M, Ohta K, Yamasoba T. Local increase in IgE and class switch recombination to IgE in nasal polyps in chronic rhinosinusitis. Clin Exp Allergy 2014; 44:701-12. [PMID: 24931597 DOI: 10.1111/cea.12287] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 01/09/2014] [Accepted: 02/03/2014] [Indexed: 01/30/2023]
Abstract
BACKGROUND Chronic rhinosinusitis with nasal polyps is generally characterized by local Th2 inflammation and is categorized into two subtypes in Japan: eosinophilic chronic rhinosinusitis (similar to chronic rhinosinusitis with nasal polyps in western countries) and non-eosinophilic chronic rhinosinusitis (characterized by Th1-dominant inflammation). OBJECTIVE To investigate local IgE production and class switch recombination to IgE in these two subtypes of chronic rhinosinusitis with nasal polyps. METHODS The identity of IgE-positive cells was determined using double-immunofluorescent staining for IgE and cell-type-specific molecular markers. To investigate the local class switch recombination to IgE and IgE synthesis in the mucosa, we performed real-time polymerase chain reaction to examine the mRNA expression of Th2 cytokines and class-switch-related molecules, including IL-4, IL-5, IL-13, ε germline gene transcripts, IgE mature transcript, IgG mature transcript, RAG1, RAG2 and activation-induced cytidine deaminase in eosinophilic polyps, non-eosinophilic polyps and controls. RESULTS The concentrations of total IgE and number of IgE-positive cells were significantly higher in the eosinophilic polyps compared with control and non-eosinophilic polyps. IgE-positive cells were predominantly mast cells in eosinophilic polyps and significantly correlated with the number of FcεR1-positive cells in the subepithelial layer. IL-5 and IL-13 mRNA and ε germline gene transcripts expression levels were significantly higher in eosinophilic polyps compared with control and non-eosinophilic polyps. In contrast, the number of plasma cells and the expression of IgG mature transcripts were increased in non-eosinophilic polyps compared with eosinophilic polyps. RAG2 mRNA was significantly increased in both eosinophilic and non-eosinophilic polyps compared with control mucosa. CONCLUSION AND CLINICAL RELEVANCE The current study suggests local class switching to IgE, production of IgE and IgE localization to the surface of mast cells in eosinophilic chronic rhinosinusitis in the Japanese population. The difference in the IgE-related profiles between eosinophilic chronic rhinosinusitis and non-eosinophilic chronic rhinosinusitis suggests heterogeneity in the pathogenesis of chronic rhinosinusitis with nasal polyps.
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Affiliation(s)
- S Baba
- Department of Otolaryngology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Ushio M, Miki T, Balser TC. A coexisting fungal-bacterial community stabilizes soil decomposition activity in a microcosm experiment. PLoS One 2013; 8:e80320. [PMID: 24260368 PMCID: PMC3832447 DOI: 10.1371/journal.pone.0080320] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 10/07/2013] [Indexed: 11/25/2022] Open
Abstract
How diversity influences the stability of a community function is a major question in ecology. However, only limited empirical investigations of the diversity–stability relationship in soil microbial communities have been undertaken, despite the fundamental role of microbial communities in driving carbon and nutrient cycling in terrestrial ecosystems. In this study, we conducted a microcosm experiment to investigate the relationship between microbial diversity and stability of soil decomposition activities against changes in decomposition substrate quality by manipulating microbial community using selective biocides. We found that soil respiration rates and degradation enzyme activities by a coexisting fungal and bacterial community (a taxonomically diverse community) are more stable against changes in substrate quality (plant leaf materials) than those of a fungi-dominated or a bacteria-dominated community (less diverse community). Flexible changes in the microbial community composition and/or physiological state in the coexisting community against changes in substrate quality, as inferred by the soil lipid profile, may be the mechanism underlying this positive diversity–stability relationship. Our experiment demonstrated that the previously found positive diversity–stability relationship could also be valid in the soil microbial community. Our results also imply that the functional/taxonomic diversity and community ecology of soil microbes should be incorporated into the context of climate–ecosystem feedbacks. Changes in substrate quality, which could be induced by climate change, have impacts on decomposition process and carbon dioxide emission from soils, but such impacts may be attenuated by the functional diversity of soil microbial communities.
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Affiliation(s)
- Masayuki Ushio
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
- Department of Soil Science, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
| | - Takeshi Miki
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Teri C. Balser
- Department of Soil Science, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Soil and Water Science, University of Florida IFAS, Gainesville, Florida, United States of America
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Abstract
As predator-prey interactions are inherently size-dependent, predator and prey body sizes are key to understanding their feeding relationships. To describe predator-prey size relationships (PPSRs) when predators can consume prey larger than themselves, we conducted field observations targeting three aquatic hemipteran bugs, and assessed their body masses and those of their prey for each hunting event. The data revealed that their PPSR varied with predator size and species identity, although the use of the averaged sizes masked these effects. Specifically, two predators had slightly decreased predator-prey mass ratios (PPMRs) during growth, whereas the other predator specialized on particular sizes of prey, thereby showing a clear positive size-PPMR relationship. We discussed how these patterns could be different from fish predators swallowing smaller prey whole.
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Abstract
We investigated whole-plant leaf area in relation to ontogenetic variation in leaf-size for a forest perennial herb, Cardiocrinum cordatum. The 200-fold ontogenetic variability in C. cordatum leaf area followed a power-law dependence on total leaf number, a measure of developmental stage. When we normalized for plant size, the function describing the size of single leaves along the stem was similar among different-sized plants, implying that the different-sized canopies observed at different times in the growth trajectory were fundamentally similar to each other. We conclude that the growth trajectory of a population of C. cordatum plant leaves obeyed a dynamic scaling law, the first reported for a growth trajectory at the whole-plant level.
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Affiliation(s)
- Kohei Koyama
- Department of Environmental Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan.
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Takeuchi Y, Salcher MM, Ushio M, Shimizu-Inatsugi R, Kobayashi MJ, Diway B, von Mering C, Pernthaler J, Shimizu KK. In situ enzyme activity in the dissolved and particulate fraction of the fluid from four pitcher plant species of the genus Nepenthes. PLoS One 2011; 6:e25144. [PMID: 21949872 PMCID: PMC3174996 DOI: 10.1371/journal.pone.0025144] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 08/26/2011] [Indexed: 12/04/2022] Open
Abstract
The genus Nepenthes, a carnivorous plant, has a pitcher to trap insects and digest them in the contained fluid to gain nutrient. A distinctive character of the pitcher fluid is the digestive enzyme activity that may be derived from plants and dwelling microbes. However, little is known about in situ digestive enzymes in the fluid. Here we examined the pitcher fluid from four species of Nepenthes. High bacterial density was observed within the fluids, ranging from 7×10(6) to 2.2×10(8) cells ml(-1). We measured the activity of three common enzymes in the fluid: acid phosphatases, β-D-glucosidases, and β-D-glucosaminidases. All the tested enzymes detected in the liquid of all the pitcher species showed activity that considerably exceeded that observed in aquatic environments such as freshwater, seawater, and sediment. Our results indicate that high enzyme activity within a pitcher could assist in the rapid decomposition of prey to maximize efficient nutrient use. In addition, we filtered the fluid to distinguish between dissolved enzyme activity and particle-bound activity. As a result, filtration treatment significantly decreased the activity in all enzymes, while pH value and Nepenthes species did not affect the enzyme activity. It suggested that enzymes bound to bacteria and other organic particles also would significantly contribute to the total enzyme activity of the fluid. Since organic particles are themselves usually colonized by attached and highly active bacteria, it is possible that microbe-derived enzymes also play an important role in nutrient recycling within the fluid and affect the metabolism of the Nepenthes pitcher plant.
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Affiliation(s)
- Yayoi Takeuchi
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland.
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Kitayama K, Aiba SI, Ushio M, Seino T, Fujiki Y. The Ecology of Podocarps in Tropical Montane Forests of Borneo: Distribution, Population Dynamics, and Soil Nutrient Acquisition. ACTA ACUST UNITED AC 2011. [DOI: 10.5479/si.0081024x.95.101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Miki T, Ushio M, Fukui S, Kondoh M. Functional diversity of microbial decomposers facilitates plant coexistence in a plant-microbe-soil feedback model. Proc Natl Acad Sci U S A 2010; 107:14251-6. [PMID: 20663953 PMCID: PMC2922608 DOI: 10.1073/pnas.0914281107] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Theory and empirical evidence suggest that plant-soil feedback (PSF) determines the structure of a plant community and nutrient cycling in terrestrial ecosystems. The plant community alters the nutrient pool size in soil by affecting litter decomposition processes, which in turn shapes the plant community, forming a PSF system. However, the role of microbial decomposers in PSF function is often overlooked, and it remains unclear whether decomposers reinforce or weaken litter-mediated plant control over nutrient cycling. Here, we present a theoretical model incorporating the functional diversity of both plants and microbial decomposers. Two fundamental microbial processes are included that control nutrient mineralization from plant litter: (i) assimilation of mineralized nutrient into the microbial biomass (microbial immobilization), and (ii) release of the microbial nutrients into the inorganic nutrient pool (net mineralization). With this model, we show that microbial diversity may act as a buffer that weakens plant control over the soil nutrient pool, reversing the sign of PSF from positive to negative and facilitating plant coexistence. This is explained by the decoupling of litter decomposability and nutrient pool size arising from a flexible change in the microbial community composition and decomposition processes in response to variations in plant litter decomposability. Our results suggest that the microbial community plays a central role in PSF function and the plant community structure. Furthermore, the results strongly imply that the plant-centered view of nutrient cycling should be changed to a plant-microbe-soil feedback system, by incorporating the community ecology of microbial decomposers and their functional diversity.
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Affiliation(s)
- Takeshi Miki
- Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan.
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Ushio M, Miki T, Kitayama K. Phenolic control of plant nitrogen acquisition through the inhibition of soil microbial decomposition processes: a plant-microbe competition model. Microbes Environ 2009; 24:180-7. [PMID: 21566372 DOI: 10.1264/jsme2.me09107] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Phenolics are a dominant class of plant secondary metabolites that have strong effects on various ecosystem processes. The ecological significance of these compounds, however, is still poorly understood. We hypothesized that the inhibitory effects of phenolics on microbial activity could enhance plant nitrogen acquisition by relaxing competition between plants and microbes. To test this hypothesis theoretically, we constructed a novel and simple mechanistic model by unifying two concepts: one is a new paradigm of nitrogen cycling which considers the uptake of organic nitrogen by plants, and the other is that phenolics can regulate nitrogen cycling by inhibiting microbial decomposition processes. Our plant-microbe competition model consists of five compartments (plants, soil microbes, debris, organic nitrogen and inorganic nitrogen) and incorporates the essential processes of nitrogen cycling: plant uptake of monomers, competition between plants and microbes, and the depolymerization process. Our analysis showed that plant nitrogen acquisition was maximized at intermediate levels of phenolics, but only when plants could utilize organic nitrogen. Furthermore, this pattern occurred over a broad range of parameter conditions. Our study successfully demonstrated the potential role of phenolics in plant nitrogen acquisition throughout natural environments.
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Affiliation(s)
- Masayuki Ushio
- Center for Ecological Research, Kyoto University, 509-3 Hirano 2-chome, Otsu, Shiga, 520-2113, Japan.
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Murofushi T, Iwasaki S, Ozeki H, Nakahar H, Ushio M, Chihara Y. P07.23 Tone burst-galvanic ratio of vestibular evoked myogenic potentials: An indicator of labyrinthine damages? Clin Neurophysiol 2006. [DOI: 10.1016/j.clinph.2006.06.292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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