Evaluating the soil microbe community-level physiological profile using EcoPlate and soil properties at 33 forest sites across Japan

Masahiro Nakamura; Chisato Terada; Kinya Ito; Kazuaki Matsui; Shigeru Niwa; Masae Ishihara; Tanaka Kenta; Tetsuro Yoshikawa; Taku Kadoya; Tsutom Hiura; Hiroyuki Muraoka; Ken Ishida; Naoki Agetsuma; Ryosuke Nakamura; Hitoshi Sakio; Masahiro Takagi; Akira S. Mori; Megumi K. Kimura; Hiroko Kurokawa; Tsutomu Enoki; Tatsuyuki Seino; Atsushi Takashima; Hajime Kobayashi; Kazuho Matsumoto; Koichi Takahashi; Ryunosuke Tateno; Tomohiro Yoshida; Tatsuro Nakaji; Masayuki Maki; Kazutaka Kobayashi; Karibu Fukuzawa; Kazuhiko Hoshizaki; Kazuhide Ohta; Keito Kobayashi; Motohiro Hasegawa; Satoshi N. Suzuki; Michinori Sakimoto; Yoichiro Kitagawa; Akiko Sakai; Hirofumi Kondo; Tomoaki Ichie; Koji Kageyama; Ayaka Hieno; Shogo Kato; Tatsuya Otani; Yasuhiro Utsumi; Tomonori Kume; Kosuke Homma; Koju Kishimoto; Kazuhiko Masaka; Kenta Watanabe; Motomu Toda; Dai Nagamatsu; Yuko Miyazaki; Tamon Yamashita; Naoko Tokuchi

doi:10.1111/1440-1703.12293

Evaluating the soil microbe community-level physiological profile using EcoPlate and soil properties at 33 forest sites across Japan

Masahiro Nakamura, Chisato Terada, Kinya Ito, Kazuaki Matsui, Shigeru Niwa, Masae Ishihara, Tanaka Kenta, Tetsuro Yoshikawa, Taku Kadoya, Tsutom Hiura, Hiroyuki Muraoka, Ken Ishida, Naoki Agetsuma, Ryosuke Nakamura, Hitoshi Sakio, Masahiro Takagi, Akira S. Mori, Megumi K. Kimura, Hiroko Kurokawa, Tsutomu EnokiTatsuyuki Seino, Atsushi Takashima, Hajime Kobayashi, Kazuho Matsumoto, Koichi Takahashi, Ryunosuke Tateno, Tomohiro Yoshida, Tatsuro Nakaji, Masayuki Maki, Kazutaka Kobayashi, Karibu Fukuzawa, Kazuhiko Hoshizaki, Kazuhide Ohta, Keito Kobayashi, Motohiro Hasegawa, Satoshi N. Suzuki, Michinori Sakimoto, Yoichiro Kitagawa, Akiko Sakai, Hirofumi Kondo, Tomoaki Ichie, Koji Kageyama, Ayaka Hieno, Shogo Kato, Tatsuya Otani, Yasuhiro Utsumi, Tomonori Kume, Kosuke Homma, Koju Kishimoto, Kazuhiko Masaka, Kenta Watanabe, Motomu Toda, Dai Nagamatsu, Yuko Miyazaki, Tamon Yamashita, Naoko Tokuchi

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Abstract

We present the largest freely available EcoPlate dataset for Japan, comprising data collected from a network of 33 natural forest sites (77 plots) in regions of East Asia ranging from cool temperate to subtropical. EcoPlate is a 96-well microplate that contains three repeated sets of 31 response wells with different sole carbon substrates. The utilization of each carbon substrate by the microbial community is quantified by the color density of the well during incubation. EcoPlate can provide a multifunctional index of a soil microbial community. Soil properties (water content, carbon [C] and nitrogen [N] contents, the C/N ratio, and pH) that are essential for interpreting the EcoPlate results were also measured. The network is part of the Forest and Grassland Survey of the Monitoring Sites 1000 Project established by the Ministry of the Environment. Using a standardized protocol, soil was sampled between September and December 2020. A preliminary principal component analysis was performed on the temporal integration of color density using 31 substrates. For the temporal integration, we calculated the cumulative amount of color development by integrating the color density development curve. PC1 contributed 55.6% and is thought to represent the magnitude of the overall absorbance of all substrates. The model of environmental factors including elevation and the model of soil properties, including water content and pH, were selected as the best-fit models for variation in PC1. EcoPlate data enable the meta-analysis of comparative studies among forest types and testing community ecology and ecosystem function hypotheses at broad spatial scales. The complete data set for this abstract published in the Data Paper section of the journal is available in electronic format in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2022-01.1/jalter-en.

Original language	English
Pages (from-to)	432-445
Number of pages	14
Journal	Ecological Research
Volume	37
Issue number	3
DOIs	https://doi.org/10.1111/1440-1703.12293
Publication status	Published - 2022 May

Keywords

microbial community
multifunctional index
site-network survey
standardized protocol
the Monitoring Sites 1000 Project

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics

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10.1111/1440-1703.12293

Cite this

Nakamura, M., Terada, C., Ito, K., Matsui, K., Niwa, S., Ishihara, M., Kenta, T., Yoshikawa, T., Kadoya, T., Hiura, T., Muraoka, H., Ishida, K., Agetsuma, N., Nakamura, R., Sakio, H., Takagi, M., Mori, A. S., Kimura, M. K., Kurokawa, H., ... Tokuchi, N. (2022). Evaluating the soil microbe community-level physiological profile using EcoPlate and soil properties at 33 forest sites across Japan. Ecological Research, 37(3), 432-445. https://doi.org/10.1111/1440-1703.12293

Nakamura, M, Terada, C, Ito, K, Matsui, K, Niwa, S, Ishihara, M, Kenta, T, Yoshikawa, T, Kadoya, T, Hiura, T, Muraoka, H, Ishida, K, Agetsuma, N, Nakamura, R, Sakio, H, Takagi, M, Mori, AS, Kimura, MK, Kurokawa, H, Enoki, T, Seino, T, Takashima, A, Kobayashi, H, Matsumoto, K, Takahashi, K, Tateno, R, Yoshida, T, Nakaji, T, Maki, M, Kobayashi, K, Fukuzawa, K, Hoshizaki, K, Ohta, K, Kobayashi, K, Hasegawa, M, Suzuki, SN, Sakimoto, M, Kitagawa, Y, Sakai, A, Kondo, H, Ichie, T, Kageyama, K, Hieno, A, Kato, S, Otani, T, Utsumi, Y, Kume, T, Homma, K, Kishimoto, K, Masaka, K, Watanabe, K, Toda, M, Nagamatsu, D, Miyazaki, Y, Yamashita, T & Tokuchi, N 2022, 'Evaluating the soil microbe community-level physiological profile using EcoPlate and soil properties at 33 forest sites across Japan', Ecological Research, vol. 37, no. 3, pp. 432-445. https://doi.org/10.1111/1440-1703.12293

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title = "Evaluating the soil microbe community-level physiological profile using EcoPlate and soil properties at 33 forest sites across Japan",

abstract = "We present the largest freely available EcoPlate dataset for Japan, comprising data collected from a network of 33 natural forest sites (77 plots) in regions of East Asia ranging from cool temperate to subtropical. EcoPlate is a 96-well microplate that contains three repeated sets of 31 response wells with different sole carbon substrates. The utilization of each carbon substrate by the microbial community is quantified by the color density of the well during incubation. EcoPlate can provide a multifunctional index of a soil microbial community. Soil properties (water content, carbon [C] and nitrogen [N] contents, the C/N ratio, and pH) that are essential for interpreting the EcoPlate results were also measured. The network is part of the Forest and Grassland Survey of the Monitoring Sites 1000 Project established by the Ministry of the Environment. Using a standardized protocol, soil was sampled between September and December 2020. A preliminary principal component analysis was performed on the temporal integration of color density using 31 substrates. For the temporal integration, we calculated the cumulative amount of color development by integrating the color density development curve. PC1 contributed 55.6% and is thought to represent the magnitude of the overall absorbance of all substrates. The model of environmental factors including elevation and the model of soil properties, including water content and pH, were selected as the best-fit models for variation in PC1. EcoPlate data enable the meta-analysis of comparative studies among forest types and testing community ecology and ecosystem function hypotheses at broad spatial scales. The complete data set for this abstract published in the Data Paper section of the journal is available in electronic format in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2022-01.1/jalter-en.",

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author = "Masahiro Nakamura and Chisato Terada and Kinya Ito and Kazuaki Matsui and Shigeru Niwa and Masae Ishihara and Tanaka Kenta and Tetsuro Yoshikawa and Taku Kadoya and Tsutom Hiura and Hiroyuki Muraoka and Ken Ishida and Naoki Agetsuma and Ryosuke Nakamura and Hitoshi Sakio and Masahiro Takagi and Mori, {Akira S.} and Kimura, {Megumi K.} and Hiroko Kurokawa and Tsutomu Enoki and Tatsuyuki Seino and Atsushi Takashima and Hajime Kobayashi and Kazuho Matsumoto and Koichi Takahashi and Ryunosuke Tateno and Tomohiro Yoshida and Tatsuro Nakaji and Masayuki Maki and Kazutaka Kobayashi and Karibu Fukuzawa and Kazuhiko Hoshizaki and Kazuhide Ohta and Keito Kobayashi and Motohiro Hasegawa and Suzuki, {Satoshi N.} and Michinori Sakimoto and Yoichiro Kitagawa and Akiko Sakai and Hirofumi Kondo and Tomoaki Ichie and Koji Kageyama and Ayaka Hieno and Shogo Kato and Tatsuya Otani and Yasuhiro Utsumi and Tomonori Kume and Kosuke Homma and Koju Kishimoto and Kazuhiko Masaka and Kenta Watanabe and Motomu Toda and Dai Nagamatsu and Yuko Miyazaki and Tamon Yamashita and Naoko Tokuchi",

note = "Funding Information: The authors are grateful to Rie Kurokawa, Hiroko Ikuma, Hikaru Iguchi, Mahoko Noguchi. The authors also thank all individuals who have contributed to collect the data. The study was partly supported by Climate Change Adaptation Research Program, National Institute for Environmental Studies, Japan. Publisher Copyright: {\textcopyright} 2022 The Ecological Society of Japan.",

year = "2022",

month = may,

doi = "10.1111/1440-1703.12293",

language = "English",

volume = "37",

pages = "432--445",

journal = "Ecological Research",

issn = "0912-3814",

publisher = "Springer Japan",

number = "3",

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T1 - Evaluating the soil microbe community-level physiological profile using EcoPlate and soil properties at 33 forest sites across Japan

AU - Nakamura, Masahiro

AU - Terada, Chisato

AU - Ito, Kinya

AU - Matsui, Kazuaki

AU - Niwa, Shigeru

AU - Ishihara, Masae

AU - Kenta, Tanaka

AU - Yoshikawa, Tetsuro

AU - Kadoya, Taku

AU - Hiura, Tsutom

AU - Muraoka, Hiroyuki

AU - Ishida, Ken

AU - Agetsuma, Naoki

AU - Nakamura, Ryosuke

AU - Sakio, Hitoshi

AU - Takagi, Masahiro

AU - Mori, Akira S.

AU - Kimura, Megumi K.

AU - Kurokawa, Hiroko

AU - Enoki, Tsutomu

AU - Seino, Tatsuyuki

AU - Takashima, Atsushi

AU - Kobayashi, Hajime

AU - Matsumoto, Kazuho

AU - Takahashi, Koichi

AU - Tateno, Ryunosuke

AU - Yoshida, Tomohiro

AU - Nakaji, Tatsuro

AU - Maki, Masayuki

AU - Kobayashi, Kazutaka

AU - Fukuzawa, Karibu

AU - Hoshizaki, Kazuhiko

AU - Ohta, Kazuhide

AU - Kobayashi, Keito

AU - Hasegawa, Motohiro

AU - Suzuki, Satoshi N.

AU - Sakimoto, Michinori

AU - Kitagawa, Yoichiro

AU - Sakai, Akiko

AU - Kondo, Hirofumi

AU - Ichie, Tomoaki

AU - Kageyama, Koji

AU - Hieno, Ayaka

AU - Kato, Shogo

AU - Otani, Tatsuya

AU - Utsumi, Yasuhiro

AU - Kume, Tomonori

AU - Homma, Kosuke

AU - Kishimoto, Koju

AU - Masaka, Kazuhiko

AU - Watanabe, Kenta

AU - Toda, Motomu

AU - Nagamatsu, Dai

AU - Miyazaki, Yuko

AU - Yamashita, Tamon

AU - Tokuchi, Naoko

N1 - Funding Information: The authors are grateful to Rie Kurokawa, Hiroko Ikuma, Hikaru Iguchi, Mahoko Noguchi. The authors also thank all individuals who have contributed to collect the data. The study was partly supported by Climate Change Adaptation Research Program, National Institute for Environmental Studies, Japan. Publisher Copyright: © 2022 The Ecological Society of Japan.

PY - 2022/5

Y1 - 2022/5

N2 - We present the largest freely available EcoPlate dataset for Japan, comprising data collected from a network of 33 natural forest sites (77 plots) in regions of East Asia ranging from cool temperate to subtropical. EcoPlate is a 96-well microplate that contains three repeated sets of 31 response wells with different sole carbon substrates. The utilization of each carbon substrate by the microbial community is quantified by the color density of the well during incubation. EcoPlate can provide a multifunctional index of a soil microbial community. Soil properties (water content, carbon [C] and nitrogen [N] contents, the C/N ratio, and pH) that are essential for interpreting the EcoPlate results were also measured. The network is part of the Forest and Grassland Survey of the Monitoring Sites 1000 Project established by the Ministry of the Environment. Using a standardized protocol, soil was sampled between September and December 2020. A preliminary principal component analysis was performed on the temporal integration of color density using 31 substrates. For the temporal integration, we calculated the cumulative amount of color development by integrating the color density development curve. PC1 contributed 55.6% and is thought to represent the magnitude of the overall absorbance of all substrates. The model of environmental factors including elevation and the model of soil properties, including water content and pH, were selected as the best-fit models for variation in PC1. EcoPlate data enable the meta-analysis of comparative studies among forest types and testing community ecology and ecosystem function hypotheses at broad spatial scales. The complete data set for this abstract published in the Data Paper section of the journal is available in electronic format in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2022-01.1/jalter-en.

AB - We present the largest freely available EcoPlate dataset for Japan, comprising data collected from a network of 33 natural forest sites (77 plots) in regions of East Asia ranging from cool temperate to subtropical. EcoPlate is a 96-well microplate that contains three repeated sets of 31 response wells with different sole carbon substrates. The utilization of each carbon substrate by the microbial community is quantified by the color density of the well during incubation. EcoPlate can provide a multifunctional index of a soil microbial community. Soil properties (water content, carbon [C] and nitrogen [N] contents, the C/N ratio, and pH) that are essential for interpreting the EcoPlate results were also measured. The network is part of the Forest and Grassland Survey of the Monitoring Sites 1000 Project established by the Ministry of the Environment. Using a standardized protocol, soil was sampled between September and December 2020. A preliminary principal component analysis was performed on the temporal integration of color density using 31 substrates. For the temporal integration, we calculated the cumulative amount of color development by integrating the color density development curve. PC1 contributed 55.6% and is thought to represent the magnitude of the overall absorbance of all substrates. The model of environmental factors including elevation and the model of soil properties, including water content and pH, were selected as the best-fit models for variation in PC1. EcoPlate data enable the meta-analysis of comparative studies among forest types and testing community ecology and ecosystem function hypotheses at broad spatial scales. The complete data set for this abstract published in the Data Paper section of the journal is available in electronic format in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2022-01.1/jalter-en.

KW - microbial community

KW - multifunctional index

KW - site-network survey

KW - standardized protocol

KW - the Monitoring Sites 1000 Project

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ER -

Evaluating the soil microbe community-level physiological profile using EcoPlate and soil properties at 33 forest sites across Japan

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