Spatial structure of fungal DNA assemblages revealed with eDNA metabarcoding in a forest river network in western Japan

Shunsuke Matsuoka; Yoriko Sugiyama; Hirotoshi Sato; Izumi Katano; Ken Harada; Hideyuki Doi

doi:10.3897/mbmg.3.36335

Peggy Heine, Jonas Hausen, Richard Ottermanns, Martina Roß-Nickoll (2021)
Comparing eDNA metabarcoding with morphological analyses: Fungal species richness and community composition of differently managed stages along a forest conversion of Norway spruce towards European beech in Germany. Forest Ecology and Management 496: 119429.

DOI: 10.1016/j.foreco.2021.119429

Indunil C. Senanayake, Dhandevi Pem, Achala R. Rathnayaka, Subodini N. Wijesinghe, Saowaluck Tibpromma, Dhanushka N. Wanasinghe, Rungtiwa Phookamsak, Nuwan D. Kularathnage, Deecksha Gomdola, Dulanjalee Harishchandra, Lakmali S. Dissanayake, Mei-mei Xiang, Anusha H. Ekanayaka, Eric H. C. McKenzie, Kevin D. Hyde, Hao-xing Zhang, Ning Xie (2022)
Predicting global numbers of teleomorphic ascomycetes. Fungal Diversity 114: 237.

DOI: 10.1007/s13225-022-00498-w

Shunsuke Matsuoka, Yoriko Sugiyama, Yoshito Shimono, Masayuki Ushio, Hideyuki Doi (2021)
Evaluation of seasonal dynamics of fungal DNA assemblages in a flow‐regulated stream in a restored forest using eDNA metabarcoding. Environmental Microbiology 23: 4797.

DOI: 10.1111/1462-2920.15669

Shota Masumoto, Ryo Kitagawa, Ryo Kaneko, Keita Nishizawa, Shunsuke Matsuoka, Masaki Uchida, Akira S Mori (2023)
Discrepancies of fungi and plants in the pattern of beta-diversity with environmental gradient imply a comprehensive community assembly rule. FEMS Microbiology Ecology 99: .

DOI: 10.1093/femsec/fiac157

Haile Yang, Hao Du, Hongfang Qi, Luxian Yu, Xindong Hou, Hui Zhang, Junyi Li, Jinming Wu, Chengyou Wang, Qiong Zhou, Qiwei Wei (2021)
Effectiveness assessment of using riverine water eDNA to simultaneously monitor the riverine and riparian biodiversity information. Scientific Reports 11: .

DOI: 10.1038/s41598-021-03733-7

Leho Tedersoo, Mohammad Bahram, Lucie Zinger, R. Henrik Nilsson, Peter G. Kennedy, Teng Yang, Sten Anslan, Vladimir Mikryukov (2022)
Best practices in metabarcoding of fungi: From experimental design to results. Molecular Ecology 31: 2769.

DOI: 10.1111/mec.16460

Yoriko Sugiyama, Shunsuke Matsuoka, Yoshito Shimono, Masayuki Ushio, Hideyuki Doi (2024)
Do aquatic fungal environmental DNA assemblages reflect the surrounding terrestrial sporocarp communities?. Fungal Ecology 67: 101311.

DOI: 10.1016/j.funeco.2023.101311

Noriko Uchida, Kengo Kubota, Shunsuke Aita, So Kazama (2020)
Aquatic insect community structure revealed by eDNA metabarcoding derives indices for environmental assessment. PeerJ 8: e9176.

DOI: 10.7717/peerj.9176

Shota Masumoto, Ryo Kitagawa, Keita Nishizawa, Takashi Osono, Motohiro Hasegawa, Yasuo Iimura, Shunsuke Matsuoka, Ryo Kaneko, Masaki Uchida, Akira S. Mori (2021)
Integrative assessment of the effects of shrub coverage on soil respiration in a tundra ecosystem. Polar Science 27: 100562.

DOI: 10.1016/j.polar.2020.100562

Corinne Biderre‐Petit, Jean‐Christophe Charvy, Gisèle Bronner, Marina Chauvet, Didier Debroas, Hélène Gardon, Claire Hennequin, Isabelle Jouan‐Dufournel, Anne Moné, Arthur Monjot, Viviane Ravet, Agnès Vellet, Cécile Lepère (2023)
FreshOmics: A manually curated and standardized –omics database for investigating freshwater microbiomes. Molecular Ecology Resources 23: 222.

DOI: 10.1111/1755-0998.13692

Aki Tanaka, Izumi Katano, Hideyuki Doi, Mami Iguchi, Shohei Koike (2023)
Applicability of environmental DNA metabarcoding for the hyporheic zone of a stream bed. Environmental DNA 5: 1667.

DOI: 10.1002/edn3.484

Shota Masumoto, Ryo Kitagawa, Keita Nishizawa, Ryo Kaneko, Takashi Osono, Motohiro Hasegawa, Shunsuke Matsuoka, Masaki Uchida, Akira S Mori (2021)
Functionally explicit partitioning of plant β-diversity reveal soil fungal assembly in the subarctic tundra. FEMS Microbiology Ecology 97: .

DOI: 10.1093/femsec/fiab129

Shunsuke Matsuoka, Hideyuki Doi, Shota Masumoto, Ryo Kitagawa, Keita Nishizawa, Kaho Tanaka, Motohiro Hasegawa, Satoru Hobara, Takashi Osono, Akira S. Mori, Masaki Uchida (2021)
Taxonomic, functional, and phylogenetic diversity of fungi in a forest-tundra ecotone in Québec. Polar Science 27: 100594.

DOI: 10.1016/j.polar.2020.100594

Lauren Cortez French, Michelle A. Jusino, Randolph M. Chambers, James Skelton (2024)
Community structure and functional diversity of aquatic fungi are correlated with water quality: Insights from multi‐marker analysis of environmental DNA in a coastal watershed. Environmental DNA 6: .

DOI: 10.1002/edn3.576

Danielle Machado Pagani, Stefânia P. R. Ventura, Duong Vu, Thairine Mendes-Pereira, Luiz Marcelo Ribeiro Tomé, Daniel Santana de Carvalho, Diogo Henrique Costa-Rezende, Rodrigo Bentes Kato, Glen Jasper Yupanqui García, József Geml, Vincent Robert, Ng Haig They, Bertram Brenig, Vasco Azevedo, Maria Lúcia Scroferneker, Patricia Valente, Aristóteles Góes-Neto (2023)
Unveiling Fungal Community Structure along Different Levels of Anthropic Disturbance in a South American Subtropical Lagoon. Journal of Fungi 9: 890.

DOI: 10.3390/jof9090890

Shunsuke Matsuoka, Yoriko Sugiyama, Mariko Nagano, Hideyuki Doi (2022)
Influence of DNA extraction kits on freshwater fungal DNA metabarcoding. PeerJ 10: e13477.

DOI: 10.7717/peerj.13477

Andrea Čačković, Katarina Kajan, Lorena Selak, Tamara Marković, Andrijana Brozičević, Petra Pjevac, Sandi Orlić, Michael J. Imperiale (2023)
Hydrochemical and Seasonally Conditioned Changes of Microbial Communities in the Tufa-Forming Freshwater Network Ecosystem. mSphere 8: .

DOI: 10.1128/msphere.00602-22

Takashi Shirouzu, Shunsuke Matsuoka, Hideyuki Doi, Nobuaki Nagata, Masayuki Ushio, Kentaro Hosaka (2020)
Complementary molecular methods reveal comprehensive phylogenetic diversity integrating inconspicuous lineages of early-diverged wood-decaying mushrooms. Scientific Reports 10: .

DOI: 10.1038/s41598-020-59620-0

Namrata Deka, Saqib Hassan, Tanveer Ahmed, George Seghal Kiran, Joseph Selvin (2022)
Freshwater Mycology. : 247.

DOI: 10.1016/B978-0-323-91232-7.00003-9

Hans-Peter Grossart, Elhagag Ahmed Hassan, Hossein Masigol, Maria Arias-Andres, Keilor Rojas-Jimenez (2022)
Encyclopedia of Inland Waters. : 667.

DOI: 10.1016/B978-0-12-819166-8.00025-6