title: Network modules and hubs in plant-root fungal biomes.
abstract: Terrestrial plants host phylogenetically and functionally diverse groups of below-ground microbes, whose community structure controls plant growth/survival in both natural and agricultural ecosystems. Therefore, understanding the processes by which whole root-associated microbiomes are organized is one of the major challenges in ecology and plant science. We here report that diverse root-associated fungi can form highly compartmentalized networks of coexistence within host roots and that the structure of the fungal symbiont communities can be partitioned into semi-discrete types even within a single host plant population. Illumina sequencing of root-associated fungi in a monodominant south beech forest revealed that the network representing symbiont-symbiont co-occurrence patterns was compartmentalized into clear modules, which consisted of diverse functional groups of mycorrhizal and endophytic fungi. Consequently, terminal roots of the plant were colonized by either of the two largest fungal species sets (represented by Oidiodendron or Cenococcum). Thus, species-rich root microbiomes can have alternative community structures, as recently shown in the relationships between human gut microbiome type (i.e., 'enterotype') and host individual health. This study also shows an analytical framework for pinpointing network hubs in symbiont-symbiont networks, leading to the working hypothesis that a small number of microbial species organize the overall root-microbiome dynamics.
authors.affiliation: Graduate School of Human and Environmental Studies, Kyoto University, Sakyo, Kyoto 606-8501, Japan toju.hirokazu.4c@kyoto-u.ac.jp.
authors.forename: Hirokazu
authors.initials: H
authors.lastname: Toju
authors.affiliation: Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-8501, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Yamamoto
authors.affiliation: National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan.
authors.forename: Akifumi S
authors.initials: AS
authors.lastname: Tanabe
authors.affiliation: Department of Wildlife Science (Nagoya Railroad Co., Ltd.), Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan Japan Monkey Centre, Inuyama, Aichi 484-0081, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Hayakawa
authors.affiliation: Department of Environmental Biology and Chemistry, Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan.
authors.forename: Hiroshi S
authors.initials: HS
authors.lastname: Ishii
mesh_terms: D005658:Fungi / Q000502:physiology*; D006801:Humans; D018517:Plant Roots / Q000382:microbiology* / Q000502:physiology*; D058441:Rhizosphere; D013559:Symbiosis / Q000502:physiology*
keywords: Illumina MiSeq; alternative stable states; community ecology; enterotypes; mutualism; network theory