Abstract
BackgroundAlthough a number of recent studies have uncovered remarkable diversity of microbes associated with plants, understanding and managing dynamics of plant microbiomes remain major scientific challenges. In this respect, network analytical methods have provided a basis for exploring “hub” microbial species, which potentially organize community-scale processes of plant–microbe interactions.MethodsBy compiling Illumina sequencing data of root-associated fungi in eight forest ecosystems across the Japanese Archipelago, we explored hubs within “metacommunity-scale” networks of plant–fungus associations. In total, the metadata included 8080 fungal operational taxonomic units (OTUs) detected from 227 local populations of 150 plant species/taxa.ResultsFew fungal OTUs were common across all the eight forests. However, in each of the metacommunity-scale networks representing northern four localities or southern four localities, diverse mycorrhizal, endophytic, and pathogenic fungi were classified as “metacommunity hubs,” which were detected from diverse host plant taxa throughout a climatic region. Specifically, Mortierella (Mortierellales), Cladophialophora (Chaetothyriales), Ilyonectria (Hypocreales), Pezicula (Helotiales), and Cadophora (incertae sedis) had broad geographic and host ranges across the northern (cool-temperate) region, while Saitozyma/Cryptococcus (Tremellales/Trichosporonales) and Mortierella as well as some arbuscular mycorrhizal fungi were placed at the central positions of the metacommunity-scale network representing warm-temperate and subtropical forests in southern Japan.ConclusionsThe network theoretical framework presented in this study will help us explore prospective fungi and bacteria, which have high potentials for agricultural application to diverse plant species within each climatic region. As some of those fungal taxa with broad geographic and host ranges have been known to promote the survival and growth of host plants, further studies elucidating their functional roles are awaited.
Highlights
A number of recent studies have uncovered remarkable diversity of microbes associated with plants, understanding and managing dynamics of plant microbiomes remain major scientific challenges
We examined whether fungal Operational taxonomic unit (OTU) placed at the core of local-level plant–fungus networks could play key topological roles within the metacommunity-scale network
Host plant species were identified based on the sequences of the genes encoding the large subunit of ribulose-1,5-bisphosphate carboxylase and the internal transcribed spacer 1 (ITS1) of the ribosomal RNA region, there were plant root samples that could not be identified to species with the rbcL and ITS1 regions [56]
Summary
A number of recent studies have uncovered remarkable diversity of microbes associated with plants, understanding and managing dynamics of plant microbiomes remain major scientific challenges. Recent studies have indicated that diverse taxonomic groups of endophytic fungi (e.g., endophytic fungi in the ascomycete orders Helotiales and Chaetothyriales) commonly interact with plant roots [10] and that those fungi play pivotal roles by providing soil nitrogen/phosphorous to their hosts [11,12,13,14,15], converting organic nitrogen into inorganic forms in the rhizosphere [16], and increasing plants’ resistance to environmental stresses [17,18,19] Because of their fundamental roles, below-ground fungi have been considered as prospective sources of ecosystem-level functioning in forest management, agriculture, and. Due to the exceptional diversity of below-ground fungi [22,23,24] and the extraordinary complexity of below-ground plant– fungus interactions [25,26,27], we are still at an early stage of managing and manipulating plant-associated microbiomes [28,29,30]
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