The kingdom Fungi is estimated to include 1.5 million or more species, playing key roles as decomposers, mutualists, and parasites in every biome on the earth. To comprehensively understand diversity ecology of this huge kingdom, DNA barcoding targeting internal transcribed spacer (ITS) region nuclear ribosomal repeat has been regarded a prerequisite procedure. By extensively surveying ITS sequences public databases, we designed new primers with improved coverage across diverse taxonomic...

Abstract Proportional and separate models able to apply different combination of substitution rate matrix (SRM) among‐site variation model (ASRVM) each locus are frequently used in phylogenetic studies multilocus data. A proportional assumes that branch lengths among partitions a partition has an independent set lengths. However, the selection from nonpartitioned (i.e., common is applied all‐loci concatenated sequences), usually based on researcher's preference rather than any information...

Taxonomic identification of biological specimens based on DNA sequence information (a.k.a. barcoding) is becoming increasingly common in biodiversity science. Although several methods have been proposed, many them are not universally applicable due to the need for prerequisite phylogenetic/machine-learning analyses, huge computational resources, or lack a firm theoretical background. Here, we propose two new barcoding and show benchmark bacterial/archeal 16S, animal COX1, fungal internal...

Abstract The application of different substitution models to each gene (a.k.a. mixed model) should be considered in model‐based phylogenetic analysis multigene sequences. However, a single molecular evolution model is still usually applied. There are no computer programs able conduct selection for multiple loci at the same time, though several recently developed types software inference can handle model. Here, I have named ‘kakusan’ that enables us solve above problems. Major running steps...

Abstract In terrestrial ecosystems, plant roots are colonized by various clades of mycorrhizal and endophytic fungi. Focused on the root systems an oak‐dominated temperate forest in J apan, we used 454 pyrosequencing to explore how phylogenetically diverse fungi constitute ecological community multiple ecotypes. total, 345 operational taxonomic units ( OTU s) were found from 159 terminal‐root samples 12 species occurring forest. Due dominance oak Q uercus serrata ), ectomycorrhizal such as R...

Although a number of recent studies have uncovered remarkable diversity microbes associated with plants, understanding and managing dynamics plant microbiomes remain major scientific challenges. In this respect, network analytical methods provided basis for exploring "hub" microbial species, which potentially organize community-scale processes plant–microbe interactions. By compiling Illumina sequencing data root-associated fungi in eight forest ecosystems across the Japanese Archipelago, we...

In terrestrial ecosystems, plant species and diverse root-associated fungi form complex networks of host-symbiont associations. Recent studies have revealed that structures those below-ground plant-fungus differ between arbuscular mycorrhizal ectomycorrhizal symbioses. Nonetheless, we still remain ignorant how ericaceous species, which dominate arctic alpine tundra, constitute with their fungi. Based on a high-throughput DNA sequencing data set, characterized the statistical properties...

Plants influence their soil environment, which affects the next generation of seedlings that can be established. While research has shown such plant-soil feedbacks occur in presence mycorrhizal fungi, it remains unclear when and how fungi mediate direction strength tree communities. Here we show arbuscular ectomycorrhizal fungal guilds differently to large-scale patterns as species coexistence succession. When are grown under same type forest, plant exhibit negative or neutral do positive...

Terrestrial plants host phylogenetically and functionally diverse groups of below-ground microbes, whose community structure controls plant growth/survival in both natural agricultural ecosystems. Therefore, understanding the processes by which whole root-associated microbiomes are organized is one major challenges ecology science. We here report that fungi can form highly compartmentalized networks coexistence within roots fungal symbiont communities be partitioned into semi-discrete types...

Plant–mycorrhizal fungal interactions are ubiquitous in forest ecosystems. While ectomycorrhizal plants and their fungi generally dominate temperate forests, arbuscular mycorrhizal symbiosis is common the tropics. In subtropical regions, however, co-occur at comparable abundances single presumably generating complex community structures of root-associated fungi. To reveal structure a mixed plants, we conducted massively-parallel pyrosequencing analysis, targeting roots 36 plant species that...

Abstract In natural forests, hundreds of fungal species colonize plant roots. The preference or specificity for partners in these symbiotic relationships is a key to understanding how the community structures root‐associated fungi and their host plants influence each other. an oak‐dominated forest Japan, we investigated based on pyrosequencing analysis roots 33 species. Of 387 taxa observed, 153 (39.5%) were identified at least two Although many mycorrhizal root‐endophytic are shared between...

Phylogenetic position of the marine biflagellate Palpitomonas bilix is intriguing, since several ultrastructural characteristics implied its evolutionary connection to Archaeplastida or Hacrobia. The origin and early evolution these two eukaryotic assemblages have yet be fully elucidated, P. may a key lineage in tracing those groups' evolution. In present study, we analyzed 'phylogenomic' alignment 157 genes clarify phylogeny. 157-gene phylogeny, was found basal clade cryptophytes,...

Most terrestrial plants interact with diverse clades of mycorrhizal and root-endophytic fungi in their roots. Through belowground plant–fungal interactions, dominant can benefit by interacting host-specific mutualistic proliferate a community based on positive plant–mutualistic fungal feedback. On the other hand, subordinate plant species may persist sharing sets (functional groups) symbionts each other. Therefore, revealing how root-associated are differentially hosted is essential for...

Abstract The nuclear 18S‐ rRNA gene has been used as a metabarcoding marker in massively parallel sequencing ( MPS )‐based environmental surveys for plankton biodiversity research. However, different hypervariable regions have studies, and their utility debated among researchers. In this study, detailed investigations into were carried out; we investigated the effective number of sequences deposited international nucleotide sequence databases INSD s), amplification bias, amplicon variability...

Abstract Environmental DNA is a powerful tool for community science‐based biodiversity surveys. However, the effectiveness of environmental education and time physical costs perceived by volunteers collecting remain unclear. Here, we evaluated science program monitoring marine fish using metabarcoding. This aimed to investigate in coastal areas along Japanese archipelago. The participants were allowed decide on date site collect DNA. They received paper manual, data sheet, sampling kit via...

Mutualisms with new host lineages can provide symbionts novel ecological opportunities to expand their geographical distribution, thereby leading evolutionary diversification. Because ectomycorrhizal (ECM) fungi ideal test the relationship between shifts and diversification, we tested whether mutualism could increase diversification rates of ECM fungi. Using a Bayesian tree inferred from 23 027-base nucleotide sequences 80 single-copy genes, rate had changed through host-shift events in...

Deep granitic aquifer is one of the largest, but least understood, microbial habitats. To avoid contamination from surface biosphere, underground drilling was conducted for 300 m deep rocks at Mizunami research laboratory (URL), Japan. Slightly alkaline groundwater characterized by low concentrations dissolved organic matter and sulfate presence > 100 nM H2 . The initial biomass highest (∼10(5) cells ml(-1) ) with dominance Hydrogenophaga spp., whereas phylum Nitrospirae became predominant...

Diverse clades of mycorrhizal and endophytic fungi are potentially involved in competitive or facilitative interactions within host-plant roots. We investigated the potential consequences these ecological on assembly process root-associated by examining co-occurrence pairs individuals. Based massively-parallel pyrosequencing, we analyzed fungal community composition for each 249 Quercus serrata 188 glauca seedlings sampled a warm-temperate secondary forest Japan. Pairs that co-occurred more...

Abstract Soil microbes are considered to be a key determinant of the aboveground plant community. They not distributed uniformly in environment, and their activity, abundance, ecosystem functioning could vary across localities, characterized by high β ‐diversity. Investigating factors that contribute ‐diversity can help infer possible mechanisms microbial community assembly, predict scale extent impacts soil have on Because systems consist multiple horizons (i.e., vertical stratification)...

Abstract We investigated the sequence variation in mitochondrial cytochrome c oxidase subunit 1 (mtCOI) gene and nuclear ribosomal internal transcribed spacers (ncITS) of calanoid copepod Acanthodiaptomus pacificus Japan. A. individuals were divided into three divergent mtCOI lineages (mt‐A, ‐B ‐C). mt‐A was distributed northernmost part Japan, from Hokkaido to northern Honshu Island, whereas mt‐C southernmost lineage, central Shikoku Kyushu Islands. mt‐B between these former two lineages,...

Lake Tanganyika, an ancient lake in the Great Rift Valley, is famous for adaptive radiation of cichlids. Five tribes Cichlidae family have acquired herbivory, with five ecomorphs: grazers, browsers, scrapers, biters and scoopers. Sixteen species herbivorous cichlids coexist on a rocky littoral slope lake. Seven them individually defend feeding territories against intruding herbivores to establish algal farms. We collected epiphyton from these at various depths also gathered fish specimens....

Root-associated fungi, including ectomycorrhizal and root-endophytic are among the most diverse important belowground plant symbionts in dipterocarp rainforests. Our study aimed to reveal biodiversity, host association, community structure of Basidiomycota root-associated Ascomycota (including Ascomycota) a lowland rainforest Southeast Asia. The chloroplast ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) region fungal internal transcribed spacer 2 (ITS2) were sequenced...