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Appl Plant Sci
2022 Mar 14;102:e11461. doi: 10.1002/aps3.11461.
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Mycobiome detection from a single subterranean gametophyte using metabarcoding techniques.
Chen KH
,
Xie QY
,
Chang CC
,
Kuo LY
.
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Premise: Several ferns and lycophytes produce subterranean gametophytes, including the Ophioglossaceae, Psilotaceae, and some members of the Schizaeaceae, Gleicheniaceae, and Lycopodiaceae. Despite the surge in plant-microbiome research, which has been particularly boosted by high-throughput sequencing techniques, the microbiomes of these inconspicuous fern gametophytes have rarely been examined. The subterranean gametophytes are peculiar due to their achlorophyllous nature, which makes them rely on fungi to obtain nutrients. Furthermore, the factors that shape the fungal communities (mycobiomes) of fern gametophytes have not been examined in depth.
Methods and Results: We present a workflow to study the mycobiome of the achlorophyllous gametophytes of Ophioderma pendulum using a high-throughput metabarcoding approach. Simultaneously, each gametophyte was investigated microscopically to detect fungal structures. Two primer sets of the nuclear ITS sequence targeting general fungi were applied, in addition to a primer set that specifically targets the nuclear small subunit ribosomal rDNA region of arbuscular mycorrhizal fungi. Both the microscopic and metabarcoding approaches revealed many diverse fungi inhabiting a single gametophyte of O. pendulum.
Discussion: This study provides methodological details and discusses precautions for the mycobiome investigation of achlorophyllous gametophytes. This research is also the first to uncover the mycobiome assembly of an achlorophyllous gametophyte of an epiphytic fern.
Figure 1. Images of the study organism, the fern Ophioderma pendulum. (A) Ophioderma pendulum growing on a tree trunk, as indicated by a white arrow. (B) The achlorophyllous subterranean gametophyte of O. pendulum
Figure 2. Workflow of a mycobiome examination in subterranean gametophytes using a combination of DNA metabarcoding and microscopy
Figure 3. Fungal structures associated with the Ophioderma pendulum gametophyte. (A) The branches of the gametophyte were fungus‐free, but the central part was densely colonized by fungal hyphae. (B) Spherical arbuscules in the cells. (C) A vesicle produced from the middle of a hypha. (D) Hyphal coils inside the plant cells. White arrow, septa; ab, arbuscules; hc, hyphal coils; v, vesicle
Figure 4. Stack barplot showing the relative abundance of fungal taxa. (A) Phylum level. (B) Class level. ITS1, ITS1 data set; ITS2, ITS2 data set; SSU, SSU data set
Benucci,
Evidence for Co-evolutionary History of Early Diverging Lycopodiaceae Plants With Fungi.
2019, Pubmed
Benucci,
Evidence for Co-evolutionary History of Early Diverging Lycopodiaceae Plants With Fungi.
2019,
Pubmed
Callahan,
DADA2: High-resolution sample inference from Illumina amplicon data.
2016,
Pubmed
Desirò,
Multigene phylogeny of Endogonales, an early diverging lineage of fungi associated with plants.
2017,
Pubmed
Fernández,
Occurrence of arbuscular mycorrhizas and dark septate endophytes in pteridophytes from a Patagonian rainforest, Argentina.
2013,
Pubmed
Hassani,
Microbial interactions within the plant holobiont.
2018,
Pubmed
Horn,
Morphological and molecular analyses of fungal endophytes of achlorophyllous gametophytes of Diphasiastrum alpinum (Lycopodiaceae).
2013,
Pubmed
Hoysted,
Mucoromycotina Fine Root Endophyte Fungi Form Nutritional Mutualisms with Vascular Plants.
2019,
Pubmed
Huson,
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data.
2016,
Pubmed
Jumpponen,
Dark septate endophytes: a review of facultative biotrophic root-colonizing fungi.
1998,
Pubmed
Liao,
Metatranscriptomic analysis of ectomycorrhizal roots reveals genes associated with Piloderma-Pinus symbiosis: improved methodologies for assessing gene expression in situ.
2014,
Pubmed
Loit,
Relative Performance of MinION (Oxford Nanopore Technologies) versus Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens.
2019,
Pubmed
Mbareche,
Comparison of the performance of ITS1 and ITS2 as barcodes in amplicon-based sequencing of bioaerosols.
2020,
Pubmed
McMurdie,
phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.
2013,
Pubmed
Morgulis,
Database indexing for production MegaBLAST searches.
2008,
Pubmed
Nilsson,
Mycobiome diversity: high-throughput sequencing and identification of fungi.
2019,
Pubmed
Nilsson,
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications.
2019,
Pubmed
Ogura-Tsujita,
Arbuscular mycorrhiza formation in cordate gametophytes of two ferns, Angiopteris lygodiifolia and Osmunda japonica.
2013,
Pubmed
Ogura-Tsujita,
Arbuscular mycorrhizal colonization in field-collected terrestrial cordate gametophytes of pre-polypod leptosporangiate ferns (Osmundaceae, Gleicheniaceae, Plagiogyriaceae, Cyatheaceae).
2016,
Pubmed
Ogura-Tsujita,
Fern gametophytes of Angiopteris lygodiifolia and Osmunda japonica harbor diverse Mucoromycotina fungi.
2019,
Pubmed
Oita,
Methodological Approaches Frame Insights into Endophyte Richness and Community Composition.
2021,
Pubmed
Opik,
The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota).
2010,
Pubmed
Petrolli,
A fine-scale spatial analysis of fungal communities on tropical tree bark unveils the epiphytic rhizosphere in orchids.
2021,
Pubmed
Pozo,
Untapping the potential of plant mycobiomes for applications in agriculture.
2021,
Pubmed
Schoch,
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi.
2012,
Pubmed
Suetsugu,
Isotopic and molecular data support mixotrophy in Ophioglossum at the sporophytic stage.
2020,
Pubmed
Swatzell,
The relationship of endophytic fungi to the gametophyte of the fern Schizaea pusilla.
1996,
Pubmed
Taberlet,
Universal primers for amplification of three non-coding regions of chloroplast DNA.
1991,
Pubmed
Taylor,
Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing.
2016,
Pubmed
Tedersoo,
PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives.
2018,
Pubmed
U'Ren,
Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi.
2014,
Pubmed
U'Ren,
Host availability drives distributions of fungal endophytes in the imperilled boreal realm.
2019,
Pubmed
Vandenkoornhuyse,
The importance of the microbiome of the plant holobiont.
2015,
Pubmed
Vági,
Simultaneous specific in planta visualization of root-colonizing fungi using fluorescence in situ hybridization (FISH).
2014,
Pubmed
Wang,
Phylogenetic distribution and evolution of mycorrhizas in land plants.
2006,
Pubmed
Wang,
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.
2007,
Pubmed
Winther,
Arbuscular mycorrhizal symbionts in Botrychium (Ophioglossaceae).
2007,
Pubmed
