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What Quality Suffices for Nanopore Metabarcoding? Reconsidering Methodology and Ectomycorrhizae in Decaying Fagus sylvatica Bark as Case Study

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-3-662-08897-5_29openalex-snapshot

Anatomical Characteristics of Identified Ectomycorrhizas: An Attempt Towards a Natural Classification

inferredcites →https://doi.org/10.1007/s00248-022-02066-wopenalex-snapshot

Forest Fire Influence on Tomicus piniperda-Associated Fungal Communities and Phloem Nutrient Availability of Colonized Pinus sylvestris

inferredcites →https://doi.org/10.1007/s00572-009-0244-3openalex-snapshot

Establishment of ectomycorrhizal fungal community on isolated Nothofagus cunninghamii seedlings regenerating on dead wood in Australian wet temperate forests: does fruit-body type matter?

inferredcites →https://doi.org/10.1007/s00572-014-0597-0openalex-snapshot

Sharing rotting wood in the shade: ectomycorrhizal communities of co-occurringbirch and hemlock seedlings

inferredcites →https://doi.org/10.1007/s00572-020-00998-0openalex-snapshot

Partner turnover and changes in ectomycorrhizal fungal communities during the early life stages of European beech (Fagus sylvatica L.)

inferredcites →https://doi.org/10.1007/s11557-006-0060-5openalex-snapshot

Lactarius sanguifluus versus Lactarius vinosus — Molecular and morphological analyses

inferredcites →https://doi.org/10.1007/s11557-019-01541-yopenalex-snapshot

Macrofungi on large decaying spruce trunks in a Central European old-growth forest: what factors affect their species richness and composition?

inferredcites →https://doi.org/10.1007/s11557-020-01637-wopenalex-snapshot

Richness and composition of macrofungi on large decaying trees in a Central European old-growth forest: a case study on silver fir (Abies alba)

inferredcites →https://doi.org/10.1007/s41348-024-00923-zopenalex-snapshot

Fungi associated with fine roots of Fraxinus excelsior affected by ash dieback detected by next-generation sequencing

inferredcites →https://doi.org/10.1016/b978-0-12-372180-8.50042-1openalex-snapshot

AMPLIFICATION AND DIRECT SEQUENCING OF FUNGAL RIBOSOMAL RNA GENES FOR PHYLOGENETICS

inferredcites →https://doi.org/10.1016/j.biocon.2006.02.004openalex-snapshot

Diversity of dead wood inhabiting fungi and bryophytes in semi-natural beech forests in Europe

inferredcites →https://doi.org/10.1016/j.biocon.2019.07.008openalex-snapshot

How citizen science boosted primary knowledge on fungal biodiversity in Denmark

inferredcites →https://doi.org/10.1016/j.funeco.2011.01.005openalex-snapshot

Do bark beetles facilitate the establishment of rot fungi in Norway spruce?

inferredcites →https://doi.org/10.1016/j.funeco.2011.05.005openalex-snapshot

RNA reveals a succession of active fungi during the decay of Norway spruce logs

inferredcites →https://doi.org/10.1016/j.funeco.2015.06.006openalex-snapshot

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

inferredcites →https://doi.org/10.1016/j.funeco.2015.08.007openalex-snapshot

Habitat models of wood-inhabiting fungi along a decay gradient of Norway spruce logs

inferredcites →https://doi.org/10.1016/j.funeco.2016.07.001openalex-snapshot

Fungi associated with decomposing deadwood in a natural beech-dominated forest

inferredcites →https://doi.org/10.1016/j.funeco.2018.11.016openalex-snapshot

Fungi associated with beetles dispersing from dead wood – Let's take the beetle bus!

inferredcites →https://doi.org/10.1016/j.scitotenv.2010.02.040openalex-snapshot

Biomass and nutrient content of sessile oak (Quercus petraea (Matt.) Liebl.) and beech (Fagus sylvatica L.) stem and branches in a mixed stand in southern Belgium

inferredcites →https://doi.org/10.1016/s0580-9517(08)70172-7openalex-snapshot

2 Characterization of Ectomycorrhiza

inferredcites →https://doi.org/10.1023/a:1022825809503openalex-snapshot

Fungal diversity on decaying beech logs – implications for sustainable forestry

inferredcites →https://doi.org/10.1038/ismej.2009.77openalex-snapshot

ClassII peroxidase-encoding genes are present in a phylogenetically wide range of ectomycorrhizal fungi

inferredcites →https://doi.org/10.1038/ismej.2013.195openalex-snapshot

Ectomycorrhizal fungi contribute to soil organic matter cycling in sub-boreal forests

inferredcites →https://doi.org/10.1038/ismej.2017.57openalex-snapshot

Interactions between soil- and dead wood-inhabiting fungal communities during the decay of Norway spruce logs

inferredcites →https://doi.org/10.1038/nmeth.3869openalex-snapshot

DADA2: High-resolution sample inference from Illumina amplicon data

inferredcites →https://doi.org/10.1038/s41467-017-01312-xopenalex-snapshot

Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

inferredcites →https://doi.org/10.1038/s41592-020-01041-yopenalex-snapshot

High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing

inferredcites →https://doi.org/10.1038/s41592-022-01520-4openalex-snapshot

Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data

inferredcites →https://doi.org/10.1038/s41598-020-74180-zopenalex-snapshot

Identification of plastic-associated species in the Mediterranean Sea using DNA metabarcoding with Nanopore MinION

inferredcites →https://doi.org/10.1046/j.0028-646x.2001.00271.xopenalex-snapshot

Populations of ectomycorrhizal Laccaria amethystina and Xerocomus spp. show contrasting colonization patterns in a mixed forest

inferredcites →https://doi.org/10.1046/j.1469-8137.1999.00502.xopenalex-snapshot

Translocation of 32P between interacting mycelia of a wood‐decomposing fungus and ectomycorrhizal fungi in microcosm systems

inferredcites →https://doi.org/10.1046/j.1469-8137.2003.00792.xopenalex-snapshot

Fine scale distribution of ectomycorrhizal fungi and roots across substrate layers including coarse woody debris in a mixed forest

inferredcites →https://doi.org/10.1073/pnas.1117018109openalex-snapshot

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

inferredcites →https://doi.org/10.1080/15572536.2006.11832767openalex-snapshot

Spore dispersal of a resupinate ectomycorrhizal fungus,Tomentella sublilacina,via soil food webs

inferredcites →https://doi.org/10.1093/bib/bbae642openalex-snapshot

Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data

inferredcites →https://doi.org/10.1093/bioinformatics/btad311openalex-snapshot

NanoPack2: population-scale evaluation of long-read sequencing data

inferredcites →https://doi.org/10.1093/nar/gkad1039openalex-snapshot

The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered

inferredcites →https://doi.org/10.1093/pnasnexus/pgae411openalex-snapshot

High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the Nanopore platform

inferredcites →https://doi.org/10.1094/pbiomes-10-22-0071-ropenalex-snapshot

Mycobiome Analysis of Tall Fescue Grass Under Drought Stress Using the Illumina MiSeq and Oxford Nanopore Technology MinION

inferredcites →https://doi.org/10.1101/074161openalex-snapshot

SINTAX: a simple non-Bayesian taxonomy classifier for 16S and ITS sequences

inferredcites →https://doi.org/10.1101/2023.06.19.544637openalex-snapshot

High-accuracy meets high-throughput for microbiome profiling with near full-length 16S rRNA amplicon sequencing on the Nanopore platform

inferredcites →https://doi.org/10.1101/2024.02.14.580249openalex-snapshot

PIMENTA: PIpeline for MEtabarcoding through Nanopore Technology used for Authentication

inferredcites →https://doi.org/10.1111/2041-210x.13561openalex-snapshot

A workflow for accurate metabarcoding using nanopore MinION sequencing

inferredcites →https://doi.org/10.1111/conl.13013openalex-snapshot

The power of citizen science to advance fungal conservation

inferredcites →https://doi.org/10.1111/j.1365-294x.1993.tb00005.xopenalex-snapshot

ITS primers with enhanced specificity for basidiomycetes ‐ application to the identification of mycorrhizae and rusts

inferredcites →https://doi.org/10.1111/j.1365-294x.2011.05392.xopenalex-snapshot

Extensive gene flow over Europe and possible speciation over Eurasia in the ectomycorrhizal basidiomycete Laccaria amethystina complex

inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05515.xopenalex-snapshot

Beech roots are simultaneously colonized by multiple genets of the ectomycorrhizal fungusLaccaria amethystinaclustered in two genetic groups

inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05723.xopenalex-snapshot

Patterns of fungal communities among and within decaying logs, revealed by 454 sequencing

inferredcites →https://doi.org/10.1111/j.1462-2920.2007.01535.xopenalex-snapshot

Forest microsite effects on community composition of ectomycorrhizal fungi on seedlings of Picea abies and Betula pendula

inferredcites →https://doi.org/10.1111/j.1462-2920.2012.02736.xopenalex-snapshot

The ectomycorrhizal fungus Paxillus involutus converts organic matter in plant litter using a trimmed brown‐rot mechanism involving Fenton chemistry

inferredcites →https://doi.org/10.1111/j.1469-8137.2005.01401.xopenalex-snapshot

Activity profiling of ectomycorrhiza communities in two forest soils using multiple enzymatic tests

inferredcites →https://doi.org/10.1111/mec.12849openalex-snapshot

Global biogeography of the ectomycorrhizal /sebacina lineage ( F ungi, S ebacinales) as revealed from comparative phylogenetic analyses

inferredcites →https://doi.org/10.1111/mec.16460openalex-snapshot

Best practices in metabarcoding of fungi: From experimental design to results

inferredcites →https://doi.org/10.1111/nph.13201openalex-snapshot

Ectomycorrhizal fungi – potential organic matter decomposers, yet not saprotrophs

inferredcites →https://doi.org/10.1128/aem.01368-19openalex-snapshot

Relative Performance of MinION (Oxford Nanopore Technologies) versus Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens

inferredcites →https://doi.org/10.1128/aem.01648-09openalex-snapshot

Vegetation and Soil Environment Influence the Spatial Distribution of Root-Associated Fungi in a Mature Beech-Maple Forest

inferredcites →https://doi.org/10.1128/aem.64.12.5004-5007.1998openalex-snapshot

Ink and Vinegar, a Simple Staining Technique for Arbuscular-Mycorrhizal Fungi

inferredcites →https://doi.org/10.1139/b82-206openalex-snapshot

First-year survival of Tsuga heterophylla without mycorrhizae and subsequent ectomycorrhizal development on decaying logs and mineral soil

inferredcites →https://doi.org/10.1139/x09-072openalex-snapshot

Response of ectomycorrhizal community structure to gap opening in natural and managed temperate beech-dominated forests

inferredcites →https://doi.org/10.1139/x82-005openalex-snapshot

Fungi from decayed wood as ectomycorrhizal symbionts of western hemlock

inferredcites →https://doi.org/10.1186/s43008-021-00064-0openalex-snapshot

Enlightening the black and white: species delimitation and UNITE species hypothesis testing in the Russula albonigra species complex

inferredcites →https://doi.org/10.1186/s43008-023-00125-6openalex-snapshot

Targeted sequencing analysis pipeline for species identification of human pathogenic fungi using long-read nanopore sequencing

inferredcites →https://doi.org/10.1264/jsme2.me14121openalex-snapshot

A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts

inferredcites →https://doi.org/10.1371/journal.pone.0061217openalex-snapshot

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

inferredcites →https://doi.org/10.14288/1.0365590openalex-snapshot

Western hemlock regeneration on coarse woody debris is facilitated by linkage into a mycorrhizal network in an old-growth forest

inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot

Cutadapt removes adapter sequences from high-throughput sequencing reads

inferredcites →https://doi.org/10.1890/08-1823.1openalex-snapshot

Associations between species and groups of sites: indices and statistical inference

inferredcites →https://doi.org/10.21436/inbor.14173748openalex-snapshot

Historic-ecological position of beech in the area of the Sonian Forest and an overview of beech-forest- related biodiversity present in the forest

inferredcites →https://doi.org/10.21825/sg.v63i0.840openalex-snapshot

Nutrient uptake of a mixed oak/beech forest in Flanders (Belgium)

inferredcites →https://doi.org/10.29203/ka.1995.309openalex-snapshot

Community structure and dynamics of wood-rotting Basidiomycetes on decomposing conifer trunks in northern Finland

inferredcites →https://doi.org/10.3114/sim.2022.106.02openalex-snapshot

Diversity of colacosome-interacting mycoparasites expands the understanding of the evolution and ecology of Microbotryomycetes

inferredcites →https://doi.org/10.32614/cran.package.aiccpermanovaopenalex-snapshot

AICcPermanova: Model Selection of PERMANOVA Models Using AICc

inferredcites →https://doi.org/10.3390/f13071036openalex-snapshot

Which Is the Best Substrate to Regenerate? A Comparative Pot Experiment for Tree Seedling Growth on Decayed Wood and in Soil

inferredcites →https://doi.org/10.3390/genes10060468openalex-snapshot

A Rapid and Accurate MinION-Based Workflow for Tracking Species Biodiversity in the Field

inferredcites →https://doi.org/10.3390/jof9080788openalex-snapshot

Does One Size Fit All? Variations in the DNA Barcode Gaps of Macrofungal Genera

inferredcites →https://doi.org/10.3390/jof9111119openalex-snapshot

Nanopore-Sequencing Metabarcoding for Identification of Phytopathogenic and Endophytic Fungi in Olive (Olea europaea) Twigs

inferredcites →https://doi.org/10.3390/soilsystems6020041openalex-snapshot

Merits and Limitations of Element Balances as a Forest Planning Tool for Harvest Intensities and Sustainable Nutrient Management—A Case Study from Germany

inferredcites →https://doi.org/10.3852/mycologia.97.4.762openalex-snapshot

Spore dispersal of a resupinate ectomycorrhizal fungus, Tomentella sublilacina, via soil food webs

inferredcites →https://doi.org/10.3897/aca.4.e65029openalex-snapshot

Decona: From demultiplexing to consensus for Nanopore amplicon data

inferredcites →https://doi.org/10.3897/biss.6.93856openalex-snapshot

UNITE Species Hypotheses Matching Analysis

inferredcites →https://doi.org/10.3897/mycokeys.45.29964openalex-snapshot

Lactifluus bicapillus (Russulales, Russulaceae), a new species from the Guineo-Congolian rainforest

inferredcites →https://doi.org/10.3897/mycokeys.56.35204openalex-snapshot

Updated taxonomy of Lactifluus section Luteoli: L. russulisporus from Australia and L. caliendrifer from Thailand

inferredcites →https://doi.org/10.5281/zenodo.8017673openalex-snapshot

Monitoring programme on strict forest reserves in Flanders (Belgium) - site level stand structure, regeneration and vegetation data

inferredcites →https://doi.org/10.5735/085.057.0101openalex-snapshot

New and Noteworthy Species of Helicogloea (Atractiellomycetes, Basidiomycota) from Europe

inferredcites →https://doi.org/10.7717/peerj.2584openalex-snapshot

VSEARCH: a versatile open source tool for metagenomics

inferredcites →https://doi.org/10.7717/peerj.4925openalex-snapshot

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.3897/imafungus.17.190198zenodo-depositor-declared

Tree identity shapes composition, substrate shifts dominance in deadwood fungi of an old-growth lowland beech forest

inferred← citeshttps://doi.org/10.1111/1755-0998.70091openalex-snapshot

Fast, Flexible, Feasible: A Transparent Framework for Evaluating eDNA Workflow Trade‐Offs in Resource‐Limited Settings

inferred← citeshttps://doi.org/10.1111/2041-210x.70250openalex-snapshot

Long‐read sequencing for biodiversity analyses—A comprehensive guide

inferred← citeshttps://doi.org/10.64898/2025.12.29.694971openalex-snapshot

RAMBO: Resolving Amplicons in Mixed Samples for Accurate DNA Barcoding with Oxford Nanopore

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