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Long‐Read Metabarcoding With Optimized Bioinformatic Analysis Outperforms Short‐Read Metabarcoding for Assessing Soil Protist Diversity and Ecology

https://doi.org/10.1002/edn3.70346
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What this work says

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

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What is the “modified” CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol
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A full‐length 18S ribosomal DNA metabarcoding approach for determining protist community diversity using Nanopore sequencing
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Assessing the performance of short 18S rDNA markers for environmental DNA metabarcoding of marine protists
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Breaking the Standard: Can Oxford Nanopore Technologies Sequencing Compete With Illumina in Protistan Amplicon Studies?
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ggplot2
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Linking biodiversity, ecosystem services, and human well-being: three challenges for designing research for sustainability
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Soil biota, ecosystem services and land productivity
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Toward the use of protists as bioindicators of multiple stresses in agricultural soils: A case study in vineyard ecosystems
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Protist metabarcoding and environmental biomonitoring: Time for change
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Protist taxonomic and functional diversity in soil, freshwater and marine ecosystems
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Soil classification and mapping in the Alps: The current state and future challenges
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Mining soil data of Switzerland: New maps for soil texture, soil organic carbon, nitrogen, and phosphorus
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Nanopore sequencing: flourishing in its teenage years
inferredcites →https://doi.org/10.1016/j.protis.2009.03.003openalex-snapshot
Helkesimastix marina n. sp. (Cercozoa: Sainouroidea superfam. n.) a Gliding Zooflagellate of Novel Ultrastructure and Unusual Ciliary Behaviour
inferredcites →https://doi.org/10.1016/j.protis.2016.08.008openalex-snapshot
The Large Subunit rDNA Sequence of Plasmodiophora brassicae Does not Contain Intra-species Polymorphism
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Diverse Applications of Environmental DNA Methods in Parasitology
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Impact of a synthetic fungicide (fosetyl-Al and propamocarb-hydrochloride) and a biopesticide (Clonostachys rosea) on soil bacterial, fungal, and protist communities
inferredcites →https://doi.org/10.1016/j.scitotenv.2023.165983openalex-snapshot
Unlocking foraminiferal genetic diversity on estuarine mudflats with eDNA metabarcoding
inferredcites →https://doi.org/10.1016/j.soilbio.2011.07.001openalex-snapshot
Tebuconazole application decreases soil microbial biomass and activity
inferredcites →https://doi.org/10.1016/j.soilbio.2020.107863openalex-snapshot
Fertilization changes soil microbiome functioning, especially phagotrophic protists
inferredcites →https://doi.org/10.1016/j.wroa.2019.100033openalex-snapshot
Organic substrate diffusibility governs microbial community composition, nutrient removal performance and kinetics of granulation of aerobic granular sludge
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A communal catalogue reveals Earth’s multiscale microbial diversity
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Improved data analysis for the MinION nanopore sequencer
inferredcites →https://doi.org/10.1038/nmeth.3869openalex-snapshot
DADA2: High-resolution sample inference from Illumina amplicon data
inferredcites →https://doi.org/10.1073/pnas.1305198110openalex-snapshot
Soil food web properties explain ecosystem services across European land use systems
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/btq461openalex-snapshot
Search and clustering orders of magnitude faster than BLAST
inferredcites →https://doi.org/10.1093/bioinformatics/bty1018openalex-snapshot
Commonly misunderstood parameters of NCBI BLAST and important considerations for users
inferredcites →https://doi.org/10.1093/femsec/fiab001openalex-snapshot
Is Oxford Nanopore sequencing ready for analyzing complex microbiomes?
inferredcites →https://doi.org/10.1093/femsre/fuy006openalex-snapshot
Soil protists: a fertile frontier in soil biology research
inferredcites →https://doi.org/10.1093/ismeco/ycaf079openalex-snapshot
Complex compositional and metabolic response of river sediment microbiomes to multiple anthropogenic stressors
inferredcites →https://doi.org/10.1093/nar/gks1160openalex-snapshot
The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy
inferredcites →https://doi.org/10.1098/rsbl.2015.0646openalex-snapshot
Photoautotrophic microorganisms as a carbon source for temperate soil invertebrates
inferredcites →https://doi.org/10.1111/jbi.13755openalex-snapshot
Soil protist diversity in the Swiss western Alps is better predicted by topo‐climatic than by edaphic variables
inferredcites →https://doi.org/10.1111/mec.12819openalex-snapshot
Effects of long‐term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach
inferredcites →https://doi.org/10.1111/nph.14776openalex-snapshot
PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives
inferredcites →https://doi.org/10.1126/science.1162986openalex-snapshot
Real-Time DNA Sequencing from Single Polymerase Molecules
inferredcites →https://doi.org/10.1371/journal.pbio.1001419openalex-snapshot
CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms
inferredcites →https://doi.org/10.1371/journal.pone.0027492openalex-snapshot
Arctic Ocean Microbial Community Structure before and after the 2007 Record Sea Ice Minimum
inferredcites →https://doi.org/10.1371/journal.pone.0095567openalex-snapshot
Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia
inferredcites →https://doi.org/10.1371/journal.pone.0131498openalex-snapshot
Taxonomic Resolutions Based on 18S rRNA Genes: A Case Study of Subclass Copepoda
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.17504/protocols.io.3byl4qe48vo5/v2openalex-snapshot
Full 18S metabarcoding of environmental samples of various substrates with Nanopore sequencing. v2
inferredcites →https://doi.org/10.18637/jss.v021.i12openalex-snapshot
Reshaping Data with the reshape Package
inferredcites →https://doi.org/10.3389/fmicb.2012.00348openalex-snapshot
Microbial control over carbon cycling in soil
inferredcites →https://doi.org/10.3389/fmicb.2016.00459openalex-snapshot
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics
inferredcites →https://doi.org/10.3390/d12030107openalex-snapshot
DNA Barcoding for Delimitation of Putative Mexican Marine Nematodes Species
inferredcites →https://doi.org/10.3390/d13070313openalex-snapshot
The Future of DNA Barcoding: Reflections from Early Career Researchers
inferredcites →https://doi.org/10.3390/microorganisms11030804openalex-snapshot
Nanopore Is Preferable over Illumina for 16S Amplicon Sequencing of the Gut Microbiota When Species-Level Taxonomic Classification, Accurate Estimation of Richness, or Focus on Rare Taxa Is Required
inferredcites →https://doi.org/10.3390/microorganisms7110493openalex-snapshot
Ciliate Environmental Diversity Can Be Underestimated by the V4 Region of SSU rDNA: Insights from Species Delimitation and Multilocus Phylogeny of Pseudokeronopsis (Protist, Ciliophora)
inferredcites →https://doi.org/10.5507/fot.2012.007openalex-snapshot
Intersection of Chlorella, Muriella and Bracteacoccus: Resurrecting the genus Chromochloris Kol et Chodat (Chlorophyceae, Chlorophyta).
inferredcites →https://doi.org/10.7717/peerj.2584openalex-snapshot
VSEARCH: a versatile open source tool for metagenomics

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inferred← uses_datahttps://doi.org/10.5281/zenodo.22010527zenodo-depositor-declared
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