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The impact of OTU sequence similarity threshold on diatom‐based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean)

https://doi.org/10.1002/ece3.4701
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What this work says

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

inferredcites →https://doi.org/10.1002/ece3.1497openalex-snapshot
Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods
inferredcites →https://doi.org/10.1002/ece3.4701openalex-snapshot
The impact of OTU sequence similarity threshold on diatom‐based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean)
inferredcites →https://doi.org/10.1002/fee.1490openalex-snapshot
Freshwater biomonitoring in the Information Age
inferredcites →https://doi.org/10.1007/978-0-387-21706-2openalex-snapshot
Modern Applied Statistics with S
inferredcites →https://doi.org/10.1007/s00248-012-0145-4openalex-snapshot
Effects of OTU Clustering and PCR Artifacts on Microbial Diversity Estimates
inferredcites →https://doi.org/10.1007/s10750-007-0729-zopenalex-snapshot
Epiphytic, littoral diatoms as bioindicators of shallow lake trophic status: Trophic Diatom Index for Lakes (TDIL) developed in Hungary
inferredcites →https://doi.org/10.1007/s10750-008-9427-8openalex-snapshot
Validation of diatoms as proxies for phytobenthos when assessing ecological status in lakes
inferredcites →https://doi.org/10.1007/s10750-012-1113-1openalex-snapshot
Are diatom diversity indices reliable monitoring metrics?
inferredcites →https://doi.org/10.1007/s10750-012-1115-zopenalex-snapshot
Identification versus counting protocols as sources of uncertainty in diatom-based ecological status assessments
inferredcites →https://doi.org/10.1007/s10750-017-3381-2openalex-snapshot
Metabarcoding of lake benthic diatoms: from structure assemblages to ecological assessment
inferredcites →https://doi.org/10.1007/s10811-008-9394-5openalex-snapshot
Harmonization is more important than experience—results of the first Nordic–Baltic diatom intercalibration exercise 2007 (stream monitoring)
inferredcites →https://doi.org/10.1007/s13127-018-0359-5openalex-snapshot
Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes
inferredcites →https://doi.org/10.1016/j.ecolind.2008.04.003openalex-snapshot
The effect of excluding diatom taxa and reducing taxonomic resolution on multivariate analyses and stream bioassessment
inferredcites →https://doi.org/10.1016/j.ecolind.2008.06.003openalex-snapshot
Improvements of the Biological Diatom Index (BDI): Description and efficiency of the new version (BDI-2006)
inferredcites →https://doi.org/10.1016/j.ecolind.2010.06.017openalex-snapshot
Evaluation of European diatom trophic indices
inferredcites →https://doi.org/10.1016/j.ecolind.2011.09.014openalex-snapshot
Biomonitoring river diatoms: Implications of taxonomic resolution
inferredcites →https://doi.org/10.1016/j.ecolind.2015.12.031openalex-snapshot
Combined eco-morphological functional groups are reliable indicators of colonisation processes of benthic diatom assemblages in a lowland stream
inferredcites →https://doi.org/10.1016/j.ecolind.2017.06.024openalex-snapshot
Assessing ecological status with diatoms DNA metabarcoding: Scaling-up on a WFD monitoring network (Mayotte island, France)
inferredcites →https://doi.org/10.1016/j.protis.2010.09.005openalex-snapshot
Barcoding Diatoms: Exploring Alternatives to COI-5P
inferredcites →https://doi.org/10.1016/j.protis.2012.04.001openalex-snapshot
Molecular Evidence for Distinct Antarctic Lineages in the Cosmopolitan Terrestrial Diatoms Pinnularia borealis and Hantzschia amphioxys
inferredcites →https://doi.org/10.1016/j.scitotenv.2015.10.161openalex-snapshot
Separate treatment of hospital and urban wastewaters: A real scale comparison of effluents and their effect on microbial communities
inferredcites →https://doi.org/10.1016/j.scitotenv.2017.07.093openalex-snapshot
Taxonomy- or trait-based ecological assessment for tropical rivers? Case study on benthic diatoms in Mayotte island (France, Indian Ocean)
inferredcites →https://doi.org/10.1016/s0043-1354(97)00157-7openalex-snapshot
USE OF THE TROPHIC DIATOM INDEX TO MONITOR EUTROPHICATION IN RIVERS
inferredcites →https://doi.org/10.1017/cbo9780511763175.005openalex-snapshot
Assessing environmental conditions in rivers and streams with diatoms
inferredcites →https://doi.org/10.1021/es506158mopenalex-snapshot
Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data
inferredcites →https://doi.org/10.1023/a:1008130202144openalex-snapshot
Is genus or species identification of periphytic diatoms required to determine the impacts of river regulation?
inferredcites →https://doi.org/10.1023/b:hydr.0000025270.10807.10openalex-snapshot
The effect of taxonomic resolution on the assessment of ecological water quality classes
inferredcites →https://doi.org/10.1038/nbt.2198openalex-snapshot
Performance comparison of benchtop high-throughput sequencing platforms
inferredcites →https://doi.org/10.1038/nmeth.2604openalex-snapshot
UPARSE: highly accurate OTU sequences from microbial amplicon reads
inferredcites →https://doi.org/10.1080/0269249x.2014.951398openalex-snapshot
Characterizing the niches of two very similarNitzschiaspecies and implications for ecological assessment
inferredcites →https://doi.org/10.1080/09670262.2014.904524openalex-snapshot
DNA-based species delimitation in algae
inferredcites →https://doi.org/10.1086/690649openalex-snapshot
Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?
inferredcites →https://doi.org/10.1093/bib/bbr009openalex-snapshot
A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis
inferredcites →https://doi.org/10.1093/database/baw016openalex-snapshot
R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring
inferredcites →https://doi.org/10.1098/rspb.2002.2218openalex-snapshot
Biological identifications through DNA barcodes
inferredcites →https://doi.org/10.1111/1755-0998.12105openalex-snapshot
Next‐generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms
inferredcites →https://doi.org/10.1111/1755-0998.12336openalex-snapshot
Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies
inferredcites →https://doi.org/10.1111/1755-0998.12668openalex-snapshot
Taxonomy‐free molecular diatom index for high‐throughput eDNA biomonitoring
inferredcites →https://doi.org/10.1111/2041-210x.12960openalex-snapshot
Avoiding quantification bias in metabarcoding: Application of a cell biovolume correction factor in diatom molecular biomonitoring
inferredcites →https://doi.org/10.1111/fwb.12520openalex-snapshot
Functional classifications and their application in phytoplankton ecology
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05470.xopenalex-snapshot
Towards next‐generation biodiversity assessment using DNA metabarcoding
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05519.xopenalex-snapshot
Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next‐generation DNA sequencing
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05538.xopenalex-snapshot
Next‐generation sequencing technologies for environmental DNA research
inferredcites →https://doi.org/10.1111/j.1529-8817.2007.00454.xopenalex-snapshot
A MOLECULAR SYSTEMATIC APPROACH TO EXPLORE DIVERSITY WITHIN THE SELLAPHORA PUPULA SPECIES COMPLEX (BACILLARIOPHYTA)1
inferredcites →https://doi.org/10.1111/jeu.12047openalex-snapshot
An Inordinate Fondness? The Number, Distributions, and Origins of Diatom Species
inferredcites →https://doi.org/10.1111/jeu.12240openalex-snapshot
Genetic and Physiological Diversity in the Diatom Nitzschia inconspicua
inferredcites →https://doi.org/10.1128/aem.00062-07openalex-snapshot
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
inferredcites →https://doi.org/10.1128/aem.00342-13openalex-snapshot
Distribution-Based Clustering: Using Ecology To Refine the Operational Taxonomic Unit
inferredcites →https://doi.org/10.1128/aem.01541-09openalex-snapshot
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
inferredcites →https://doi.org/10.1128/aem.71.3.1501-1506.2005openalex-snapshot
Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness
inferredcites →https://doi.org/10.1139/cjfas-54-8-1802openalex-snapshot
Does taxonomic resolution affect the multivariate description of the structure of freshwater benthic macroinvertebrate communities?
inferredcites →https://doi.org/10.1371/journal.pcbi.1003531openalex-snapshot
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
inferredcites →https://doi.org/10.1371/journal.pone.0125356openalex-snapshot
Estimating Bacterial Diversity for Ecological Studies: Methods, Metrics, and Assumptions
inferredcites →https://doi.org/10.1371/journal.pone.0130324openalex-snapshot
Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol
inferredcites →https://doi.org/10.1371/journal.pone.0172808openalex-snapshot
The best of both worlds: A combined approach for analyzing microalgal diversity via metabarcoding and morphology-based methods
inferredcites →https://doi.org/10.1371/journal.pone.0195770openalex-snapshot
DNA metabarcoding and microscopic analyses of sea turtles biofilms: Complementary to understand turtle behavior
inferredcites →https://doi.org/10.1899/07-077.1openalex-snapshot
Algae–P relationships, thresholds, and frequency distributions guide nutrient criterion development
inferredcites →https://doi.org/10.2216/i0031-8884-38-6-437.1openalex-snapshot
The species concept in diatoms
inferredcites →https://doi.org/10.2216/i0031-8884-43-4-459.1openalex-snapshot
The Sellaphora pupula species complex (Bacillariophyceae): morphometric analysis, ultrastructure and mating data provide evidence for five new species
inferredcites →https://doi.org/10.2307/1468322openalex-snapshot
Taxonomic resolution of benthic macroinvertebrate communities in bioassessments
inferredcites →https://doi.org/10.3732/ajb.1300306openalex-snapshot
Cryptic diversity in a cosmopolitan diatom known as Asterionellopsis glacialis (Fragilariaceae): Implications for ecology, biogeography, and taxonomy
inferredcites →https://doi.org/10.3897/rio.2.e11321openalex-snapshot
DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe
inferredcites →https://doi.org/10.4314/wsa.v40i3.14openalex-snapshot
The application and testing of diatom-based indices of stream water quality in Chinhoyi Town, Zimbabwe
inferredcites →https://doi.org/10.5507/fot.2017.013openalex-snapshot
The potential of High-Throughput Sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes
inferredcites →https://doi.org/10.5860/choice.49-6910openalex-snapshot
Standard methods for the examination of water and wastewater
inferredcites →https://doi.org/10.7717/peerj.1487openalex-snapshot
De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

What points at this work

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

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Exploring benthic diatom diversity in the West Antarctic Peninsula: insights from a morphological and molecular approach
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Diatom Taxonomy
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DNA metabarcoding effectively quantifies diatom responses to nutrients in streams
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Assessing insect biodiversity with automatic light traps in Brazil: Pearls and pitfalls of metabarcoding samples in preservative ethanol
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A Comparative Analysis of DNA Metabarcoding and Morphological Identification in Diatoms Reveals Similar Patterns of Environmental Response
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Exploring the capacity of aquatic biofilms to act as environmental DNA samplers: Test on macroinvertebrate communities in rivers
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DNA metabarcoding and morphological methods show complementary patterns in the metacommunity organization of lentic epiphytic diatoms
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Morphology and metabarcoding: a test with stream diatoms from Mexico highlights the complementarity of identification methods
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Quantifying spatial and temporal relationships between diatoms and nutrients in streams strengthens evidence of nutrient effects from monitoring data
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Environmental filtering and mass effect are two important processes driving lake benthic diatoms: Results of a DNA metabarcoding study in a large lake
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Giving the Eastern Canadian Diatom Index (IDEC) a makeover using metabarcoding: first considerations and challenges
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Characterization of the Rhizosphere Bacterial Microbiome and Coffee Bean Fermentation in the Castillo-Tambo and Bourbon Varieties in the Popayán-Colombia Plateau
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The gut microbiota of tropical marine fish is largely uncultured and distinct from surrounding water microbiota
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Succession of Microbial Community in a Small Water Body within the Alluvial Aquifer of a Large River
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