Articles producció científica> Bioquímica i Biotecnologia

Evaluation of two short overlapping rbcL markers for diatom metabarcoding of environmental samples: Effects on biomonitoring assessment and species resolution

  • Identification data

    Identifier: imarina:9280737
    Authors:
    Pérez-Burillo JMann DGTrobajo R
    Abstract:
    Two short diatom rbcL barcodes, 331 bp and 263 bp in length, have frequently been used in diatom metabarcoding studies. They overlap in a common 263-bp region but differ in the presence or absence of a 68-bp tail at the 5′ end. Though the effectiveness of both has been demonstrated in separate biomonitoring and diversity studies, the impact of the 68-bp non-shared region has not been evaluated. Here we compare the two barcodes in terms of the values of a biotic index (IPS) and the ecological status classes derived from their application to an extensive metabarcoding dataset from United Kingdom rivers; this comprised 1703 samples and was produced using the 331-bp primers. In addition, we assess the effectiveness of each barcode for discrimination of genetic variants around and below the species level. The strong correlation found in IPS values between barcodes (Pearson's R = 0.98) indicates that the choice of the barcode does not have major implications for current WFD ecological assessments, although a very few sites (55: 3.23% of those analysed) were downgraded from an acceptable WFD class (“Good”) to an unacceptable one (“Moderate”). Analyses of the taxonomic resolution of the two barcodes indicate that for many ASVs, the use of either marker – 263-bp and 331-bp – gives unambiguous assignations at species level though with differences in bootstrap confidence values. Such differences are caused by the stochasticity involved in the naïve Bayesian classifier used and by the fact that genetic distance, regarding closely related species, is increased when using the 331-bp barcode. However, in three cases, species differentiation fails with the shorter marker, leading to underestimates of species diversity. Finally, two ASVs from Nitzschia species evidenced that the use of
  • Others:

    Author, as appears in the article.: Pérez-Burillo J; Mann DG; Trobajo R
    Department: Bioquímica i Biotecnologia
    URV's Author/s: PEREZ BURILLO, JAVIER
    Keywords: Water framework directive Species discrimination Infraspecific variation High-throughput sequencing Ecological assessment Bacillariophyta species discrimination infraspecific variation high-throughput sequencing ecological assessment diversity
    Abstract: Two short diatom rbcL barcodes, 331 bp and 263 bp in length, have frequently been used in diatom metabarcoding studies. They overlap in a common 263-bp region but differ in the presence or absence of a 68-bp tail at the 5′ end. Though the effectiveness of both has been demonstrated in separate biomonitoring and diversity studies, the impact of the 68-bp non-shared region has not been evaluated. Here we compare the two barcodes in terms of the values of a biotic index (IPS) and the ecological status classes derived from their application to an extensive metabarcoding dataset from United Kingdom rivers; this comprised 1703 samples and was produced using the 331-bp primers. In addition, we assess the effectiveness of each barcode for discrimination of genetic variants around and below the species level. The strong correlation found in IPS values between barcodes (Pearson's R = 0.98) indicates that the choice of the barcode does not have major implications for current WFD ecological assessments, although a very few sites (55: 3.23% of those analysed) were downgraded from an acceptable WFD class (“Good”) to an unacceptable one (“Moderate”). Analyses of the taxonomic resolution of the two barcodes indicate that for many ASVs, the use of either marker – 263-bp and 331-bp – gives unambiguous assignations at species level though with differences in bootstrap confidence values. Such differences are caused by the stochasticity involved in the naïve Bayesian classifier used and by the fact that genetic distance, regarding closely related species, is increased when using the 331-bp barcode. However, in three cases, species differentiation fails with the shorter marker, leading to underestimates of species diversity. Finally, two ASVs from Nitzschia species evidenced that the use of the shorter marker can sometimes lead to false positives when the extent and nature of infraspecific variation are poorly known.
    Thematic Areas: Zootecnia / recursos pesqueiros Saúde coletiva Química Public health, environmental and occupational health Pollution Odontología Nutrição Medicine (miscellaneous) Medicina veterinaria Medicina ii Medicina i Materiais Interdisciplinar Health, toxicology and mutagenesis Geociências General chemistry Farmacia Environmental sciences Environmental engineering Environmental chemistry Ensino Engenharias iii Engenharias ii Engenharias i Educação física Ciências biológicas iii Ciências biológicas ii Ciências biológicas i Ciências ambientais Ciências agrárias i Ciência de alimentos Chemistry (miscellaneous) Chemistry (all) Biotecnología Biodiversidade Astronomia / física
    licence for use: https://creativecommons.org/licenses/by/3.0/es/
    Author's mail: javier.perezb@estudiants.urv.cat javier.perezb@estudiants.urv.cat
    Record's date: 2024-09-07
    Papper version: info:eu-repo/semantics/publishedVersion
    Link to the original source: https://www.sciencedirect.com/science/article/pii/S0045653522024262?via%3Dihub
    Licence document URL: https://repositori.urv.cat/ca/proteccio-de-dades/
    Papper original source: Chemosphere. 307 (pt 3): 135933-
    APA: Pérez-Burillo J; Mann DG; Trobajo R (2022). Evaluation of two short overlapping rbcL markers for diatom metabarcoding of environmental samples: Effects on biomonitoring assessment and species resolution. Chemosphere, 307(pt 3), 135933-. DOI: 10.1016/j.chemosphere.2022.135933
    Article's DOI: 10.1016/j.chemosphere.2022.135933
    Entity: Universitat Rovira i Virgili
    Journal publication year: 2022
    Publication Type: Journal Publications
  • Keywords:

    Chemistry (Miscellaneous),Environmental Chemistry,Environmental Engineering,Environmental Sciences,Health, Toxicology and Mutagenesis,Medicine (Miscellaneous),Pollution,Public Health, Environmental and Occupational Health
    Water framework directive
    Species discrimination
    Infraspecific variation
    High-throughput sequencing
    Ecological assessment
    Bacillariophyta
    species discrimination
    infraspecific variation
    high-throughput sequencing
    ecological assessment
    diversity
    Zootecnia / recursos pesqueiros
    Saúde coletiva
    Química
    Public health, environmental and occupational health
    Pollution
    Odontología
    Nutrição
    Medicine (miscellaneous)
    Medicina veterinaria
    Medicina ii
    Medicina i
    Materiais
    Interdisciplinar
    Health, toxicology and mutagenesis
    Geociências
    General chemistry
    Farmacia
    Environmental sciences
    Environmental engineering
    Environmental chemistry
    Ensino
    Engenharias iii
    Engenharias ii
    Engenharias i
    Educação física
    Ciências biológicas iii
    Ciências biológicas ii
    Ciências biológicas i
    Ciências ambientais
    Ciências agrárias i
    Ciência de alimentos
    Chemistry (miscellaneous)
    Chemistry (all)
    Biotecnología
    Biodiversidade
    Astronomia / física
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