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: 2023-04-30
Papper version: info:eu-repo/semantics/publishedVersion
Link to the original source: https://www.sciencedirect.com/science/article/pii/S0045653522024262?via%3Dihub
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
Licence document URL: http://repositori.urv.cat/ca/proteccio-de-dades/
Article's DOI: 10.1016/j.chemosphere.2022.135933
Entity: Universitat Rovira i Virgili
Journal publication year: 2022
Publication Type: Journal Publications
Repositori URV