Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches

[EN] Benthic diatoms have traditionally been used as bioindicators of aquatic ecosystems. Because diatom-based monitoring of water quality is required by European legislation, molecular-based methods had emerged as useful alternatives to classical methods based on morphological identification using...

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Autores: Borrego Ramos, María, Bécares Mantecón, Eloy, García García, Pedro, Nistal García, Alejandro, Blanco Lanza, Saúl
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2021
País:España
Institución:Universidad Rey Juan Carlos
Repositorio:BULERIA. Repositorio Institucional de la Universidad de León
OAI Identifier:oai:buleria.unileon.es:10612/18085
Acceso en línea:https://www.mdpi.com/2073-4441/13/10/1351
https://hdl.handle.net/10612/18085
Access Level:acceso abierto
Palabra clave:Ecología. Medio ambiente
Genética
Benthic diatoms
DNA barcoding
Ecological assessment
Shallow pond
2409.03 Genética de Poblaciones
2417.13 Ecología Vegetal
2417.14 Genética Vegetal
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oai_identifier_str oai:buleria.unileon.es:10612/18085
network_acronym_str ES
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spelling Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding ApproachesBorrego Ramos, MaríaBécares Mantecón, EloyGarcía García, PedroNistal García, AlejandroBlanco Lanza, SaúlEcología. Medio ambienteGenéticaBenthic diatomsDNA barcodingEcological assessmentShallow pond2409.03 Genética de Poblaciones2417.13 Ecología Vegetal2417.14 Genética Vegetal[EN] Benthic diatoms have traditionally been used as bioindicators of aquatic ecosystems. Because diatom-based monitoring of water quality is required by European legislation, molecular-based methods had emerged as useful alternatives to classical methods based on morphological identification using light microscopy. The aim of this study was to test the reliability of DNA metabarcoding combined with High-Throughput Sequencing (HTS) techniques in the bioassessment of the trophic status of 22 Mediterranean shallow ponds in NW Spain. For each pond, the Trophic Diatom Index (TDI) was calculated from inventories obtained by identification using light microscopy (LM) followed by high-throughput sequencing (HTS) at the molecular level. Ponds were subsequently classified into five water quality classes. The results showed a good correspondence between both methods, especially after applying a correction factor that depended on the biovolume of the cells. This correspondence led to the assignment to the same quality class in 59% of the ponds. The determination and quantification of valves or DNA sequences was one of the main pitfalls, which mainly included those related to the variability in the relative abundances of some species. Accordingly, ponds with similar relative abundances for the dominant species were assigned to the same quality class. Moreover, other difficulties leading the discrepancies were the misidentification of some species due to the presence of semi-cryptic taxa, the incompleteness of the reference database and the bioinformatic protocol. Thus, the validation of DNA-based methods for the identification of freshwater diatoms represents an important goal, as an alternative to using traditional methods in Mediterranean shallow pondsSIThis research was funded by the Spanish Ministry of Economy and Industry, project CGL2017-84176R (METAPONDS) and Fundación Biodiversidad, Ministerio para la Transición Ecológica y el Reto Demográfico project BT-2019MDPIGeneticaFacultad de Ciencias Biologicas y Ambientales2021info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttps://www.mdpi.com/2073-4441/13/10/1351https://hdl.handle.net/10612/18085reponame:BULERIA. Repositorio Institucional de la Universidad de Leóninstname:Universidad Rey Juan CarlosInglésinfo:eu-repo/grantAgreement/AEI/Programa Estatal de I+D+i Orientada a los Retos de la Sociedad/CGL2017-84176Rhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:buleria.unileon.es:10612/180852026-06-24T12:43:27Z
dc.title.none.fl_str_mv Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches
title Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches
spellingShingle Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches
Borrego Ramos, María
Ecología. Medio ambiente
Genética
Benthic diatoms
DNA barcoding
Ecological assessment
Shallow pond
2409.03 Genética de Poblaciones
2417.13 Ecología Vegetal
2417.14 Genética Vegetal
title_short Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches
title_full Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches
title_fullStr Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches
title_full_unstemmed Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches
title_sort Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches
dc.creator.none.fl_str_mv Borrego Ramos, María
Bécares Mantecón, Eloy
García García, Pedro
Nistal García, Alejandro
Blanco Lanza, Saúl
author Borrego Ramos, María
author_facet Borrego Ramos, María
Bécares Mantecón, Eloy
García García, Pedro
Nistal García, Alejandro
Blanco Lanza, Saúl
author_role author
author2 Bécares Mantecón, Eloy
García García, Pedro
Nistal García, Alejandro
Blanco Lanza, Saúl
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Genetica
Facultad de Ciencias Biologicas y Ambientales
dc.subject.none.fl_str_mv Ecología. Medio ambiente
Genética
Benthic diatoms
DNA barcoding
Ecological assessment
Shallow pond
2409.03 Genética de Poblaciones
2417.13 Ecología Vegetal
2417.14 Genética Vegetal
topic Ecología. Medio ambiente
Genética
Benthic diatoms
DNA barcoding
Ecological assessment
Shallow pond
2409.03 Genética de Poblaciones
2417.13 Ecología Vegetal
2417.14 Genética Vegetal
description [EN] Benthic diatoms have traditionally been used as bioindicators of aquatic ecosystems. Because diatom-based monitoring of water quality is required by European legislation, molecular-based methods had emerged as useful alternatives to classical methods based on morphological identification using light microscopy. The aim of this study was to test the reliability of DNA metabarcoding combined with High-Throughput Sequencing (HTS) techniques in the bioassessment of the trophic status of 22 Mediterranean shallow ponds in NW Spain. For each pond, the Trophic Diatom Index (TDI) was calculated from inventories obtained by identification using light microscopy (LM) followed by high-throughput sequencing (HTS) at the molecular level. Ponds were subsequently classified into five water quality classes. The results showed a good correspondence between both methods, especially after applying a correction factor that depended on the biovolume of the cells. This correspondence led to the assignment to the same quality class in 59% of the ponds. The determination and quantification of valves or DNA sequences was one of the main pitfalls, which mainly included those related to the variability in the relative abundances of some species. Accordingly, ponds with similar relative abundances for the dominant species were assigned to the same quality class. Moreover, other difficulties leading the discrepancies were the misidentification of some species due to the presence of semi-cryptic taxa, the incompleteness of the reference database and the bioinformatic protocol. Thus, the validation of DNA-based methods for the identification of freshwater diatoms represents an important goal, as an alternative to using traditional methods in Mediterranean shallow ponds
publishDate 2021
dc.date.none.fl_str_mv 2021
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://www.mdpi.com/2073-4441/13/10/1351
https://hdl.handle.net/10612/18085
url https://www.mdpi.com/2073-4441/13/10/1351
https://hdl.handle.net/10612/18085
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv info:eu-repo/grantAgreement/AEI/Programa Estatal de I+D+i Orientada a los Retos de la Sociedad/CGL2017-84176R
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
dc.source.none.fl_str_mv reponame:BULERIA. Repositorio Institucional de la Universidad de León
instname:Universidad Rey Juan Carlos
instname_str Universidad Rey Juan Carlos
reponame_str BULERIA. Repositorio Institucional de la Universidad de León
collection BULERIA. Repositorio Institucional de la Universidad de León
repository.name.fl_str_mv
repository.mail.fl_str_mv
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