Advances in the use of molecular tools in ecological and biodiversity assessment of aquatic ecosystems
ABSTRACT: Conservation and sustainable management of aquatic ecosystems is a priority in environmental programs worldwide. However, these aims are highly dependent on the efficiency, accuracy and cost of existent methods for the detection of keystone species and monitoring of biological communities....
| Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Fecha de publicación: | 2020 |
| País: | España |
| Institución: | Universidad de Cantabria (UC) |
| Repositorio: | UCrea Repositorio Abierto de la Universidad de Cantabria |
| Idioma: | inglés |
| OAI Identifier: | oai:repositorio.unican.es:10902/26335 |
| Acceso en línea: | https://hdl.handle.net/10902/26335 |
| Access Level: | acceso abierto |
| Palabra clave: | EDNA Metabarcoding Conservation Ecological quality Species detection Rivers Lakes Thermal springs Estuaries Lagoons |
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Advances in the use of molecular tools in ecological and biodiversity assessment of aquatic ecosystems |
| title |
Advances in the use of molecular tools in ecological and biodiversity assessment of aquatic ecosystems |
| spellingShingle |
Advances in the use of molecular tools in ecological and biodiversity assessment of aquatic ecosystems Feio, Maria João EDNA Metabarcoding Conservation Ecological quality Species detection Rivers Lakes Thermal springs Estuaries Lagoons |
| title_short |
Advances in the use of molecular tools in ecological and biodiversity assessment of aquatic ecosystems |
| title_full |
Advances in the use of molecular tools in ecological and biodiversity assessment of aquatic ecosystems |
| title_fullStr |
Advances in the use of molecular tools in ecological and biodiversity assessment of aquatic ecosystems |
| title_full_unstemmed |
Advances in the use of molecular tools in ecological and biodiversity assessment of aquatic ecosystems |
| title_sort |
Advances in the use of molecular tools in ecological and biodiversity assessment of aquatic ecosystems |
| dc.creator.none.fl_str_mv |
Feio, Maria João Filipe, Ana Filipa García Raventós, Aina Ardura, Alba Calapez, Ana Raquel Pujante, Ana María Mortágua, Andreia Múrria, Cesc Díaz de Quijano, Daniel Martins, Filipa MS Duarte, Sofia Saínz Bariáin, Marta Cordeiro, Rita Rivera, Sinziana F. Väisänen, Leif O. S. Fonseca, Amélia Gonçalves, Vítor García Vázquez, Eva Vieites Rodríguez, David Ivanova, Elena A. Costa, Filipe O. Barquín Ortiz, José|||0000-0003-1897-2636 Rojo, Verónica Vierna, Joaquín Fais, Maria Suárez, Marcos Nieminen, Marko Hammers- Wirtz, Monica Kolmakova, Olesia V. Trusova, Maria Y. Beja, Pedro González, Raquel Planes, Serge Almeida, Salomé FP |
| author |
Feio, Maria João |
| author_facet |
Feio, Maria João Filipe, Ana Filipa García Raventós, Aina Ardura, Alba Calapez, Ana Raquel Pujante, Ana María Mortágua, Andreia Múrria, Cesc Díaz de Quijano, Daniel Martins, Filipa MS Duarte, Sofia Saínz Bariáin, Marta Cordeiro, Rita Rivera, Sinziana F. Väisänen, Leif O. S. Fonseca, Amélia Gonçalves, Vítor García Vázquez, Eva Vieites Rodríguez, David Ivanova, Elena A. Costa, Filipe O. Barquín Ortiz, José|||0000-0003-1897-2636 Rojo, Verónica Vierna, Joaquín Fais, Maria Suárez, Marcos Nieminen, Marko Hammers- Wirtz, Monica Kolmakova, Olesia V. Trusova, Maria Y. Beja, Pedro González, Raquel Planes, Serge Almeida, Salomé FP |
| author_role |
author |
| author2 |
Filipe, Ana Filipa García Raventós, Aina Ardura, Alba Calapez, Ana Raquel Pujante, Ana María Mortágua, Andreia Múrria, Cesc Díaz de Quijano, Daniel Martins, Filipa MS Duarte, Sofia Saínz Bariáin, Marta Cordeiro, Rita Rivera, Sinziana F. Väisänen, Leif O. S. Fonseca, Amélia Gonçalves, Vítor García Vázquez, Eva Vieites Rodríguez, David Ivanova, Elena A. Costa, Filipe O. Barquín Ortiz, José|||0000-0003-1897-2636 Rojo, Verónica Vierna, Joaquín Fais, Maria Suárez, Marcos Nieminen, Marko Hammers- Wirtz, Monica Kolmakova, Olesia V. Trusova, Maria Y. Beja, Pedro González, Raquel Planes, Serge Almeida, Salomé FP |
| author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
| dc.contributor.none.fl_str_mv |
Universidad de Cantabria |
| dc.subject.none.fl_str_mv |
EDNA Metabarcoding Conservation Ecological quality Species detection Rivers Lakes Thermal springs Estuaries Lagoons |
| topic |
EDNA Metabarcoding Conservation Ecological quality Species detection Rivers Lakes Thermal springs Estuaries Lagoons |
| description |
ABSTRACT: Conservation and sustainable management of aquatic ecosystems is a priority in environmental programs worldwide. However, these aims are highly dependent on the efficiency, accuracy and cost of existent methods for the detection of keystone species and monitoring of biological communities. Rapid advances in eDNA, barcoding and metabarcoding promoted by high-throughput sequencing technologies are generating millions of sequences in a fast way, with a promising cost reduction, and overcoming some difficulties of the traditional taxonomic approaches. This paper provides an updated broad perspective of the current developments in this dynamic field presented in the special session (SS) “The use of molecular tools in ecological and biodiversity assessment of aquatic ecosystems” of the XIX Congress of the Iberian Association of Limnology (AIL2018), held in Coimbra, Portugal. Developments presented are mainly focused on the Iberian Peninsula (Portugal and Spain, including Atlantic Macaronesian islands) but include studies in France, Germany, Finland, Russia (Siberia) and South America. The networks within which these researchers are involved are yet even broader, profiting from existing molecular facilities, and traditional taxonomic expertise, which can be viewed as a characteristic of this new research area. It was evident in the SS that the use of molecular tools is widespread, being used to study a diversity of aquatic systems, from rivers’ headwaters to estuaries and coastal lagoons, and volcanic, mountain and frozen lakes to hot springs. The organisms targeted are likewise varied and include fish, macroinvertebrates, meiofauna, microalgae such as diatoms and dinoflagellates, other protists, fungi, and bacteria (cyanobacteria and other). Some studies address the whole biodiversity (i.e., all species present independently of the taxonomic group) from environmental samples of water, biofilms and preservative solution from field samples (e.g., ethanol from macroinvertebrate samples). Great advances were acknowledged in the special session, namely in the use of metabarcoding for detecting hidden biodiversity, juvenile stages, low-abundance species, non-indigenous species and toxicity potential, and ultimately for ecological monitoring of diatoms and invertebrates. Yet, several drawbacks were highlighted and need further work, which include: taxonomic gaps in the reference databases (including gaps at species level and on intraspecific variability) or absence of public databases (e.g. for meiofauna), still high sequencing costs, the need of a substantial bioinformatics effort, difficulties in establishing the amount of environmental sample necessary for a good DNA extraction and the need for testing different genetic markers to obtain accurate results. |
| publishDate |
2020 |
| dc.date.none.fl_str_mv |
2020 2020-01-01 |
| dc.type.none.fl_str_mv |
journal article http://purl.org/coar/resource_type/c_6501 NA http://purl.org/coar/version/c_be7fb7dd8ff6fe43 |
| dc.type.openaire.fl_str_mv |
info:eu-repo/semantics/article |
| format |
article |
| dc.identifier.none.fl_str_mv |
https://hdl.handle.net/10902/26335 |
| url |
https://hdl.handle.net/10902/26335 |
| dc.language.none.fl_str_mv |
Inglés eng |
| language_invalid_str_mv |
Inglés |
| language |
eng |
| dc.rights.none.fl_str_mv |
open access http://purl.org/coar/access_right/c_abf2 Attribution-NonCommercial 4.0 International http://creativecommons.org/licenses/by-nc/4.0/ |
| dc.rights.openaire.fl_str_mv |
info:eu-repo/semantics/openAccess |
| rights_invalid_str_mv |
open access http://purl.org/coar/access_right/c_abf2 Attribution-NonCommercial 4.0 International http://creativecommons.org/licenses/by-nc/4.0/ |
| eu_rights_str_mv |
openAccess |
| dc.publisher.none.fl_str_mv |
Asociación Ibérica de Limnología |
| publisher.none.fl_str_mv |
Asociación Ibérica de Limnología |
| dc.source.none.fl_str_mv |
Limnetica, 2020, 39(1), 419-440 reponame:UCrea Repositorio Abierto de la Universidad de Cantabria instname:Universidad de Cantabria (UC) |
| instname_str |
Universidad de Cantabria (UC) |
| reponame_str |
UCrea Repositorio Abierto de la Universidad de Cantabria |
| collection |
UCrea Repositorio Abierto de la Universidad de Cantabria |
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| _version_ |
1869424649126805504 |
| spelling |
Advances in the use of molecular tools in ecological and biodiversity assessment of aquatic ecosystemsFeio, Maria JoãoFilipe, Ana FilipaGarcía Raventós, AinaArdura, AlbaCalapez, Ana RaquelPujante, Ana MaríaMortágua, AndreiaMúrria, CescDíaz de Quijano, DanielMartins, Filipa MSDuarte, SofiaSaínz Bariáin, MartaCordeiro, RitaRivera, Sinziana F.Väisänen, Leif O. S.Fonseca, AméliaGonçalves, VítorGarcía Vázquez, EvaVieites Rodríguez, DavidIvanova, Elena A.Costa, Filipe O.Barquín Ortiz, José|||0000-0003-1897-2636Rojo, VerónicaVierna, JoaquínFais, MariaSuárez, MarcosNieminen, MarkoHammers- Wirtz, MonicaKolmakova, Olesia V.Trusova, Maria Y.Beja, PedroGonzález, RaquelPlanes, SergeAlmeida, Salomé FPEDNAMetabarcodingConservationEcological qualitySpecies detectionRiversLakesThermal springsEstuariesLagoonsABSTRACT: Conservation and sustainable management of aquatic ecosystems is a priority in environmental programs worldwide. However, these aims are highly dependent on the efficiency, accuracy and cost of existent methods for the detection of keystone species and monitoring of biological communities. Rapid advances in eDNA, barcoding and metabarcoding promoted by high-throughput sequencing technologies are generating millions of sequences in a fast way, with a promising cost reduction, and overcoming some difficulties of the traditional taxonomic approaches. This paper provides an updated broad perspective of the current developments in this dynamic field presented in the special session (SS) “The use of molecular tools in ecological and biodiversity assessment of aquatic ecosystems” of the XIX Congress of the Iberian Association of Limnology (AIL2018), held in Coimbra, Portugal. Developments presented are mainly focused on the Iberian Peninsula (Portugal and Spain, including Atlantic Macaronesian islands) but include studies in France, Germany, Finland, Russia (Siberia) and South America. The networks within which these researchers are involved are yet even broader, profiting from existing molecular facilities, and traditional taxonomic expertise, which can be viewed as a characteristic of this new research area. It was evident in the SS that the use of molecular tools is widespread, being used to study a diversity of aquatic systems, from rivers’ headwaters to estuaries and coastal lagoons, and volcanic, mountain and frozen lakes to hot springs. The organisms targeted are likewise varied and include fish, macroinvertebrates, meiofauna, microalgae such as diatoms and dinoflagellates, other protists, fungi, and bacteria (cyanobacteria and other). Some studies address the whole biodiversity (i.e., all species present independently of the taxonomic group) from environmental samples of water, biofilms and preservative solution from field samples (e.g., ethanol from macroinvertebrate samples). Great advances were acknowledged in the special session, namely in the use of metabarcoding for detecting hidden biodiversity, juvenile stages, low-abundance species, non-indigenous species and toxicity potential, and ultimately for ecological monitoring of diatoms and invertebrates. Yet, several drawbacks were highlighted and need further work, which include: taxonomic gaps in the reference databases (including gaps at species level and on intraspecific variability) or absence of public databases (e.g. for meiofauna), still high sequencing costs, the need of a substantial bioinformatics effort, difficulties in establishing the amount of environmental sample necessary for a good DNA extraction and the need for testing different genetic markers to obtain accurate results.We are grateful to all participants of the special session “The use of molecular tools in ecological and biodiversity assessment of aquatic ecosystems” for the productive discussions during the AIL 2018 meeting (XIX Iberian Association of Limnology meeting in Coimbra (Portugal, June 2018). M.J. Feio is supported by MARE strategic program (UID/MAR/04292/2013); SFP Almeida is supported by GeoBioTec strategic program UID/GEO/04035/2019. R. Cordeiro was supported by a Ph.D. Grant (M3.1.a/F/017/2011) from Fundo Regional da Ciência e Tecnologia (FRCT); A.F. Filipe and A. Garcia-Raventos were supported by FRESHING Project “Next-generation biomonitoring: freshwater bioassessment and species conservation improved with metagenomics” funded by the Portuguese Foundation for Science and Technology (FCT) and COMPETE (PTDC/AAG-MAA/2261/2014 – POCI-01-0145FEDER-356 016824); F.M.S. Martins was supported by a FCT PhD grant (SFRH/BD/ 104703/2014); A.R. Calapez was supported by a grant from the FCT-PhD programme FLUVIO (PD\BD\52510\2014); A.M. Pujante acknowledges the BIOWAT-KIT_E!11892 Eurostars project; Maria Fais and Sofia Duarte were supported, respectively, by a PhD (SFRH/BD/ 113547/2015) and a post-doc fellowship (SFRH/BPD/109842/2015), from FCT; and C. Múrria acknowledges the Fundació Aigües de Barcelona for funding his research.Asociación Ibérica de LimnologíaUniversidad de Cantabria20202020-01-01journal articlehttp://purl.org/coar/resource_type/c_6501NAhttp://purl.org/coar/version/c_be7fb7dd8ff6fe43info:eu-repo/semantics/articlehttps://hdl.handle.net/10902/26335Limnetica, 2020, 39(1), 419-440reponame:UCrea Repositorio Abierto de la Universidad de Cantabriainstname:Universidad de Cantabria (UC)Inglésengopen accesshttp://purl.org/coar/access_right/c_abf2Attribution-NonCommercial 4.0 Internationalhttp://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccessoai:repositorio.unican.es:10902/263352026-06-02T12:39:31Z |
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15,300719 |