Molecular techniques like metabarcoding, while promising for exploring diversity of communities, are often impeded by the lack of reference DNA sequences available for taxonomic annotation. Our study explores the benefits of combining targeted DNA barcoding and morphological taxonomy to improve metabarcoding efficiency, using beach meiofauna as a case study. Beaches are globally important ecosystems and are inhabited by meiofauna, microscopic animals living in the interstitial space between the sand grains, which play a key role in coastal biodiversity and ecosystem dynamics. However, research on meiofauna faces challenges due to limited taxonomic expertise and sparse sampling. We generated 775 new cytochrome c oxidase I DNA barcodes from meiofauna specimens collected along the Netherlands' west coast and combined them with the NCBI GenBank database. We analysed alpha and beta diversity in 561 metabarcoding samples from 24 North Sea beaches, a region extensively studied for meiofauna, using both the enriched reference database and the NCBI database without the additional reference barcodes. Our results show a 2.5-fold increase in sequence annotation and a doubling of species-level Operational Taxonomic Units (OTUs) identification when annotating the metabarcoding data with the enhanced database. Additionally, our analyses revealed a bell-shaped curve of OTU richness across the intertidal zone, aligning more closely with morphological analysis patterns, and more defined community dissimilarity patterns between supralittoral and intertidal sites. Our research highlights the importance of expanding molecular reference databases and combining morphological taxonomy with molecular techniques for biodiversity assessments, ultimately improving our understanding of coastal ecosystems.

Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna / Macher, Jan‐niklas; Martínez, Alejandro; Çakir, Sude; Cholley, Pierre‐etienne; Christoforou, Eleni; Curini , ; Gallett, Marco; van Galen, Lotte; García‐cobo, Marta; Jondelius, Ulf; de Jong, Daphne; Leasi, Francesca; Lemke, Michael; Rubio , ; Lopez, Iñigo; Sánchez, Nuria; Sørensen Martin, Vinther; Todaro, Mary Antonio Donatello; Renema, Willem; Fontaneto, Diego. - In: MOLECULAR ECOLOGY RESOURCES. - ISSN 1755-098X. - (2024), pp. 1-13. [10.1111/1755-0998.13997]

Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna

Todaro M. Antonio;
2024

Abstract

Molecular techniques like metabarcoding, while promising for exploring diversity of communities, are often impeded by the lack of reference DNA sequences available for taxonomic annotation. Our study explores the benefits of combining targeted DNA barcoding and morphological taxonomy to improve metabarcoding efficiency, using beach meiofauna as a case study. Beaches are globally important ecosystems and are inhabited by meiofauna, microscopic animals living in the interstitial space between the sand grains, which play a key role in coastal biodiversity and ecosystem dynamics. However, research on meiofauna faces challenges due to limited taxonomic expertise and sparse sampling. We generated 775 new cytochrome c oxidase I DNA barcodes from meiofauna specimens collected along the Netherlands' west coast and combined them with the NCBI GenBank database. We analysed alpha and beta diversity in 561 metabarcoding samples from 24 North Sea beaches, a region extensively studied for meiofauna, using both the enriched reference database and the NCBI database without the additional reference barcodes. Our results show a 2.5-fold increase in sequence annotation and a doubling of species-level Operational Taxonomic Units (OTUs) identification when annotating the metabarcoding data with the enhanced database. Additionally, our analyses revealed a bell-shaped curve of OTU richness across the intertidal zone, aligning more closely with morphological analysis patterns, and more defined community dissimilarity patterns between supralittoral and intertidal sites. Our research highlights the importance of expanding molecular reference databases and combining morphological taxonomy with molecular techniques for biodiversity assessments, ultimately improving our understanding of coastal ecosystems.
2024
1
13
Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna / Macher, Jan‐niklas; Martínez, Alejandro; Çakir, Sude; Cholley, Pierre‐etienne; Christoforou, Eleni; Curini , ; Gallett, Marco; van Galen, Lotte; García‐cobo, Marta; Jondelius, Ulf; de Jong, Daphne; Leasi, Francesca; Lemke, Michael; Rubio , ; Lopez, Iñigo; Sánchez, Nuria; Sørensen Martin, Vinther; Todaro, Mary Antonio Donatello; Renema, Willem; Fontaneto, Diego. - In: MOLECULAR ECOLOGY RESOURCES. - ISSN 1755-098X. - (2024), pp. 1-13. [10.1111/1755-0998.13997]
Macher, Jan‐niklas; Martínez, Alejandro; Çakir, Sude; Cholley, Pierre‐etienne; Christoforou, Eleni; Curini , ; Gallett, Marco; van Galen, Lotte; ...espandi
File in questo prodotto:
File Dimensione Formato  
Macher et al-2024-Netherlands.pdf

Open access

Tipologia: Versione pubblicata dall'editore
Dimensione 3.19 MB
Formato Adobe PDF
3.19 MB Adobe PDF Visualizza/Apri
Pubblicazioni consigliate

Licenza Creative Commons
I metadati presenti in IRIS UNIMORE sono rilasciati con licenza Creative Commons CC0 1.0 Universal, mentre i file delle pubblicazioni sono rilasciati con licenza Attribuzione 4.0 Internazionale (CC BY 4.0), salvo diversa indicazione.
In caso di violazione di copyright, contattare Supporto Iris

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11380/1350286
Citazioni
  • ???jsp.display-item.citation.pmc??? 1
  • Scopus ND
  • ???jsp.display-item.citation.isi??? ND
social impact