How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs?
Abstract Quantifying fish species diversity in rich tropical marine environments remains challenging. Environmental DNA (eDNA) metabarcoding is a promising tool to face this challenge through the filtering, amplification, and sequencing of DNA traces from water samples. However, because eDNA concent...
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2021
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oai:doaj.org-article:99d934e539ef4ef8a8c535955580b9d52021-11-08T17:10:40ZHow many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs?2045-775810.1002/ece3.8150https://doaj.org/article/99d934e539ef4ef8a8c535955580b9d52021-11-01T00:00:00Zhttps://doi.org/10.1002/ece3.8150https://doaj.org/toc/2045-7758Abstract Quantifying fish species diversity in rich tropical marine environments remains challenging. Environmental DNA (eDNA) metabarcoding is a promising tool to face this challenge through the filtering, amplification, and sequencing of DNA traces from water samples. However, because eDNA concentration is low in marine environments, the reliability of eDNA to detect species diversity can be limited. Using an eDNA metabarcoding approach to identify fish Molecular Taxonomic Units (MOTUs) with a single 12S marker, we aimed to assess how the number of sampling replicates and filtered water volume affect biodiversity estimates. We used a paired sampling design of 30 L per replicate on 68 reef transects from 8 sites in 3 tropical regions. We quantified local and regional sampling variability by comparing MOTU richness, compositional turnover, and compositional nestedness. We found strong turnover of MOTUs between replicated pairs of samples undertaken in the same location, time, and conditions. Paired samples contained non‐overlapping assemblages rather than subsets of one another. As a result, non‐saturated localized diversity accumulation curves suggest that even 6 replicates (180 L) in the same location can underestimate local diversity (for an area <1 km). However, sampling regional diversity using ~25 replicates in variable locations (often covering 10 s of km) often saturated biodiversity accumulation curves. Our results demonstrate variability of diversity estimates possibly arising from heterogeneous distribution of eDNA in seawater, highly skewed frequencies of eDNA traces per MOTU, in addition to variability in eDNA processing. This high compositional variability has consequences for using eDNA to monitor temporal and spatial biodiversity changes in local assemblages. Avoiding false‐negative detections in future biomonitoring efforts requires increasing replicates or sampled water volume to better inform management of marine biodiversity using eDNA.Salomé StaufferMeret JuckerThomas KegginVirginie MarquesMarco AndrelloSandra BessudoMarie‐Charlotte CheutinGiomar Helena Borrero‐PérezEilísh RichardsTony DejeanRégis HocdéJean‐Baptiste JuhelFelipe LadinoTom B. LetessierNicolas LoiseauEva MaireDavid MouillotMaria Mutis MartinezguerraStéphanie ManelAndrea Polanco FernándezAlice ValentiniLaure VelezCamille AlbouyLoïc PellissierConor WaldockWileyarticlebiomonitoringcoral reef diversityenvironmental DNAMOTUsampling variabilitytropical marine ecosystemsEcologyQH540-549.5ENEcology and Evolution, Vol 11, Iss 21, Pp 14630-14643 (2021) |
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| language |
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| topic |
biomonitoring coral reef diversity environmental DNA MOTU sampling variability tropical marine ecosystems Ecology QH540-549.5 |
| spellingShingle |
biomonitoring coral reef diversity environmental DNA MOTU sampling variability tropical marine ecosystems Ecology QH540-549.5 Salomé Stauffer Meret Jucker Thomas Keggin Virginie Marques Marco Andrello Sandra Bessudo Marie‐Charlotte Cheutin Giomar Helena Borrero‐Pérez Eilísh Richards Tony Dejean Régis Hocdé Jean‐Baptiste Juhel Felipe Ladino Tom B. Letessier Nicolas Loiseau Eva Maire David Mouillot Maria Mutis Martinezguerra Stéphanie Manel Andrea Polanco Fernández Alice Valentini Laure Velez Camille Albouy Loïc Pellissier Conor Waldock How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs? |
| description |
Abstract Quantifying fish species diversity in rich tropical marine environments remains challenging. Environmental DNA (eDNA) metabarcoding is a promising tool to face this challenge through the filtering, amplification, and sequencing of DNA traces from water samples. However, because eDNA concentration is low in marine environments, the reliability of eDNA to detect species diversity can be limited. Using an eDNA metabarcoding approach to identify fish Molecular Taxonomic Units (MOTUs) with a single 12S marker, we aimed to assess how the number of sampling replicates and filtered water volume affect biodiversity estimates. We used a paired sampling design of 30 L per replicate on 68 reef transects from 8 sites in 3 tropical regions. We quantified local and regional sampling variability by comparing MOTU richness, compositional turnover, and compositional nestedness. We found strong turnover of MOTUs between replicated pairs of samples undertaken in the same location, time, and conditions. Paired samples contained non‐overlapping assemblages rather than subsets of one another. As a result, non‐saturated localized diversity accumulation curves suggest that even 6 replicates (180 L) in the same location can underestimate local diversity (for an area <1 km). However, sampling regional diversity using ~25 replicates in variable locations (often covering 10 s of km) often saturated biodiversity accumulation curves. Our results demonstrate variability of diversity estimates possibly arising from heterogeneous distribution of eDNA in seawater, highly skewed frequencies of eDNA traces per MOTU, in addition to variability in eDNA processing. This high compositional variability has consequences for using eDNA to monitor temporal and spatial biodiversity changes in local assemblages. Avoiding false‐negative detections in future biomonitoring efforts requires increasing replicates or sampled water volume to better inform management of marine biodiversity using eDNA. |
| format |
article |
| author |
Salomé Stauffer Meret Jucker Thomas Keggin Virginie Marques Marco Andrello Sandra Bessudo Marie‐Charlotte Cheutin Giomar Helena Borrero‐Pérez Eilísh Richards Tony Dejean Régis Hocdé Jean‐Baptiste Juhel Felipe Ladino Tom B. Letessier Nicolas Loiseau Eva Maire David Mouillot Maria Mutis Martinezguerra Stéphanie Manel Andrea Polanco Fernández Alice Valentini Laure Velez Camille Albouy Loïc Pellissier Conor Waldock |
| author_facet |
Salomé Stauffer Meret Jucker Thomas Keggin Virginie Marques Marco Andrello Sandra Bessudo Marie‐Charlotte Cheutin Giomar Helena Borrero‐Pérez Eilísh Richards Tony Dejean Régis Hocdé Jean‐Baptiste Juhel Felipe Ladino Tom B. Letessier Nicolas Loiseau Eva Maire David Mouillot Maria Mutis Martinezguerra Stéphanie Manel Andrea Polanco Fernández Alice Valentini Laure Velez Camille Albouy Loïc Pellissier Conor Waldock |
| author_sort |
Salomé Stauffer |
| title |
How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs? |
| title_short |
How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs? |
| title_full |
How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs? |
| title_fullStr |
How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs? |
| title_full_unstemmed |
How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs? |
| title_sort |
how many replicates to accurately estimate fish biodiversity using environmental dna on coral reefs? |
| publisher |
Wiley |
| publishDate |
2021 |
| url |
https://doaj.org/article/99d934e539ef4ef8a8c535955580b9d5 |
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