Accumulation curves of environmental DNA sequences predict coastal fish diversity in the Coral Triangle

Juhel, Jean‐Baptiste; Utama, Rizkie Satriya; Marques, Virginie; Vimono, Indra Bayu; Sugeha, Hagi Yulia; kadarusman, kadarusman; Pouyaud, Laurent; Déjean, Tony; Mouillot, David; Hocd, R gis

doi:10.22541/au.158082947.75232617

Cited by 5 publications

(29 citation statements)

References 3 publications

(3 reference statements)

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“…This unexpected result suggests that there may be an upper limit to the amount of diversity eDNA can capture within a single liter of seawater. As such, eDNA studies in high diversity ecosystems will require much greater sampling intensity, a result consistent with Juhel et al (2020). Given that our models indicate that high biodiversity regions like Raja Ampat may require in excess of 300 one-liter samples to capture all fish diversity present, eDNA surveys in high diversity areas will either need to increase the numbers of samples or volume of water per sample to be maximally informative.…”

Section: Discussionsupporting

confidence: 61%

“…Similarly, most coral reef eDNA studies to date have occurred in Japan, Central Pacific, Western Australia, and the Red Sea (Alexander et al 2020;Bessey et al 2020; DiBattista et al 2017; Lafferty et al 2020; Oka et al 2020;Stat et al 2017; Stat et al 2019; West et al 2020), where fish biodiversity is far lower than the Coral Triangle (Bellwood & Meyer, 2009; Roberts et al, 2002). Most recently, Juhel et al (2020) used eDNA to examine fish diversity in Raja Ampat, Indonesia, home to the world’s most diverse reef fish fauna (Allen, 2002), reporting a strong correlation between eDNA results and checklists from visual data. However, species accumulation curves indicated that eDNA greatly under sampled species diversity, suggesting that the methods, sampling design, and bioinformatics approaches employed in temperate eDNA studies may not be equally effective in megadiverse tropical regions like the Coral Triangle.…”

Section: Introductionmentioning

confidence: 99%

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Environmental DNA in a Global Biodiversity Hotspot: Lessons from Coral Reef Fish Diversity Across the Indonesian Archipelago

Marwayana

Gold

Barber

2021

Preprint

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Indonesia is the heart of the Coral Triangle, the world's most diverse marine ecosystem. Preserving the biological and economic value of this marine biodiversity requires efficient and economical ecosystem monitoring, yet our understanding of marine biodiversity in this region remains limited. This study uses environmental DNA (eDNA) to survey fish communities across a pronounced biodiversity gradient in Indonesia. A total of 12,939,690 sequence reads of MiFish 12S rRNA from 39 sites spanning 7 regions of Indonesia revealed 4,146 Amplified Sequence Variants (ASVs). Regional patterns of fish diversity based on eDNA broadly conformed to expectations based on traditional biodiversity survey methods, with the highest fish biodiversity in Raja Ampat and generally lower diversity in Western Indonesia. However, eDNA performed relatively poorly compared to visual survey methods in site-by-site comparisons, both in terms of total number of taxa recovered and ability to assign species names to ASVs. This result stands in a stark contrast to eDNA studies of temperate and tropical ecosystems with lower diversity. Analyses show that while sequencing depth was sufficient to capture all fish diversity within individual seawater samples, variation among samples from individual localities was high, and sampling effort was insufficient to capture all fish diversity at a given sampling site. Interestingly, mean ASVs recovered per one-liter seawater was surprisingly similar across sites, despite substantial differences in total diversity, suggesting a limit to total ASVs (~200) per one-liter eDNA sample. Combined, results highlight two major challenges of eDNA in highly diverse ecosystems such as the Coral Triangle. First, reference databases are incomplete and insufficient for effective ASV taxonomic assignment. Second, eDNA sampling design developed from lower diversity temperate marine ecosystems are inadequate to fully capture diversity of biodiversity hotspots like the Coral Triangle.

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Section: Discussionsupporting

confidence: 61%

Section: Introductionmentioning

confidence: 99%

Environmental DNA in a Global Biodiversity Hotspot: Lessons from Coral Reef Fish Diversity Across the Indonesian Archipelago

Marwayana

Gold

Barber

2021

Preprint

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“…We performed the aggregation into MOTUs using the teleo primers, as the bioinformatics clustering pipeline using SWARM has only been developed and fully tested with this primer (Juhel et al., 2020; Marques et al., 2020). In Providencia, the eDNA clustering pipeline identified 227 distinct MOTUs, and we detected an average of 26.2 ± 12.6 MOTUs per filter.…”

Section: Resultsmentioning

confidence: 99%

“…eDNA metabarcoding is now widely employed in various aquatic ecosystems (Deiner et al., 2017), but some uncertainties remain as regard to sampling design (Valentini et al., 2016) and the choice of markers (Collins et al., 2019; Stat et al., 2017) and bioinformatics pipeline (Calderón‐Sanou et al., 2020; Juhel et al., 2020). We tested three different primer sets for the 12S region looking for fish taxa, but we did not find a universal marker able to detect all taxa.…”

Section: Discussionmentioning

confidence: 99%

“…Several applications demonstrated that eDNA can recover multiple components of marine ecosystems, including species richness (Jerde et al., 2019), seasonal composition variation (Djurhuus et al., 2020), rare species (Weltz et al., 2017), abundance or biomass (Knudsen et al., 2019; Thomsen et al., 2016), and the occurrence of invasive species (Nevers et al., 2018). Nevertheless, a range of methodological challenges still hampers the broad use of eDNA for the reliable monitoring of marine ecosystems, linked to the choice of markers (Collins et al., 2019; Freeland, 2017), primers sets (Stat et al., 2017), laboratory and sequencing protocols (Deiner et al., 2017; Goldberg et al., 2016), and bioinformatic analyses (Calderón‐Sanou et al., 2020; Juhel et al., 2020), which implies further testing of the eDNA methodology in situ.…”

Section: Introductionmentioning

confidence: 99%

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Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes

Marques

Fopp

et al. 2020

Environmental DNA

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Environmental DNA (eDNA) analysis is a revolutionary method to monitor marine biodiversity from animal DNA traces. Examining the capacity of eDNA to provide accurate biodiversity measures in species‐rich ecosystems such as coral reefs is a prerequisite for their application in long‐term monitoring. Here, we surveyed two Colombian tropical marine reefs, the island of Providencia and Gayraca Bay near Santa Marta, using eDNA and underwater visual census (UVC) methods. We collected a large quantity of surface water (30 L per filter) above the reefs and applied a metabarcoding protocol using three different primer sets targeting the 12S mitochondrial DNA, which are specific to the vertebrates Actinopterygii and Elasmobranchii. By assigning eDNA sequences to species using a public reference database, we detected the presence of 107 and 85 fish species, 106 and 92 genera, and 73 and 57 families in Providencia and Gayraca Bay, respectively. Of the species identified using eDNA, 32.7% (Providencia) and 18.8% (Gayraca) were also found in the UVCs. We further found congruence in genus and species richness and abundance between eDNA and UVC approaches in Providencia but not in Gayraca Bay. Mismatches between eDNA and UVC had a phylogenetic and ecological signal, with eDNA detecting a broader phylogenetic diversity and more effectively detecting smaller species, pelagic species and those in deeper habitats. Altogether, eDNA can be used for fast and broad biodiversity surveys and is applicable to species‐rich ecosystems in the tropics, but improved coverage of the reference database is required before this new method could serve as an effective complement to traditional census methods.

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Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding

et al. 2022

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Increasing speed and magnitude of global change threaten the world's biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems. We analysed 226 environmental DNA (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central and Southwest Pacific, Coral Triangle and Western Indian Ocean) and compared those to 2047 underwater visual censuses from the Reef Life Survey in 1224 stations. Environmental DNA reveals a higher (16%) fish biodiversity, with 2650 taxa, and 25% more families than underwater visual surveys. By identifying more pelagic, reef-associated and crypto-benthic species, eDNA offers a fresh view on assembly rules across spatial scales. Nevertheless, the reef life survey identified more species than eDNA in 47 shared families, which can be due to incomplete sequence assignment, possibly combined with incomplete detection in the environment, for some species. Combining eDNA metabarcoding and extensive visual census offers novel insights on the spatial organization of the richest marine ecosystems.

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Accumulation curves of environmental DNA sequences predict coastal fish diversity in the Coral Triangle

Cited by 5 publications

References 3 publications

Environmental DNA in a Global Biodiversity Hotspot: Lessons from Coral Reef Fish Diversity Across the Indonesian Archipelago

Environmental DNA in a Global Biodiversity Hotspot: Lessons from Coral Reef Fish Diversity Across the Indonesian Archipelago

Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes

Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding

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