How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs?

Background Effective biodiversity monitoring is fundamental in tracking changes in ecosystems as it relates to commercial, recreational, and conservation interests. Current approaches to survey coral reef ecosystems center on the use of indicator species and repeat surveying at specific sites. However, such approaches are often limited by the narrow snapshot of total marine biodiversity that they describe and are thus hindered in their ability to contribute to holistic ecosystem-based monitoring. In tandem, environmental DNA (eDNA) and next-generation sequencing metabarcoding methods provide a new opportunity to rapidly assess the presence of a broad spectrum of eukaryotic organisms within our oceans, ranging from microbes to macrofauna. Methods We here investigate the potential for rapid universal metabarcoding surveys (RUMS) of eDNA in sediment samples to provide snapshots of eukaryotic subtropical biodiversity along a depth gradient at two coral reefs in Okinawa, Japan based on 18S rRNA. Results Using 18S rRNA metabarcoding, we found that there were significant separations in eukaryotic community assemblages (at the family level) detected in sediments when compared across different depths ranging from 10 to 40 m (p = 0.001). Significant depth zonation was observed across operational taxonomic units assigned to the class Demospongiae (sponges), the most diverse class (contributing 81% of species) within the phylum Porifera; the oldest metazoan phylum on the planet. However, zonation was not observed across the class Anthozoa (i.e., anemones, stony corals, soft corals, and octocorals), suggesting that the former may serve as a better source of indicator species based on sampling over fine spatial scales and using this universal assay. Furthermore, despite their abundance on the examined coral reefs, we did not detect any octocoral DNA, which may be due to low cellular shedding rates, assay sensitivities, or primer biases. Discussion Overall, our pilot study demonstrates the importance of exploring depth effects in eDNA and suggest that RUMS may be applied to provide a baseline of information on eukaryotic marine taxa at coastal sites of economic and conservation importance.

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Alpine freshwater fish biodiversity assessment: an intercalibration test for metabarcoding method set up

ARPHA Conference Abstracts ◽

10.3897/aca.4.e64927 ◽

2021 ◽

Vol 4 ◽

Author(s):

Giulia Riccioni ◽

Isabelle Domaizon ◽

Andrea Gandolfi ◽

Massimo Pindo ◽

Marine Vautier ◽

...

Keyword(s):

Freshwater Fish ◽

Population Decline ◽

Environmental Dna ◽

Well Being ◽

Taxonomic Resolution ◽

Anthropogenic Pressure ◽

Biodiversity Assessment ◽

Good Efficiency ◽

Essential Information ◽

Fish Biodiversity

Environmental DNA (eDNA) based methods (Fig. 1) are proving to be a promising tool for freshwater fish biodiversity assessment in Europe within the Water Framework Directive (WFD, 2000/60/EC) especially for large rivers and lakes where current fish monitoring techniques have known shortcomings. Freshwater fish are actively involved in aquatic ecosystems functioning and diversity, contributing to the health, well-being and economy in every geographic realm. Unfortunately, many freshwater fish are experiencing critical population decline with risk of local or global extinction because of intense anthropogenic pressure. Within the EU project Eco-AlpsWater, advanced high throughput sequencing (HTS) techniques are used to improve the traditional WFD monitoring approaches by using environmental DNA (eDNA) collected in Alpine waterbodies. To evaluate the performance of the metabarcoding approach specifically designed to measure freshwater fish biodiversity in Alpine lakes and rivers, an intercalibration test was performed. This exercise forecasted the use of mock samples containing either tissue-extracted DNA of different target species or water collected from aquaculture tanks to mimic real environmental water sampling and processing. Moreover, three water samples collected in Lake Bourget (France) were used to compare the efficiency of taxonomic assignments in natural and mock community samples. Our results highlighted a good efficiency of the molecular laboratory protocols for HTS and a good amplification success of the selected primers, providing essential information concerning the taxonomic resolution of the 12S mitochondrial marker. As further confirmation, different concentration of species DNA in the mock samples were well represented by the relative read abundance. This preliminary test confirmed the applicability of eDNA metabarcoding analyses for the biomonitoring of freshwater fish inhabiting Alpine and perialpine lakes and rivers.

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Environmental DNA reveals quantitative patterns of fish biodiversity in large rivers despite its downstream transportation

Scientific Reports ◽

10.1038/s41598-018-28424-8 ◽

2018 ◽

Vol 8 (1) ◽

Cited By ~ 95

Author(s):

Didier Pont ◽

Mathieu Rocle ◽

Alice Valentini ◽

Raphaël Civade ◽

Pauline Jean ◽

...

Keyword(s):

Environmental Dna ◽

Large Rivers ◽

Fish Biodiversity

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Peer Review #1 of "Assessment of fish biodiversity in four Korean rivers using environmental DNA metabarcoding (v0.1)"

10.7287/peerj.9508v0.1/reviews/1 ◽

2020 ◽

Keyword(s):

Peer Review ◽

Environmental Dna ◽

Fish Biodiversity ◽

Dna Metabarcoding

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More Than Expected From Old Sponge Samples: A Natural Sampler DNA Metabarcoding Assessment of Marine Fish Diversity in Nha Trang Bay (Vietnam)

Frontiers in Marine Science ◽

10.3389/fmars.2020.605148 ◽

2020 ◽

Vol 7 ◽

Author(s):

Marta Turon ◽

Carlos Angulo-Preckler ◽

Adrià Antich ◽

Kim Præbel ◽

Owen S. Wangensteen

Keyword(s):

Coral Reefs ◽

Fish Species ◽

Fish Communities ◽

Environmental Dna ◽

Pcr Primers ◽

Tropical Fish ◽

Sponge Species ◽

Fish Diversity ◽

Biodiversity Patterns ◽

Nha Trang Bay

Sponges have recently been proposed as ideal candidates to act as natural samplers for environmental DNA due to their efficiency in filtering water. However, validation of the usefulness of DNA recovered from sponges to reveal vertebrate biodiversity patterns in Marine Protected Areas is still needed. Additionally, nothing is known about how different sponge species and morphologies influence the capture of environmental DNA and whether biodiversity patterns obtained from sponges are best described by quantitative or qualitative measures. In this study, we amplified and sequenced a vertebrate specific 12S barcode with a set of universal PCR primers (MiFish) for metabarcoding environmental DNA from fishes, to unveil fine-scale patterns of fish communities from natural-sampler DNA retrieved from 64 sponges (16 species) located in eutrophic and well-preserved coral reefs in Nha Trang Bay (central Vietnam). Ninety tropical fish species were identified from the sponges, corresponding to one third of the total local ichthyofauna reported from previous extensive conventional surveys. Significant differentiation in fish communities between eutrophic and well-preserved environments was observed, albeit eutrophication only explained a modest proportion of the variation between fish communities. Differences in efficiency of capturing fish environmental DNA among sponge species or morphologies were not observed. Overall, the majority of detected fish species corresponded to reef-associated small-sized species, as expected in coral reefs environments. Remarkably, pelagic, migratory, and deep-sea fish species were also recovered from sponge tissues, pointing out the ability of sponge natural sampled DNA to detect fishes that were not permanently associated to the biomes where the sponges were sampled. These results highlight the suitability of natural samplers as a cost-effective way to assess vertebrate diversity in hyper-diverse environments.

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