Environmental DNA metabarcoding for biodiversity monitoring of a highly-diverse tropical fish community in a coral-reef lagoon: Estimation of species richness and detection of habitat segregation

AbstractAn environmental DNA (eDNA) metabarcoding approach has been widely used for biodiversity monitoring of fishes, although it has rarely been applied to tropical and subtropical aquatic ecosystems, where species diversity is remarkably high. This study examined the extent to which species richness can be estimated in a small coral reef lagoon (1500 × 900 m) near Okinawa Island, southern Japan, where the surrounding waters are likely to harbor more than 1500 species of fish. During 2015–2017, a total of 16 capture-based surveys were conducted to create a faunal list of fish species, followed by eDNA metabarcoding based on seawater samples taken from 11 sites in the lagoon on a day in May 2019. We also tested whether eDNA metabarcoding could detect differences between adjacent fish communities inhabiting the offshore reef edge and shore-side seagrass beds within the lagoon. A total of 217 fish species were confirmed by the capture-based samplings, while 291 fish species were detected by eDNA metabarcoding, identifying a total of 410 species distributed across 119 families and 193 genera. Of these 410 species, only 96 (24% of the total) were commonly identified by both methods, indicating that capture-based surveys failed to collect a number of species detected by eDNA metabarcoding. Interestingly, two different approaches to estimate species richness based on eDNA data yielded values close to the 410 species, including one that suggested an additional three or more eDNA surveys from 11 sites (36 samples) would detect 90% of the 410 species. In addition, non-metric multi-dimensional scaling for fish assemblages clearly distinguished between the fish communities of the offshore reef edge and those of the shore-side seagrass beds.

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Environmental DNA metabarcoding for biodiversity monitoring of a highly diverse tropical fish community in a coral reef lagoon: Estimation of species richness and detection of habitat segregation

Environmental DNA ◽

10.1002/edn3.132 ◽

2020 ◽

Cited By ~ 3

Author(s):

Shin‐ichiro Oka ◽

Hideyuki Doi ◽

Kei Miyamoto ◽

Nozomi Hanahara ◽

Tetsuya Sado ◽

...

Keyword(s):

Species Richness ◽

Coral Reef ◽

Fish Community ◽

Environmental Dna ◽

Tropical Fish ◽

Habitat Segregation ◽

Biodiversity Monitoring ◽

Reef Lagoon ◽

Dna Metabarcoding ◽

Coral Reef Lagoon

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Microbiological nitrogen transformation in carbonate sediments of a coral-reef lagoon and associated seagrass beds

Marine Ecology Progress Series ◽

10.3354/meps217273 ◽

2001 ◽

Vol 217 ◽

pp. 273-286 ◽

Cited By ~ 45

Author(s):

T Miyajima ◽

M Suzumura ◽

Y Umezawa ◽

I Koike

Keyword(s):

Coral Reef ◽

Nitrogen Transformation ◽

Seagrass Beds ◽

Carbonate Sediments ◽

Reef Lagoon ◽

Coral Reef Lagoon

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Circumglobal distribution of fish environmental DNA in coral reefs

ARPHA Conference Abstracts ◽

10.3897/aca.4.e64792 ◽

2021 ◽

Vol 4 ◽

Author(s):

Laetitia Mathon ◽

Virginie Marques ◽

David Mouillot ◽

Camille Albouy ◽

Marco Andrello ◽

...

Keyword(s):

Species Richness ◽

Coral Reef ◽

Coral Reefs ◽

Survey Data ◽

Fish Species ◽

Environmental Dna ◽

Fish Diversity ◽

Visual Census ◽

Biodiversity Patterns ◽

Distribution Of Fish

Coral reefs host the highest fish diversity on Earth despite covering less than 0.1% of the ocean’s seafloor. At the same time they are also extremely threatened. Data syntheses over decades of surveys estimate the total number of coral reef fishes to vary from 2,400 to 8,000 species distributed among roughly 100 families. But this diversity remains largely unknown. Here, we investigated how environmental DNA (eDNA) could describe the distribution of fish diversity in coral reefs. We generated 504,457,267 raw 12S ribosomal DNA (rDNA) sequence reads from 251 samples (2,693 PCR replicates) collected at 25 sites in 145 stations covering five regions across the Indian, Pacific and Atlantic Oceans. Bioinformatic analysis clustered these sequences into 2,160 molecular operational taxonomic units (MOTUs) corresponding to distinct species (Marques 2020) We compared our results, with visual census surveys from Reef Life Survey, on 2,813 transects in tropical regions. Our outcomes demonstrate the capacity of eDNA metabarcoding from water samples to reconstruct well-known biogeographic patterns of fish diversity on coral reefs, such as species richness gradients towards the coral triangle, and family proportion stability across sites (Bellwood and Hughes 2001). Additionally, eDNA survey data documented a higher fish species (16%) and family (50%) diversity than estimates obtained with underwater visual surveys carried out on 20 times more sites. MOTU richness per family retrieved with eDNA closely matched fish species richness within families recorded in visual census data. However, eDNA revealed higher richness of reef-associated species and species from adjacent habitats, of cryptobenthic or nocturnal species, but also of pelagic and wide-ranging species. eDNA survey data showed that fish diversity is characterized by spatially heterogeneous species assemblages among regions, with more dissimilarity among adjacent coral reefs than detected with visual survey data. Unlike visual surveys, eDNA metabarcoding revealed the same prevalence of rarity as expected under the neutral theory of biodiversity, suggesting the predominance of random processes and ecological equivalence within trophic groups at large scale to explain fish biodiversity patterns on coral reefs. Our study demonstrates how sequencing eDNA from water provides a rapid and effective approach to characterize and assess coral reef diversity across large spatial scales, thereby also uncovering hidden biodiversity patterns.

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