scholarly journals Circumglobal distribution of fish environmental DNA in coral reefs

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.

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

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.

scholarly journals Assessing the Condition of Coral Reefs and the Indicator Fish (Family: Chaetodontidae) in Coastal Waters of Jayapura City, Papua Province, Indonesia

2019 ◽  
Vol 5 (2) ◽  
pp. 126-132
Author(s):  
Baigo Hamuna ◽  
John Dominggus Kalor ◽  
Adinda Intan Rachmadani
Keyword(s):  
Coral Reef ◽  
Coral Reefs ◽  
Fish Species ◽  
Coastal Waters ◽  
Good Condition ◽  
Live Coral ◽  
Visual Census ◽  
Fish Family ◽  
Reef Condition

Abstract The aim of this study was to find out the condition of coral reef coverage and the presence of Chaetodontidae fish in coastal waters of Jayapura City, Indonesia. The observation of coral reef coverage was performed using point intercept transect (PIT) method; meanwhile the observation of the presence of Chaetodontidae fish used visual census method. The result of this study described that coral reef condition in the study site was in severely damage (live coral 0%) in the DOK II site at 6 m depth, moderately damage (live coral 32.00% ± 2.13% to 42.00% ± 13.18%) in Kayu Pulo Island and the DOK II at 3 m depth, and good condition (live coral 56.00% ± 7.48% to 60.00% ± 5.55%) in the Tanjung Kayu Batu. There were 9 Chaetodontidae fish species from Chaetodon genus, Forcipiger genus, and Heniochus genus. The number of Chaetodontidae fish was 95, of which Heniochus acuminatus was the most dominant, as many as 46 individuals.

scholarly journals 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

2020 ◽  
Author(s):  
Shin-ichiro Oka ◽  
Hideyuki Doi ◽  
Kei Miyamoto ◽  
Nozomi Hanahara ◽  
Tetsuya Sado ◽  
...  
Keyword(s):  
Species Richness ◽  
Coral Reef ◽  
Fish Species ◽  
Environmental Dna ◽  
Seagrass Beds ◽  
Biodiversity Monitoring ◽  
Reef Lagoon ◽  
Coral Reef Lagoon ◽  
Offshore Reef ◽  
Reef Edge

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.

scholarly journals Complementarity of Rotating Video and Underwater Visual Census for Assessing Species Richness, Frequency and Density of Reef Fish on Coral Reef Slopes

PLoS ONE ◽  
2014 ◽  
Vol 9 (1) ◽  
pp. e84344 ◽  
Author(s):  
Delphine Mallet ◽  
Laurent Wantiez ◽  
Soazig Lemouellic ◽  
Laurent Vigliola ◽  
Dominique Pelletier
Keyword(s):  
Species Richness ◽  
Coral Reef ◽  
Reef Fish ◽  
Visual Census ◽  
Underwater Visual Census

scholarly journals Experimental reef communities persist under future ocean acidification and warming

2021 ◽  
Author(s):  
Christopher Jury ◽  
Keisha Bahr ◽  
Evan Barba ◽  
Russell Brainard ◽  
Annick Cros ◽  
...  
Keyword(s):  
Experimental Study ◽  
Species Richness ◽  
Coral Reef ◽  
Coral Reefs ◽  
Ocean Acidification ◽  
Community Composition ◽  
Functional State ◽  
Reef Communities ◽  
Paris Climate Agreement

Abstract Coral reefs are among the most sensitive ecosystems affected by ocean acidification and warming, and are predicted to shift from net accreting calcifier-dominated systems to net eroding algal-dominated systems over the coming decades. Here we present a long-term experimental study examining the responses of entire mesocosm coral reef communities to acidification (-0.2 pH units), warming (+ 2°C), and combined future ocean (-0.2 pH, + 2°C) treatments. We show that under future ocean conditions, net calcification rates declined yet remained positive, corals showed reduced abundance yet were not extirpated, and community composition shifted while species richness was maintained. Our results suggest that under Paris Climate Agreement targets, coral reefs could persist in an altered functional state rather than collapse.

scholarly journals KONDISI IKAN KARANG FAMILI CHAETODONTIDAE DI DAERAH PERLINDUNGAN LAUT DESA BAHOI KECAMATAN LIKUPANG BARAT KABUPATEN MINAHASA UTARA

2015 ◽  
Vol 2 (3) ◽  
pp. 92
Author(s):  
Jacqline Laikun ◽  
Ari B Rondonuwu ◽  
Unstain N.W.J. Rembet
Keyword(s):  
Spatial Distribution ◽  
Coral Reef ◽  
Coral Reefs ◽  
Protected Areas ◽  
Reef Fish ◽  
Marine Protected Areas ◽  
Visual Census ◽  
Fish Family ◽  
Marine Life ◽  
Reef Condition

The coral reefs are a sundry of marine life. Which one is reef fish in family Chaetodontidae. This fish is  indicator of the coral reef condition. The aim from the research is : discover of spatial distribution of the reef fish family Chaetodontidae and find out of the intercourse of reef fish family Chaetodontidae with the coral reef presence based on growth of coral form. The research was do in the coral reef at Marine Protected Areas in Bahoi Village District of West Likupang North Minahasa Regency, on Tuesday, December 23rd, 2014. The research is using to do the surveying method. The data is collecting distribution of the fish Chaetodontidae (amount from species and individuals to using by technic visual census). The total of reef fish family Chaetodontidae those found in Marina Protected Areas in Bahoi Village is about 20 species, with total of the individuals at a depth of 3 meters and 10 meters is (56,66 and 57,33 individuals/150m2). Keywords : Coral reefs, Chaetodontidae, Bahoi   ABSTRAK Terumbu karang merupakan tempat berbagai macam biota laut. Salah satu Ikan karang adalah ikan famili Chaetodontidae. Ikan ini merupakan ikan indikator terumbu karang. Tujuan dari penelitian ini : mengetahui kelimpahan dari ikan karang famili Chaetodontidae. Penelitian ini dilakukan di Daerah Perlindungan Laut Desa Bahoi Kecamatan Likupang Barat Kabupaten Minahasa Utara, pada hari selasa, tanggal 23 Desember 2014. Penelitian ini menggunakan metode survey. Data yang dikumpulkan adalah kelimpahan ikan Chaetodontidae (Jumlah spesies dan individu dengan menggunakan teknik sensus visual). Jumlah ikan karang famili Chaetodontidae yang di temukan di Daerah Perlindungan Laut Desa Bahoi berjumlah 20 spesies, dengan jumlah individu pada kedalaman 3 meter dan 10 meter berjumlah (56,66 individu/150m2 dan 57,33/150m2 individu). Kata kunci : Terumbu karang, Chaetodontidae, Bahoi 1Bagian dari skripsi 2Mahasiswa Program Studi Manajemen Sumberdaya Perairan FPIK-UNSRAT 3Staf pengajar Fakultas Perikanan dan Ilmu Kelautan Universitas Sam Ratulangi

scholarly journals Abundance of Herbivorous Fish at Fish Apartment in Tangah Island Coastal Waters of Pariaman City, West Sumatera

2019 ◽  
Vol 6 (1) ◽  
pp. 97
Author(s):  
Suci Frimanozi ◽  
Indra Junaidi Zakaria ◽  
Jabang Nurdin
Keyword(s):  
Coral Reef ◽  
Coral Reefs ◽  
Habitat Quality ◽  
Coastal Waters ◽  
Herbivorous Fish ◽  
Coral Recruitment ◽  
Visual Census ◽  
West Sumatra ◽  
And Control ◽  
Reef Condition

Herbivorous fish have an influence on habitat quality and a major factor in determining coral reef community. This herbivorous fish used as indicator of  monitoring refers to reef resilience since of its ability to retain and restore the coral reef condition after disturbance. The presence of herbivores is important in influencing succession of algae, it can reduce and control algae on coral reefs. It’s causes in the availability of space or substrate for corals to recruit. So the research conducted that aims to know the abundance of herbivorous fish in fish apartment as one indicator of monitoring based on endurance. This study had conducted after six months of fish apartment placed in the coastal waters of Tangah Island, Pariaman City, West Sumatra. Then, the observation had done every month for six months in July 2015 - January 2016 at the location of the fish apartment. Observation abundance of herbivorous fish had done by visual census method at fish apartment location. From the results of observations for six months found 10 species of herbivorous fish with total as many as 289 individuals. Zebrasoma scopas is a species with the most individuals than 97 individu. However, to see the effect of herbivorous fish on coral recruitment in fish apartment needs to do further research. Keywords: abundance, herbivorous fish, fish apartment

scholarly journals FISH DIVERSITY OF GHODAGHODI LAKE IN KAILALI, FAR-WEST NEPAL

2017 ◽  
Vol 22 (1) ◽  
pp. 120-126
Author(s):  
Dipendra Joshi ◽  
Bijaya K. C.
Keyword(s):  
Species Richness ◽  
Community Structure ◽  
Fish Species ◽  
Diversity Index ◽  
Fish Diversity ◽  
Channa Striatus ◽  
Illegal Fishing ◽  
Dominant Fish ◽  
Fish Catch ◽  
Excessive Proliferation

Ghodaghodi Lake is an ox-bow perennial lake of Ghodaghodi Lake Complex, situated in Kailali district. The present study was conducted to understand the fish diversity, community structure and distribution pattern in Ghodaghodi Lake. A total of 13 fish species were recorded from the different section of Ghodaghodi Lake, belonging to five order, eight family and eleven genera. According to fish catch the dominant order and family of Ghodaghodi Lake were found to be Cypriniformes (40%) and Cyprinidae (40%) respectively. The dominant fish species of Ghodaghodi Lake was Labeo gonius followed by Mystus tengara, Nandus nandus and Channa striatus. The highest diversity index (2.46), species richness (6.14) and evenness (0.96) of fish were recorded from station III during the month of January. Lowest diversity index (1.75) and evenness (0.90) was found in station II and during the month of October (2.25 and 0.88). Similarly, lowest species richness was found in station I (3.91) and during the month of July (5.82). Fish diversity and number in Ghodaghodi Lake were found to have decreased. This could be due to pollution, illegal fishing and excessive proliferation of aquatic weeds.Journal of Institute of Science and TechnologyVolume 22, Issue 1, July 2017, page: 120-126

scholarly journals Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6379 ◽  
Author(s):  
Joseph D. DiBattista ◽  
James D. Reimer ◽  
Michael Stat ◽  
Giovanni D. Masucci ◽  
Piera Biondi ◽  
...  
Keyword(s):  
Coral Reef ◽  
Coral Reefs ◽  
Indicator Species ◽  
18S Rrna ◽  
Spatial Scales ◽  
Environmental Dna ◽  
Marine Biodiversity ◽  
Depth Gradient ◽  
Coral Reef Ecosystems ◽  
Eukaryotic Organisms

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.

Sign in / Sign up

Export Citation Format

Share Document