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 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 Testing the performance of environmental DNA metabarcoding for surveying highly diverse tropical fish communities: A case study from Lake Tanganyika

2019 ◽  
Vol 2 (1) ◽  
pp. 24-41 ◽  
Author(s):  
Christopher J. Doble ◽  
Helen Hipperson ◽  
Walter Salzburger ◽  
Gavin J. Horsburgh ◽  
Chacha Mwita ◽  
...  
Keyword(s):  
Lake Tanganyika ◽  
Fish Communities ◽  
Environmental Dna ◽  
Tropical Fish ◽  
Dna Metabarcoding

scholarly journals Mapping biodiversity hotspots of fish communities in subtropical streams through environmental DNA

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rosetta C. Blackman ◽  
Maslin Osathanunkul ◽  
Jeanine Brantschen ◽  
Cristina Di Muri ◽  
Lynsey R. Harper ◽  
...  
Keyword(s):  
Large Scale ◽  
Fish Communities ◽  
Environmental Dna ◽  
River Network ◽  
Fish Diversity ◽  
Conservation Areas ◽  
Anthropogenic Pressures ◽  
Sampling Campaign ◽  
Chao Phraya River ◽  
River Catchments

AbstractLarge tropical and subtropical rivers are among the most biodiverse ecosystems worldwide, but also suffer from high anthropogenic pressures. These rivers are hitherto subject to little or no routine biomonitoring, which would be essential for identification of conservation areas of high importance. Here, we use a single environmental DNA multi-site sampling campaign across the 200,000 km2 Chao Phraya river basin, Thailand, to provide key information on fish diversity. We found a total of 108 fish taxa and identified key biodiversity patterns within the river network. By using hierarchical clustering, we grouped the fish communities of all sites across the catchment into distinct clusters. The clusters not only accurately matched the topology of the river network, but also revealed distinct groups of sites enabling informed conservation measures. Our study reveals novel opportunities of large-scale monitoring via eDNA to identify relevant areas within whole river catchments for conservation and habitat protection.

scholarly journals Monitoring fish communities through environmental DNA metabarcoding in the fish pass system of the second largest hydropower plant in the world

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Giorgi Dal Pont ◽  
Camila Duarte Ritter ◽  
Andre Olivotto Agostinis ◽  
Paula Valeska Stica ◽  
Aline Horodesky ◽  
...  
Keyword(s):  
Fish Communities ◽  
Environmental Dna ◽  
Hydropower Plant ◽  
Southeastern Brazil ◽  
Fish Diversity ◽  
Pass System ◽  
Fish Pass ◽  
Dna Metabarcoding ◽  
The World ◽  
The Impact

AbstractThe Itaipu Hydroelectric Power Plant is the second largest in the world in power generation. The artificial barrier created by its dam imposes an obstacle for fish migration. Thus, in 2002, a fish pass system, named Piracema Channel, was built to allow fish to access areas upstream of the reservoir. We tested the potential of environmental DNA metabarcoding to monitor the impact of both the dam and associated fish pass system in the Paraná River fish communities and to compare it with traditional monitoring methods. Using a fragment of the 12S gene, we characterized richness and community composition based on amplicon sequence variants, operational taxonomic units, and zero-radius OTUs. We combined GenBank and in-house data for taxonomic assignment. We found that different bioinformatics approaches showed similar results. Also, we found a decrease in fish diversity from 2019 to 2020 probably due to the recent extreme drought experienced in southeastern Brazil. The highest alpha diversity was recorded in the mouth of the fish pass system, located in a protected valley with the highest environmental heterogeneity. Despite the clear indication that the reference databases need to be continuously improved, our results demonstrate the analytical efficiency of the metabarcoding to monitor fish species.

scholarly journals Diversity and Structure of the Ichthyologic Communities in the Diving Sites in Holguin (Cuba)

2020 ◽  
Vol 22 (3) ◽  
pp. 57-82
Author(s):  
Enrique Reynaldo De La Cruz ◽  
María Eugenia Vega Cendejas ◽  
Sheila Rodríguez Machado ◽  
Franklin Garcia Fernández ◽  
Antonio Vega Torres
Keyword(s):  
Species Richness ◽  
Coral Reefs ◽  
Marine Fish ◽  
Fish Species ◽  
Fish Communities ◽  
Reef System ◽  
Poor State ◽  
Number Of Species

Abstract This study is aimed to determine the diversity and structure of the ichthyologic communities in the coral reefs of Holguín, Cuba. A total of 85 fish species were recorded, including in 32 families and 53 genera. Low species richness and equitability were estimated at different sampling sites throughout the reef system. Cadena de Vita and Canto Chiquito are the sites with the highest number of species 47 and 46 respectively. Cueva 1 and Punta Naranjo were the places with the highest equitability 0.76. Replacement of fish species among the reef sites studied is poor. Canto Azul with Canto Pionero and La Llanita, sharing 29 species. These results reflect a poor state of conservation of the marine fish communities in Holguín.

scholarly journals MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

2015 ◽  
Vol 2 (7) ◽  
pp. 150088 ◽  
Author(s):  
M. Miya ◽  
Y. Sato ◽  
T. Fukunaga ◽  
T. Sado ◽  
J. Y. Poulsen ◽  
...  
Keyword(s):  
Fish Species ◽  
Survey Methods ◽  
Hypervariable Region ◽  
Environmental Dna ◽  
Pcr Primers ◽  
12S Rrna ◽  
Rrna Gene ◽  
Sufficient Information ◽  
Diverse Range ◽  
Spatial And Temporal Scales

We developed a set of universal PCR primers (MiFish-U/E) for metabarcoding environmental DNA (eDNA) from fishes. Primers were designed using aligned whole mitochondrial genome (mitogenome) sequences from 880 species, supplemented by partial mitogenome sequences from 160 elasmobranchs (sharks and rays). The primers target a hypervariable region of the 12S rRNA gene (163–185 bp), which contains sufficient information to identify fishes to taxonomic family, genus and species except for some closely related congeners. To test versatility of the primers across a diverse range of fishes, we sampled eDNA from four tanks in the Okinawa Churaumi Aquarium with known species compositions, prepared dual-indexed libraries and performed paired-end sequencing of the region using high-throughput next-generation sequencing technologies. Out of the 180 marine fish species contained in the four tanks with reference sequences in a custom database, we detected 168 species (93.3%) distributed across 59 families and 123 genera. These fishes are not only taxonomically diverse, ranging from sharks and rays to higher teleosts, but are also greatly varied in their ecology, including both pelagic and benthic species living in shallow coastal to deep waters. We also sampled natural seawaters around coral reefs near the aquarium and detected 93 fish species using this approach. Of the 93 species, 64 were not detected in the four aquarium tanks, rendering the total number of species detected to 232 (from 70 families and 152 genera). The metabarcoding approach presented here is non-invasive, more efficient, more cost-effective and more sensitive than the traditional survey methods. It has the potential to serve as an alternative (or complementary) tool for biodiversity monitoring that revolutionizes natural resource management and ecological studies of fish communities on larger spatial and temporal scales.

scholarly journals Mapping biodiversity hotspots of fish communities in subtropical streams through environmental DNA

2021 ◽  
Vol 4 ◽  
Author(s):  
Rosetta Blackman ◽  
Maslin Osathanunkula ◽  
Jeanine Brantschen ◽  
Cristina Di Muri ◽  
Lynsey Harper ◽  
...  
Keyword(s):  
Large Scale ◽  
Global Climate ◽  
Fish Communities ◽  
Environmental Dna ◽  
River Network ◽  
Fish Diversity ◽  
Protection Measures ◽  
Alpha And Beta Diversity ◽  
Sampling Campaign ◽  
Chao Phraya River

Tropical and subtropical freshwater habitats are among the most biodiverse ecosystems worldwide, containing a characteristic fauna and high numbers of endemic species. However, exploitation of organisms, global climate change, pollution and the introduction of invasive species are severely threatening this diversity. Implementation of appropriate conservation and protection measures in tropical freshwater systems depends on comprehensive knowledge of state and change in biodiversity, which however, has been barely feasible due to logistic, technical and taxonomic challenges abound in tropical and subtropical ecosystems. Here we use a single environmental DNA (eDNA) multi-site sampling campaign distributed evenly through the 200,000 km2 Chao Phraya river basin, Thailand, to provide key information on freshwater fish diversity. We found a total of 108 fish taxa and identified key biodiversity patterns within the river network with respect to alpha- and beta-diversity patterns. By using a hierarchical clustering, we grouped the fish communities of all sites across the catchment into distinct clusters. Mapping these clusters over the catchment not only accurately matched the topology of the river network, but also revealed distinct groups of sites which should each be considered of high conservation value. Our study demonstrates a key application of large-scale monitoring (via eDNA) to identify distinct areas within a catchment for conservation and habitat protection.

scholarly journals Contrasting patterns in the abundance of fish communities targeted by fishers on two coral reefs in southern Mozambique

2020 ◽  
Vol 42 (1) ◽  
pp. 95-107
Author(s):  
T Sancelme ◽  
J Goetze ◽  
S Jaquemet ◽  
MG Meekan ◽  
A Flam ◽  
...  
Keyword(s):  
Coral Reefs ◽  
Fish Communities

scholarly journals Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tatsuhiko Hoshino ◽  
Ryohei Nakao ◽  
Hideyuki Doi ◽  
Toshifumi Minamoto
Keyword(s):  
Fish Species ◽  
High Throughput Sequencing ◽  
Correlation Coefficients ◽  
Environmental Dna ◽  
Digital Pcr ◽  
Absolute Quantification ◽  
Taqman Probe ◽  
Individual Species ◽  
Natural Environments ◽  
Target Sequence

AbstractThe combination of high-throughput sequencing technology and environmental DNA (eDNA) analysis has the potential to be a powerful tool for comprehensive, non-invasive monitoring of species in the environment. To understand the correlation between the abundance of eDNA and that of species in natural environments, we have to obtain quantitative eDNA data, usually via individual assays for each species. The recently developed quantitative sequencing (qSeq) technique enables simultaneous phylogenetic identification and quantification of individual species by counting random tags added to the 5′ end of the target sequence during the first DNA synthesis. Here, we applied qSeq to eDNA analysis to test its effectiveness in biodiversity monitoring. eDNA was extracted from water samples taken over 4 days from aquaria containing five fish species (Hemigrammocypris neglectus, Candidia temminckii, Oryzias latipes, Rhinogobius flumineus, and Misgurnus anguillicaudatus), and quantified by qSeq and microfluidic digital PCR (dPCR) using a TaqMan probe. The eDNA abundance quantified by qSeq was consistent with that quantified by dPCR for each fish species at each sampling time. The correlation coefficients between qSeq and dPCR were 0.643, 0.859, and 0.786 for H. neglectus, O. latipes, and M. anguillicaudatus, respectively, indicating that qSeq accurately quantifies fish eDNA.

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