scholarly journals Calibrating Environmental DNA Metabarcoding to Conventional Surveys for Measuring Fish Species Richness

2020 ◽  
Vol 8 ◽  
Author(s):  
Mary E. McElroy ◽  
Terra L. Dressler ◽  
Georgia C. Titcomb ◽  
Emily A. Wilson ◽  
Kristy Deiner ◽  
...  
Keyword(s):  
Species Richness ◽  
Fish Species ◽  
Environmental Dna ◽  
Dna Metabarcoding

scholarly journals Improving the detection of rare native fish species in environmental DNA metabarcoding surveys

2021 ◽  
Author(s):  
Jack Rojahn ◽  
Dianne M. Gleeson ◽  
Elise Furlan ◽  
Tim Haeusler ◽  
Jonas Bylemans
Keyword(s):  
Fish Species ◽  
Environmental Dna ◽  
Native Fish ◽  
Dna Metabarcoding

scholarly journals Environmental DNA metabarcoding reveals and unpacks a biodiversity conservation paradox in Mediterranean marine reserves

2021 ◽  
Vol 288 (1949) ◽  
Author(s):  
Emilie Boulanger ◽  
Nicolas Loiseau ◽  
Alice Valentini ◽  
Véronique Arnal ◽  
Pierre Boissery ◽  
...  
Keyword(s):  
Species Richness ◽  
Fish Species ◽  
Fish Assemblages ◽  
Marine Reserves ◽  
Marked Change ◽  
Environmental Dna ◽  
Biodiversity Loss ◽  
Conclusive Evidence ◽  
Anthropogenic Pressure ◽  
Local Species Richness

Although we are currently experiencing worldwide biodiversity loss, local species richness does not always decline under anthropogenic pressure. This conservation paradox may also apply in protected areas but has not yet received conclusive evidence in marine ecosystems. Here, we survey fish assemblages in six Mediterranean no-take reserves and their adjacent fishing grounds using environmental DNA (eDNA) while controlling for environmental conditions. We detect less fish species in marine reserves than in nearby fished areas. The paradoxical gradient in species richness is accompanied by a marked change in fish species composition under different managements. This dissimilarity is mainly driven by species that are often overlooked by classical visual surveys but detected with eDNA: cryptobenthic, pelagic, and rare fishes. These results do not negate the importance of reserves in protecting biodiversity but shed new light on how under-represented species groups can positively react to fishing pressure and how conservation efforts can shape regional biodiversity patterns.

scholarly journals Quantitative assessment of multiple fish species around artificial reefs combining environmental DNA metabarcoding and acoustic survey

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Masaaki Sato ◽  
Nariaki Inoue ◽  
Ryogen Nambu ◽  
Naoki Furuichi ◽  
Tomohito Imaizumi ◽  
...  
Keyword(s):  
Fish Species ◽  
Internal Standard ◽  
Environmental Dna ◽  
Artificial Reefs ◽  
Sampling Station ◽  
Biodiversity Monitoring ◽  
Dna Metabarcoding ◽  
Positive Correlations ◽  
Multiple Species ◽  
Echo Sounder

AbstractSince the early 1970s, many artificial reefs (ARs) have been deployed in Japanese coastal waters to create fisheries grounds. Recently, researchers began to use environmental DNA (eDNA) methods for biodiversity monitoring of aquatic species. A metabarcoding approach using internal standard DNAs [i.e., quantitative MiSeq sequencing (qMiSeq)] makes it possible to monitor eDNA concentrations of multiple species simultaneously. This method can improve the efficiency of monitoring AR effects on fishes. Our study investigated distributions of marine fishes at ARs and surrounding stations in the open oceanographic environment of Tateyama Bay, central Japan, using qMiSeq and echo sounder survey. Using the qMiSeq with 12S primers, we found higher quantities of fish eDNAs at the ARs than at surrounding stations and different fish species compositions between them. Comparisons with echo sounder survey also showed positive correlations between fish eDNA concentration and echo intensity, which indicated a highly localized signal of eDNA at each sampling station. These results suggest that qMiSeq is a promising technique to complement conventional methods to monitor distributions of multiple fish species.

scholarly journals Evaluation of biodiversity in estuaries using environmental DNA metabarcoding

2020 ◽  
Author(s):  
Hyojin Ahn ◽  
Manabu Kume ◽  
Yuki Terashima ◽  
Feng Ye ◽  
Satoshi Kameyama ◽  
...  
Keyword(s):  
Fish Species ◽  
Environmental Conditions ◽  
Environmental Dna ◽  
Aquatic Biodiversity ◽  
Non Invasive ◽  
Dna Metabarcoding ◽  
And Migration ◽  
Low Degrees ◽  
River Mouths ◽  
Rare Fishes

AbstractBiodiversity is an important parameter for the evaluation of the extant environmental conditions. Here, we used environmental DNA (eDNA) metabarcoding to investigate fish biodiversity in five different estuaries in Japan. Water samples for eDNA were collected from river mouths and adjacent coastal areas of two estuaries with high degrees of development (the Tama and Miya Rivers) and three estuaries with relatively low degrees of development (the Aka, Takatsu, and Sendai Rivers). A total of 182 fish species across 67 families were detected. Among them, 11 species occurred in all the rivers studied. Rare fishes including endangered species were successfully detected in rich natural rivers. Biodiversity was the highest in the Sendai River and lowest in the Tama River, reflecting the degree of human development along each river. Even though nutrient concentration was low in both the Aka and Sendai Rivers, the latter exhibited greater diversity, including many tropical or subtropical species, owing to its more southern location. Species composition detected by eDNA varied among rivers, reflecting the distribution and migration of fishes. Our results are in accordance with the ecology of each fish species and environmental conditions of each river, suggesting the potential of eDNA for non-invasive assessment of aquatic biodiversity.

scholarly journals Environmental DNA revealed the fish community of Hokkaido Island, Japan, after invasion by rainbow trout

2020 ◽  
Vol 8 ◽  
Author(s):  
Akio Imamura ◽  
Kana Hayami ◽  
Masayuki Sakata ◽  
Toshifumi Minamoto
Keyword(s):  
Invasive Species ◽  
Species Richness ◽  
Rainbow Trout ◽  
Fish Species ◽  
Seasonal Changes ◽  
Fish Community ◽  
Environmental Dna ◽  
Native Fish ◽  
Native Salmonids ◽  
Hokkaido Island

In freshwater ecosystems, invasive salmonid fishes can have a significant impact on native fish species. Detecting the invasion and its negative effects is critical for the conservation of native fish communities. We examined the species composition and seasonal changes in the freshwater fish community, including salmonids, on the Kamikawa Plain, Hokkaido Island, Japan, using environmental DNA (eDNA) metabarcoding. We detected 23 fish species in 176 samples collected from 16 sites over 12 months (October 2018 – August 2019). Between 11 and 20 species were detected at each site, including five native salmonids (Oncorhynchus masou, Oncorhynchus keta, Parahucho perryi, Salvelinus leucomaenis leucomaenis and Salvelinus malma krascheninnikova). The invasive alien rainbow trout Oncorhynchus mykiss was detected at all 16 sites and it was the most commonly detected salmonid. Although we found no obvious competitive exclusion of native salmonids by rainbow trout in the study area, the invasive species occurred more often and at more sites than any of the natives. We also determined the occurrence and seasonal changes in the fish community, classified as native salmonids, invasive rainbow trout, Cypriniformes and other benthic fishes. There were fewer species overall in winter, but the sites with higher species richness in winter were on the lower reaches of the river. In addition, we detected domestic invaders, such as the topmouth gudgeon, Pseudorasbora parva, although they were less prevalent than rainbow trout. These results show the effectiveness of eDNA metabarcoding, which can be used for surveying species richness at an ecosystem scale. In particular, the detection of the early stages of establishment and spread of invasive species can be achieved by eDNA monitoring.

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 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 Vascular plants are strong predictors of multi-taxon species richness

2018 ◽  
Author(s):  
Ane Kirstine Brunbjerg ◽  
Hans Henrik Bruun ◽  
Lars Dalby ◽  
Camilla Fløjgaard ◽  
Tobias G. Frøslev ◽  
...  
Keyword(s):  
Species Richness ◽  
Vascular Plants ◽  
Environmental Dna ◽  
Plant Species Richness ◽  
Carabid Beetles ◽  
Data Set ◽  
Total Species Richness ◽  
Dna Metabarcoding ◽  
Total Species ◽  
Positive Effect

AbstractPlants regulate soils and microclimate, provide substrate for heterotrophic taxa, are easy to observe and identify and have a stable taxonomy, which strongly justifies the use of plants as bioindicators in monitoring and conservation. However, insects and fungi make up the vast majority of species. Surprisingly, it remains untested whether plants are strong predictors of total multi-taxon species richness. To answer this question, we collected an extensive data set on species richness of vascular plants, bryophytes, macrofungi, lichens, plant-galling arthropods, gastropods, spiders, carabid beetles, hoverflies and OTU richness from environmental DNA metabarcoding. Plant species richness per se was a moderate predictor of richness of other taxa. Taking an ecospace approach to modelling, the addition of plant-derived bioindicators revealed 1) a consistently positive effect of plant richness on other taxa, 2) prediction of 12-55% of variation in other taxa and 48 % of variation in the total species richness.

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