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138 results for “fish metabarcoding”
F I G U R E 3 in The future of fish-based ecological assessment of European rivers: from traditional EU Water Framework Directive compliant methods to eDNA metabarcoding-based approaches
F I G U R E 3 Comparison of trait-based metrics expressed in relative number of individuals computed from eDNA () and traditional electro-fishing (TEF;) samples in the five river stretches (RS), A, B, C, D and E. Trait categories: BEN, benthic; EUR, eurytopic; INS, insectivorous; OMN, omnivorous; PHY, phytophilic; POT, potamodromous; RHE, rheophilic; TOL, tolerant; PEL pelagic. Significance of the differences between eDNA and TEF metrics are shown: ns, not significant (P> 0.05)
F I G U R E 4 in The future of fish-based ecological assessment of European rivers: from traditional EU Water Framework Directive compliant methods to eDNA metabarcoding-based approaches
F I G U R E 4 Boxplots (, median value;, interquartile range;, full range;, outliers) showing the variability in the eDNAadapted fish index (six metrics) computed at three sites (Brangues, Rhins and Usses) where 10 eDNA water samples were collected once. At each site, the eDNA-based six-metric fish index was computed for each of the 45 possible pairs of samples
F I G U R E 2 in The future of fish-based ecological assessment of European rivers: from traditional EU Water Framework Directive compliant methods to eDNA metabarcoding-based approaches
F I G U R E 2 Comparison of trait-based metrics expressed in number of species computed from eDNA () and traditional electrofishing (TEF;) samples in the five river stretches (RS), A, B, C, D and E. Trait categories: BEN, benthic; EUR, eurytopic; INS, insectivorous; OMN, omnivorous; PHY, phytophilic; POT, potamodromous; RHE, rheophilic; TOL, tolerant; PEL pelagic. Significance of the differences between eDNA and TEF metrics are shown: P <0.05; P <0.01; ns, not significant (P> 0.05)
F I G U R E 1 in The future of fish-based ecological assessment of European rivers: from traditional EU Water Framework Directive compliant methods to eDNA metabarcoding-based approaches
F I G U R E 1 Sampling locations along river stretches (RS) A to E () of the main channel of the Rhône River, France, using both traditional electro-fishing (TEF) and eDNA., Sites sampled every 2 months (September 2015– August 2016);, sites where ten eDNA water samples (filtration capsules) were collected once;, sites located on the tributaries or the Rhône River itself sampled once for eDNA. The 10 metric fish index and the adapted six-metric fish index were computed at all sites with a black filled symbol within natural water bodies
Niche partitioning between planktivorous fish in the pelagic Baltic Sea assessed by DNA metabarcoding, qPCR and microscopy: Data and Analyses
<p class="MsoNormal"><span>Marine communities undergo rapid changes because of human-induced ecosystem pressures. The Baltic Sea pelagic food web has experienced several regime shifts during the past century, resulting in a system where competition between planktivorous mesopredators is assumed to be high. While the two clupeids sprat and herring reveal signs of competition, the stickleback population has increased drastically during the past decades. Here, we investigate diet overlap between the three dominating planktivorous fish in the Baltic Sea, utilizing DNA metabarcoding on the <em>18S rRNA</em> gene and the <em>COI </em>gene, targeted qPCR, and microscopy. Our results show niche differentiation between clupeids and stickleback and that rotifers play an important function in niche partitioning of stickleback, as a resource that is not being used, neither by the clupeids nor by other zooplankton. <span>We further show that all the diet assessment methods used in this study are consistent but DNA metabarcoding describes the plankton-fish link at the highest taxonomic resolution. </span>This study suggests that rotifers and other understudied soft-bodied prey may have an important function in the pelagic food web and that the growing population of pelagic stickleback is supported by the unutilized feeding niche offered by the rotifers.</span></p>
Data from: Using environmental DNA metabarcoding to monitor fish communities in small rivers and large brooks: Insights on the spatial scale of information
<p><span>Monitoring fish communities is central to the evaluation of ecological health of rivers. Not only presence/absence of species is important to assess, but also the species composition of local fish assemblages is a crucial parameter. Lotic fish communities are traditionally monitored via electrofishing, characterized by a known limited efficiency and high survey costs. The use of environmental DNA-based analyses could serve as a non-destructive alternative, but this approach requires further insights in practical sampling schemes incorporating transport and dilution of the eDNA fragments; as well as optimization of molecular detection in terms of predictive power and quality assurance. By introducing fifteen species known to occur in Belgian waters via a controlled cage experiment, we aim to extend the knowledge on streamreach of eDNA in small rivers and large brooks, as laid out in the European Water Framework Directive's water typology. Introducing fish communities in two transects of a species poor river characterized by contrasting river discharge rates, we found strong and significant correlations between the eDNA relative abundances and the relative biomass per species in the cage community. Despite a decreasing correlation over distance, the underlying community composition remained stable over a distance of 300 m up to 1 km downstream of the cages, depending on the river discharge rate. Such decrease in similarity between relative source biomass and the corresponding eDNA-based community profile with increasing distance downstream from the source, can partly be attributed to variation in species-specific eDNA persistence. Our findings offer novel insights on eDNA behaviour and characterization of riverine fish communities. We conclude that water sampled from a relatively small river offers an adequate snapshot of the total fish community composition occurring within an upstream perimeter ranging between 300 and 1000 meters. The potential application for other river systems is discussed in this study. </span></p>
Data for: Optimizing a metabarcoding marker portfolio for species detection from complex mixtures of globally diverse fishes
<p>DNA metabarcoding is used to enumerate and identify taxa in both environmental samples and tissue mixtures, but the effectiveness of particular markers depends on their sensitivity to the taxa involved. Using multiple primer sets that amplify different genes can mitigate biases in amplification efficiency, sequence resolution, and reference data availability, but few empirical studies have evaluated markers for complementary performance. Here, we assess the individual and joint performance of 22 markers for detecting species in a DNA pool of 98 species of marine and freshwater bony fishes from geographically and phylogenetically diverse origins. We find that a portfolio of four markers targeting 12S, 16S, and two regions of COI identifies 100% of reference taxa to family and nearly 60% to species. We then use these four markers to evaluate metabarcoding of heterogeneous tissue mixtures, using experimental fishmeal to test: 1) the tissue input threshold to ensure detection; 2) how read depth scales with tissue abundance; and 3) the effect of non-target material in the mixture on recovery of target taxa. We consistently detect taxa that make up >1% of fishmeal mixtures and can detect taxa at the lowest input level of 0.01%, but rare taxa (<1%) were detected inconsistently across markers and replicates. Read counts showed only a weak correlation with tissue input, suggesting they are not a reliable quantitative proxy for relative abundance. Despite the limitations arising from primer specificity and reference data availability, our results demonstrate that a modest portfolio of markers can perform well in detecting and identifying aquatic species in complex mixtures despite heterogeneity in tissue representation, phylogenetic affinities, and from a broad geographic range.</p>
Integration of environmental DNA metabarcoding technique to reinforce fish biodiversity assessments in seagrass ecosystems: A case study of Gazi Bay Seagrass meadows
<p><span>Assessing biodiversity in marine nearshore ecosystems is crucial for effective management, especially in the context of climate change and overexploitation of marine resources. Conventional methods often fall short in providing comprehensive information for managing seagrass ecosystems. However, the emergence of environmental DNA (eDNA) techniques has transformed the field by enabling non-invasive surveys that are cost-effective and provide detailed information with high resolution. In this study, we utilized eDNA to assess fish diversity and compared its effectiveness to conventional techniques such as catch assessment surveys and underwater surveys. </span>We sampled three habitats (A: mangrove-seagrass, B: seagrass only, and C: coral-seagrass) with 4 replicates. Site A recorded 8 fish species, site B had 16 species, and site C, characterized by coral and seagrass habitats, exhibited the highest fish diversity with 45 species (mean H' index = 2.455), underscoring its ecological importance. To ensure accurate taxonomic identification, we utilized an updated MiFish reference database containing a larger number of fish species compared to the initial library. This expanded reference database with 9,569 fish species, facilitated more precise identification and enhanced the reliability of our findings. Notably, the eDNA technique outperformed conventional methods by detecting 23 additional fish species that went undetected using traditional surveys. Moreover, our study documented five fish species previously unknown to occur within the study region, further emphasizing the value of eDNA analysis in uncovering hidden biodiversity. These findings strongly advocate for integrating eDNA techniques into the monitoring and assessment of biodiversity in shallow tropical habitats of the Western Indian Ocean. By leveraging eDNA surveys, we can gain valuable insights into fish diversity, discover hidden species, and make informed decisions for the conservation and management of these ecologically significant areas.</p>
Tidewater goby and estuarine fish records from seining, qPCR and metabarcoding data for Southern California estuaries in 2023
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Data from: Reduced sampling intensity through key sampling site selection for optimal characterization of riverine fish communities by eDNA metabarcoding
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Data from: Using environmental DNA metabarcoding to monitor fish communities in small rivers and large brooks: Insights on the spatial scale of information
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Niche partitioning between planktivorous fish in the pelagic Baltic Sea assessed by DNA metabarcoding, qPCR and microscopy: Data and Analyses
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Data for: Optimizing a metabarcoding marker portfolio for species detection from complex mixtures of globally diverse fishes
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Integration of environmental DNA metabarcoding technique to reinforce fish biodiversity assessments in seagrass ecosystems: A case study of Gazi Bay Seagrass meadows
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Effects of sampling seasons and locations on fish environmental DNA metabarcoding in dam reservoirs
<p>Environmental DNA (eDNA) analysis has seen rapid development in the last decade, as a novel biodiversity monitoring method. Previous studies have evaluated optimal strategies, at several experimental steps of eDNA metabarcoding, for the simultaneous detection of fish species. However, optimal sampling strategies, especially the season and the location of water sampling, have not been evaluated thoroughly. To identify optimal sampling seasons and locations, we performed sampling monthly or at two-monthly intervals throughout the year in three dam reservoirs. Water samples were collected from 15 and 9 locations in the Miharu and Okawa dam reservoirs in Fukushima Prefecture, respectively, and 5 locations in the Sugo dam reservoir in Hyogo Prefecture, Japan. One liter of water was filtered with glass-fiber filters and eDNA was extracted. By performing MiFish metabarcoding, we successfully detected a total of 21, 24, and 22 fish species in Miharu, Okawa, and Sugo reservoirs, respectively. From these results, the eDNA metabarcoding method had a similar level of performance compared to conventional long-term data. Furthermore, it was found to be effective in evaluating entire fish communities. The number of species detected by eDNA survey peaked in May in Miharu and Okawa reservoirs, and in March and June in Sugo reservoir, which corresponds with the breeding seasons of many of fish species inhabiting the reservoirs. In addition, the number of detected species was significantly higher in shore, compared to offshore samples in the Miharu reservoir, and a similar tendency was found in the other two reservoirs. Based on these results, we can conclude that the efficiency of species detection by eDNA metabarcoding could be maximized by collecting water from shore locations during the breeding seasons of the inhabiting fish. These results will contribute in the determination of sampling seasons and locations for fish fauna survey via eDNA metabarcoding, in the future.</p>
Bioinformatic pipeline from: Increasing confidence for discerning species and population compositions from metabarcoding assays of environmental samples: case studies of fishes in the Laurentian Great Lakes and Wabash River
<p>Community composition data are essential for conservation management, facilitating identification of rare native and invasive species, along with abundant ones. However, traditional capture-based morphological surveys require considerable taxonomic expertise, are time consuming and expensive, can kill rare taxa and damage habitats, and often are prone to false negatives. Alternatively, metabarcode assays can be used to assess the genetic identity and compositions of entire communities from environmental samples, comprising a more sensitive, less damaging, and relatively time- and cost-efficient approach. However, there is a trade-off between the stringency of bioinformatic filtering needed to remove false positives and the potential for false negatives. The present investigation thus evaluated use of four mitochondrial (mt) DNA metabarcode assays and a customized bioinformatic pipeline to increase confidence in species identifications by removing false positives, while achieving high detection probability. Positive controls were used to calculate sequencing error, and results that fell below those cutoff values were removed, unless found with multiple assays. The performance of this approach was tested to discern and identify North American freshwater fishes using lab experiments (mock communities and aquarium experiments) and processing of a bulk ichthyoplankton sample. The method then was applied to field environmental (e)DNA water samples taken concomitant with electrofishing surveys and morphological identifications. This protocol detected 100% of species present in concomitant electrofishing surveys in the Wabash River and an additional 21 that were absent from traditional sampling. Using single 1 L water samples collected from just four locations, the metabarcoding assays discerned 73% of the total fish species that were discerned in comparison to four months of an extensive electrofishing river survey in the Maumee River, along with an additional nine species. In both rivers, total fish species diversity was best resolved when all four metabarcode assays were used together, which identified 35 additional species missed by electrofishing. Ecological distinction and diversity levels among the fish communities also were better resolved with the metabarcode assays than with morphological sampling and identifications, especially with the combined assays. At the population-level, metabarcode analyses targeting the invasive round goby <i>Neogobius melanostomus</i> and the silver carp <i>Hypophthalmichthys molitrix</i> identified all population haplotype variants found using Sanger sequencing of morphologically sampled fish, along with additional intra-specific diversity, meriting further investigation. Overall findings demonstrated that the use of multiple metabarcode assays and custom bioinformatics that filter potential error from true positive detections improves confidence in evaluating biodiversity.</p>
Data from: Dietary partitioning among three cryptobentic reef fish mesopredators revealed by visual analysis, metabarcoding of gut content, and stable isotope analysis
<p>Understanding how mesopredators partition their diet and the identity of consumed prey can assist in understanding the ecological role predators and prey play in ecosystem trophodynamics. Here, we assessed the diet of three common coral reef mesopredators; <em>Pseudochromis flavivertex</em>, <em>Pseudochromis fridmani</em>, and <em>Pseudochromis olivaceus</em> from the family Pseudochromidae, commonly known as dottybacks, using a combination of i) visual stomach content analysis, ii) stomach content DNA metabarcoding (18S, COI), and iii) stable isotope analysis (δ<sup>15</sup>N, δ<sup>13</sup>C). In addition, <em>P. flavivertex</em> is found in two distinct color morphs in the Red Sea, providing an opportunity to analyze intra-morph differences. These techniques revealed partitioning in the dietary composition and resource use among species. Arthropods comprised the main dietary component of <em>P. flavivertex</em> (18S > 60%; COI > 10%), and <em>P. olivaceus</em> (18S = 57.2%) while <em>P. fridmani</em> ingested predominantly mollusks (18S = 51.3%, COI = 24.6%). Despite being small predators, microplastics were found in the gut content of some of these fishes. Stable isotope analysis showed differences in species' isotopic niche breadth and trophic position. <em>Pseudochromis olivaceus</em> presented the largest isotopic niche (SEA<sub>C</sub> = 1.61‰<sup>2</sup>), while <em>P. fridmani</em> showed the smallest isotopic niche (SEA<sub>C</sub> = 0.45‰<sup>2</sup>) among species. Although the two techniques used for stomach content analysis did not show differences in the diet within color morphs of <em>P. flavivertex</em>, they differed in the isotopic niche and resource use. Despite our limited sampling, our findings provide evidence of species-specific differences in the trophic ecology of dottybacks and demonstrate their important role as predators of cryptic invertebrates and small fishes. This study highlights the importance of combining several approaches (short-term: visual analysis and DNA metabarcoding; and long-term: isotope analysis) when assessing the feeding habits of coral reef fish, as they provide complementary information necessary to delimit their niches and understand the role that small mesopredators play in coral reef ecosystems.</p>
Metabarcoding to decipher the fish diet of Eurasian otters and seals
<p><span>Long-lived top predators shape biodiversity structure in their ecosystems and predator-prey interactions are critical in decoding how communities function. </span><span>Studies on the foraging ecology of seals and Eurasian otters in Western Europe are outdated and most studies solely performed traditional hard part analysis. </span><span>Molecular metabarcoding can be used as an innovative non-invasive diet analysis tool, which has proven efficient and complementary to hard part analysis, however lacking application in the </span><span>wider North Sea area. In this study, DNA from digesta, collected between 2014-2020, were used to identify fish species in the diet of 47 Eurasian otters, 54 harbour seals and 21 grey seals by applying a next-generation metabarcoding approach. A newly designed 16S rRNA primer, providing the best coverage of >130 local marine and freshwater fish species, was used to amplify prey DNA from seal scats and otter gut content sampled from the North Sea and regional freshwater bodies. Frequent fish species included</span><span> </span><span>tench</span><span>, ninespine stickleback and white bream in otters; hooknose and common roach in grey seals and Pleuronectidae and sand gobies in harbour seals. Bipartite network analysis showed a strong overlap of harbour and grey seal diets. Otter diet intersected with both seal species in terms of freshwater species. </span><span>This study provides new knowledge about dietary composition and community assemblage of fish prey in otters and seals in the North Sea and regional freshwaters, and a new molecular tool to elucidate predator-prey interactions and interspecies competition in complex and changing ecosystems under pressure from anthropogenic activities.</span></p>
Data from: Development and validation of targeted environmental DNA (eDNA) metabarcoding for early detection of 69 invasive fishes and aquatic invertebrates
<p>Invasive species are of concern due to their impacts on ecosystems and economies, but they pose significant control challenges. Environmental DNA (eDNA) is a powerful tool in the detection of aquatic organisms at low densities due to high sensitivity and ease of collection. Aquatic eDNA analyses have increased worldwide and are generally either applied to a few target species (quantitative PCR) or for broad taxonomic applications (metabarcoding). Here we describe the development and testing of a hybrid approach that utilized high sensitivity PCR primer sets and high-throughput sequencing (HTS), referred to as <em>targeted metabarcoding</em>, to detect 69 fishes and invertebrates. We identified target species based on reports of globally important invasive species and developed two independent PCR primers for each species (CO1 and a second mtDNA region). We assessed sensitivity and eDNA interference for all 138 primers (2 per species, 69 species) using standard end-point PCR and tested them on 10 eDNA samples spiked with various amounts of one or more of the target species' DNA. The sensitivity of the 138 primer sets ranged between 1.5×10<sup>-5</sup> and 2.64 ng template DNA (mean = 0.069 ng). Primers were also tested for interference effects using plankton eDNA to simulate field conditions. The inclusion of interfering plankton DNA reduced the sensitivity for most primer sets by one or more orders of magnitude (range 0 to 3). Overall, our targeted metabarcoding resulted in the detection of ~ 98% of species in the DNA spiked samples, and, perhaps more importantly, the HTS read count was positively related to the quantity of spiked DNA (P < 0.002). We envision this technique being particularly useful for the early detection of species at low population densities; however, there are diverse applications of targeted metabarcoding for monitoring aquatic community composition and quantifying ecosystem change and health.</p>
Data from: Environmental DNA metabarcoding reflects spatiotemporal patterns of fish community shifts in the Scheldt estuary
<p>Estuarine ecosystems face increasing anthropogenic pressures, necessitating effective monitoring methods to mitigate their impacts on the biodiversity they harbour. The use of environmental DNA (eDNA) based detection methods is increasingly recognized as a promising tool to complement other, potentially invasive monitoring techniques. Integrating such eDNA analyses into monitoring frameworks for large spatial ecosystems is still challenging and requires a deeper understanding of the scale and resolution at which eDNA patterns may offer insights in species presence and community composition space and time. The Scheldt estuary, characterized by its diverse habitats and complex currents, is one of the largest Western European tidal river systems. Until now, it remains challenging to obtain accurate information on fish communities living in and migrating through this large ecosystem, consequently confining our knowledge to specific locations. To explore the potential of eDNA-based monitoring, we simultaneously combine stow net fishing with eDNA metabarcoding, to assess the Scheldt estuary's fish communities in space and time. In total, we detected 71 fish species in the estuary using eDNA metabarcoding, partly overlapping with historic fish community data gathered at the different study locations and in contrast to only 42 species using stow net fishing during the same survey period. Community compositions found by both detection methods varied amongst sampling locations, driven by a clear correlation to the salinity gradient. Limited effects of sampling depth and tide were observed on the eDNA metabarcoding data, allowing a significant reduction of the eDNA sampling effort for future eDNA fish monitoring campaigns in this study system. Our results further demonstrate that seasonal shifts in fish species occurrence can be detected using eDNA metabarcoding. Combining eDNA metabarcoding and stow net fishing further enhances our understanding of this vital waterway's diverse fish populations, allowing a higher resolution and more efficient monitoring strategy.</p>
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Allen Brain Atlas
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