MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples

Fisheries Science, Год журнала: 2020, Номер 86(6), С. 939 - 970

Опубликована: Сен. 15, 2020

Abstract We reviewed the current methodology and practices of DNA metabarcoding approach using a universal PCR primer pair MiFish, which co-amplifies short fragment fish (approx. 170 bp from mitochondrial 12S rRNA gene) across wide variety taxa. This method has mostly been applied to biodiversity monitoring environmental (eDNA) shed and, coupled with next-generation sequencing technologies, enabled massively parallel several hundred eDNA samples simultaneously. Since publication its technical outline in 2015, this widely used various aquatic environments around six continents, MiFish primers have demonstrably outperformed other competing primers. Here, we progress over last 5 years highlight some case studies on marine, freshwater, estuarine communities. Additionally, discuss applications non-fish organisms, single-species detection systems, quantitative monitoring, bulk than eDNA. By recognizing strengths limitations, argue that is useful for ecosystem conservation strategies sustainable use fishery resources “ecosystem-based management” through continuous at multiple sites.

Язык: Английский

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Environmental DNA Metabarcoding: A Novel Method for Biodiversity Monitoring of Marine Fish Communities

Annual Review of Marine Science, Год журнала: 2021, Номер 14(1), С. 161 - 185

Опубликована: Авг. 5, 2021

Environmental DNA (eDNA) is genetic material that has been shed from macroorganisms. It received increased attention as an indirect marker for biodiversity monitoring. This article reviews the current status of eDNA metabarcoding (simultaneous detection multiple species) a noninvasive and cost-effective approach monitoring marine fish communities discusses prospects this growing field. coamplifies short fragments across wide variety taxa and, coupled with high-throughput sequencing technologies, allows massively parallel to be performed simultaneously dozens hundreds samples. can predict species richness in given area, detect habitat segregation biogeographic patterns small large spatial scales, monitor spatiotemporal dynamics communities. In addition, it anthropogenic impact on through evaluation their functional diversity. Recognizing strengths limitations will help ensure continuous at sites useful ecosystem conservation sustainable use fishery resources, possibly contributing achieving targets United Nations' Sustainable Development Goal 14 2030.

Язык: Английский

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Meta‐analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment

Molecular Ecology, Год журнала: 2022, Номер 31(6), С. 1820 - 1835

Опубликована: Янв. 25, 2022

Abstract DNA metabarcoding is increasingly used for the assessment of aquatic communities, and numerous studies have investigated consistency this technique with traditional morpho‐taxonomic approaches. These individual to assess diversity community structure organisms both in marine freshwater systems globally over last decade. However, a systematic analysis comparability effectiveness DNA‐based across all these has hitherto been lacking. Here, we performed first meta‐analysis available comparing methods measure biological key groups, including plankton, microphytobentos, macroinvertebrates, fish. Across 215 data sets, found that provides richness estimates are consistent those obtained using methods, at local regional scale. also generates species inventories highly congruent Contrastingly, microphytobenthos macroinvertebrates by showed pronounced differences missing some taxa but same time detecting otherwise overseen diversity. The method generally sufficiently advanced study composition fish communities replace more invasive methods. For smaller organisms, like plankton microphytobenthos, may continue give complementary rather than identical compared Systematic comparable collection will increase understanding different aspects complementarity, adequate interpretation results.

Язык: Английский

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eDNA metabarcoding detection of nearshore juvenile white sharks (Carcharodon carcharias) and prey fish communities

Journal of Experimental Marine Biology and Ecology, Год журнала: 2025, Номер 583, С. 152084 - 152084

Опубликована: Янв. 31, 2025

Язык: Английский

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Are we ready to track climate‐driven shifts in marine species across international boundaries? ‐ A global survey of scientific bottom trawl data

Global Change Biology, Год журнала: 2020, Номер 27(2), С. 220 - 236

Опубликована: Окт. 17, 2020

Marine biota are redistributing at a rapid pace in response to climate change and shifting seascapes. While changes fish populations community structure threaten the sustainability of fisheries, our capacity adapt by tracking projecting marine species remains challenge due data discontinuities biological observations, lack availability, mismatch between real distributions. To assess extent this challenge, we review global status accessibility ongoing scientific bottom trawl surveys. In total, gathered metadata for 283,925 samples from 95 surveys conducted regularly 2001 2019. We identified that 59% collected not publicly available, highlighting availability is most important redistributions under change. Given primary purpose provide independent inform stock assessment commercially populations, further highlight single do cover full range main commercial demersal species. An average 18 needed least 50% ranges, demonstrating importance combining multiple evaluate shifts. potential track transboundary show differences sampling schemes inconsistency can be overcome with spatio-temporal modeling follow density redistributions. light assessment, establish framework improving management conservation migrating directions improve encourage countries share survey data, vulnerabilities, support adaptation time climate-driven ocean changes.

Язык: Английский

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The future of biodiversity monitoring and conservation utilizing environmental DNA

Environmental DNA, Год журнала: 2020, Номер 3(1), С. 3 - 7

Опубликована: Дек. 21, 2020

Technology is often looked to as a means an end. The explosion in use of environmental DNA (eDNA) for species detection great example technological discovery that fueling new possibilities study and quantify the state change, but also recovery resiliency biosphere. articles herein contribute Future Biodiversity Monitoring Conservation Utilizing Environmental DNA, by tackling methodological advances validation, shedding light on ecology different contexts, revealing eDNA observe behavior unravel diversity large hyperdiverse ecosystems. On applied side, several contributions demonstrate detecting invasions restoration populations after habitat restoration. Lastly, make efforts reduce learning curve methods inspire people about biodiversity through using surveys education. Thus, this special issue shows myriad ways which scientific community continually improving utility surveying purpose measuring, monitoring, understanding At forefront, researchers are moving beyond assess population information such abundance testing potential derive functional from RNA. Measuring population's fundamental many conservation management questions. Spear et al. (2021) progress quantities measured water samples culturally economically important sportfish, walleye, 22 lakes Wisconsin. Their observed correlation among best yet natural systems compares with adult biomass estimated mark–recapture surveys. demonstrating concentrations can have strong relationship range uncertainty similar conventional methods. They urge, though, demographic still unknown. But recent studying RNA may change outlook. Tsuri push forward idea specific tissues produce certain messenger RNAs, typing them, we could identify source their production. By tank experiments zebrafish, they mRNAs gills, skin, intestine. While proof-of-concept study, be built technique mRNA-typing eRNA future dig into not only presence abundance, even developmental state, stress, likely other aspects demography when informed biology. Several advancements continue build our established goal improve accuracy, sensitivity, better sampling design habitats. For single species, Williams compare CRISPR-Cas assay against standard qPCR approach Atlantic salmon across two watersheds northern Canada. Both showed agreement, few sites agreement opposite results. Advantages assays done isothermal reactions inhibited assays. latter need highly time-consuming purification These advantages positive more rapid onsite abilities useful contexts. biomonitoring whole communities, challenges faced Leese (2021), derived method target benthic macroinvertebrates used quality assessment. first sequenced river system primers generally amplify both prokaryotic eukaryotic knowledge total then developed desired groups while maximizing differences site-specific nontarget diversity. amplification non-target substantially reduced recovered taxa exceeded detected base morphological identification. good Carraro modeling choice how optimally sample system. Basing model's predictions hydrological terms, strategies needed depending distribution river's catchment decay rates model predictions. Having greater guide effort species. making analysis practical monitoring tool, comparison sensitivity techniques fundamental. Afzali conducted trawling survey demersal fish Estuary Gulf Saint-Lawrence, Canada, compared results metabarcoding. produced 50% consensus relative abundances were significantly correlated each other. Boivin-Delisle gillnet Rupert River, found metabarcoding larger number Moreover, read had significant captured Polanco Fernández underwater visual census bays near Santa Marta, Colombia, wider taxonomic than higher efficiency smaller body sizes those inhabiting deeper water. Overall, it was provide comparable to, or sensitive than, variety To accurate inferences space time studied, environment itself especially extra-organismal source. River particularly understand transport dynamics flow almost immediately separate its individual. Thalinger caged experiment lateral longitudinal once released seasons. show changes seasonally order same location, conditions traits determining lotic environment. most studies focus aquatic systems, Kunadiya spiked soil persistence agricultural soil-borne plant pathogen, Phytophthora cinnamomi. Detection horticulture settings crops including avocado, pineapple, peach, chestnut, macadamia. type, inoculated persist up 378 days, whereas persisted short 1–3 days. This detections indicative presence, would inference recently present soil. Moving occurrence description, increasing showcasing applying gain insights comprises illustrative examples studies. reproductive biology obvious ecological component crucial understand, standpoint. challenging requires laborious work. In contribution, Tsuji Shibata combined experimental field observations spawning (reproductive) events spikes concentration medaka (Oryzias sp.). Besides spike spawning, magnitude depended activities. As such, demonstrates usefulness tool Another facet species' pertains feeding behaviors. Here, dietary plasticity consider key factor allowing cope changes. Yet, spatio-temporal variation diet has been investigated routinely, possibly because logistical constraints. Tournayre analyze prey content nearly 2000 fecal insectivorous horseshoe bat (Rhinolophus ferrumequinum) maternal colonies France. describing diet, tested whether landscape characteristics surrounding at times year influenced composition. much diverse reported previous studies, composed core shared all secondary varied colonies. prime illustration habits elusive Advancing measure broad diversity, population-level exemplified contributions. example, Ratcliffe areas Irish Celtic seas. Concurrent larval netting equivalent estimates richness 75% agreement. Klymus (2020) freshwater mussels unique mussel Clinch watershed southeastern United States. 19 eight federally endangered Oka remarkably high coral reef lagoon Okinawa, Japan. system, clear difference communities between reef's edge shore-side seagrass bed small lagoon, suggesting segregation. Palacios Mejia three primer sets detect fauna flora sediments Mojave Desert springs California, USA. successfully groups, composition data further improvements choices required these habitats complete detection. Székely sampled seawater Disko Bay, West Greenland, bowhead whales newly species-specific real-time PCR assay. observed, enabled them mtDNA control region Sanger sequenced, haplotypes. formed "footprint," where whale just started diving, marked success transect samples. demonstrations move powerful noninvasive usage reliability branches tree life. application evaluate activities emerging provides fast potentially reliable way monitor. advance arena, Duda multiple monitor over four years dam removal project Elwha Washington, Indigenous expanded migrating area upstream side removed non-native Brook Trout suggested expand due removal. Rasmussen fungi arthropod vineyard correspondence strategy integrated, organic, biodynamic. management-dependent resulted fields. Pearman surveillance marine nonindigenous harbors intensive trading increased achieved barcoding markers. continuing accumulation case illustrate biological communities' responses anthropogenic increase restoration/management measures aiming restore conserve complementary addition now undeniable. value being collected undermined current lack standardization guidelines, which, if adopted, allow rigor comparing points time. Minamoto summarize point published "Environmental Sampling Experiment Manual," under initiative Society Japan 2018. particular, authors introduce detailed described manual, selection sites, methods, filtration extraction, report manual will assist users conducting standardized basis collecting data. national international initiatives implement methodologies local monitoring. Leading what hopefully next step standardizing steps differ various protocols collection around world. context global declines facing; becoming urgent crucially engage scale crisis efficient achieve engagement initiatives. ages horizons participate measuring surroundings create awareness. Hupało explore feasibility sequencing rapidly urban educational purposes Norway. identifying 435 15 days performed people, nicely illustrates ease purposes. convincingly openly available resources, sequence raise awareness importance biodiversity. We want honor passing colleague friend dedicating Dr. Cameron R. Turner. His exceptional infused throughout included issue. building off instrumental framework summarized put forth 'Ecology eDNA' (Barnes & Turner, 2016) regarding structure, improvement managing work cited support hypotheses, observations, comparative his keen pushed forward. he no longer us, generated live way. None declared.

Язык: Английский

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Biodiversity assessment across a dynamic riverine system: A comparison of eDNA metabarcoding versus traditional fish surveying methods

Environmental DNA, Год журнала: 2021, Номер 3(6), С. 1247 - 1266

Опубликована: Июль 21, 2021

Abstract While many studies have considered the ability of eDNA to assess animal communities in lacustrine settings, fewer riverine systems, particularly those spanning environmental gradients present large river basins. Such dynamic systems are challenging for biomonitoring due differing transport distances rivers and effects chemistry. To address this challenge, we focused on Thames River system, UK, which has exceptional historical fish records providing a baseline test accuracy metabarcoding recovering community structure across both fresh tidal zones. Two primer sets targeting 12S CO1 regions were used capture catchment, from upper freshwaters mid estuary. was collected at 35 sites, 14 simultaneously paired with traditional surveys direct comparison. We demonstrated that consistently detected more freshwater species than methods, despite extensive sampling effort using latter. In contrast, did not perform as well approaches estuarine waters, although results included novel detection protected sea lamprey. further minor variations recovery all would impact assessment simple ecological models and, thus, some variability between should be viewed serious hindrance uptake. Rather, our findings support growing consensus can reliably detect habitats.

Язык: Английский

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Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems

Environmental DNA, Год журнала: 2021, Номер 3(6), С. 1113 - 1127

Опубликована: Июль 6, 2021

Abstract Through the development of environmental DNA (eDNA) metabarcoding, in situ monitoring organisms is becoming easier and promises a revolution our approaches to detect changes biodiversity over space time. A cornerstone eDNA approach primer pairs that allow amplifying specific taxonomic groups, which then used link sequence identification. Here, we propose framework for comparing regarding (a) their capacity bind amplify broad coverage species within target clade using silico PCR, (b) not only discriminate between but also genera or families, (c) specificity efficiency across variety environments. As case study, focus on two mitochondrial 12S pairs, MiFish‐U teleo, were designed fishes. We found performance PCRs high both teleo amplified more Actinopterygii, Chondrichthyes, Petromyzontomorphi than MiFish‐U. In contrast, discriminatory power species, genera, families higher likely associated with greater length fragments. The evaluation showed recovered richness compared tropical temperate freshwater environments, generally primers perform well monitor fish species. Since detected when together, those are best combination increase ability detection.

Язык: Английский

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Comparing eDNA metabarcoding primers for assessing fish communities in a biodiverse estuary

PLoS ONE, Год журнала: 2022, Номер 17(6), С. e0266720 - e0266720

Опубликована: Июнь 17, 2022

Metabarcoding of environmental DNA is increasingly used for biodiversity assessments in aquatic communities. The efficiency and outcome these efforts are dependent upon either de novo primer design or selecting an appropriate set from the dozens that have already been published. Unfortunately, there a lack studies directly compared efficacy different metabarcoding primers marine estuarine systems. Here we evaluate five commonly sets designed to amplify rRNA barcoding genes fishes compare their performance using water samples collected sites highly biodiverse Indian River Lagoon Florida. Three portion mitochondrial 12S gene (MiFish_12S, 171bp; Riaz_12S, 106 bp; Valentini_12S, 63 bp), one amplifies 219 bp 16S (Berry_16S), other 271 nuclear 18S (MacDonald_18S). vast majority reads (> 99%) generated assigned non-target (non-fish) taxa therefore this was omitted most analyses. Using conservative 99% similarity threshold species level assignments, detected comparable number (55 49, respectively) similarly high Shannon's diversity values Riaz_12S Berry_16S sets. Meanwhile, just 34 32 were MiFish_12S Valentini_12S sets, respectively. We able both bony cartilaginous four with (>99%) former. greatest elasmobranchs (six species) suggesting it may be suitable candidate detection sharks rays. Of total 76 fish identified across all datasets, combined three 85.5% (65 while combination 93.4% (71 species). These results highlight importance employing multiple as well target genomic regions. Moreover, our suggest widely adopted not best choice, rather found effective eDNA-based surveys system.

Язык: Английский

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Assessing the utility of marine filter feeders for environmental DNA (eDNA) biodiversity monitoring

Molecular Ecology Resources, Год журнала: 2023, Номер 23(4), С. 771 - 786

Опубликована: Янв. 4, 2023

Aquatic environmental DNA (eDNA) surveys are transforming how marine ecosystems monitored. The time-consuming preprocessing step of active filtration, however, remains a bottleneck. Hence, new approaches that eliminate the need for filtration required. Filter-feeding invertebrates have been proven to collect eDNA, but side-by-side comparative studies investigate similarity between aquatic and filter-feeder eDNA signals essential. Here, we investigated differences among four sources (water; bivalve gill-tissue; sponges; ethanol in which filter-feeding organisms were stored) along vertically stratified transect Doubtful Sound, New Zealand using three metabarcoding primer sets targeting fish vertebrates. Combined, detected 59 vertebrates, while concurrent diver observed eight species. There no significant alpha beta diversity water sponge both highly correlated. Vertebrate was successfully extracted from sponges stored, although reduced number species detected. Bivalve gill-tissue dissections, on other hand, failed reliably detect eDNA. Overall, our results show vertebrate obtained samples concordant. strong demonstrates potential as an additional tool eDNA-based biodiversity surveys, by enabling incorporation larger sample numbers reducing plastic waste, simplifying collection, cost-efficient alternative. However, note importance not detrimentally impact communities by, example, nonlethal subsampling, specimen cloning, or bycatch specimens.

Язык: Английский

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