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

Fisheries Science, Journal Year: 2020, Volume and Issue: 86(6), P. 939 - 970

Published: Sept. 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.

Language: Английский

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A Comprehensive Overview of Technologies for Species and Habitat Monitoring and Conservation

BioScience, Journal Year: 2021, Volume and Issue: 71(10), P. 1038 - 1062

Published: June 24, 2021

The range of technologies currently used in biodiversity conservation is staggering, with innovative uses often adopted from other disciplines and being trialed the field. We provide first comprehensive overview current (2020) landscape technology, encompassing for monitoring wildlife habitats, as well on-the-ground management (e.g., fighting illegal activities). cover both established (routinely deployed conservation, backed by substantial field experience scientific literature) novel or technology applications (typically at trial stage, only recently conservation), providing examples types. describe that deploy sensors are fixed portable, attached to vehicles (terrestrial, aquatic, airborne) animals (biologging), complemented a section on tracking. last two sections actuators computing (including web platforms, algorithms, artificial intelligence).

Language: Английский

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Meta‐analysis shows that environmental DNA outperforms traditional surveys, but warrants better reporting standards

Ecology and Evolution, Journal Year: 2021, Volume and Issue: 11(9), P. 4803 - 4815

Published: March 18, 2021

Decades of environmental DNA (eDNA) method application, spanning a wide variety taxa and habitats, has advanced our understanding eDNA underlined its value as tool for conservation practitioners. The general consensus is that methods are more accurate cost-effective than traditional survey methods. However, they formally approved just few species globally (e.g., Bighead Carp, Silver Great Crested Newt). We conducted meta-analysis studies directly compare with surveys to evaluate the assertion consistently "better."Environmental publications multiple or single macro-organism detection were identified using Web Science, by searching "eDNA" "environmental DNA" across papers published between 1970 2020. used, focal taxa, habitats surveyed, quantitative categorical results collated analyzed determine whether under what circumstances outperforms surveys.Results show cheaper, sensitive, detect This is, however, taxa-dependent, amphibians having highest potential survey. Perhaps most strikingly, 535 reviewed 49 quantified probability both three times likely give qualitative statements performance.

Language: Английский

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Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 873, P. 162322 - 162322

Published: Feb. 18, 2023

Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this only possible an in-depth overview of technological discussion pros cons available methods. We therefore conducted systematic literature review 407 peer-reviewed papers on aquatic published between 2012 2021. observed gradual increase in annual number publications from four (2012) 28 (2018), followed growth 124 This was mirrored tremendous diversification methods all aspects workflow. For example, freezing applied preserve filter samples, whereas we recorded 12 different preservation 2021 literature. Despite ongoing standardisation debate community, field seemingly moving fast opposite direction discuss reasons implications. Moreover, compiling largest PCR-primer database date, provide information 522 141 species-specific metabarcoding primers targeting wide range organisms. works as user-friendly 'distillation' primer that hitherto scattered across hundreds papers, list also reflects which taxa are commonly studied technology environments such fish amphibians, reveals groups corals, plankton algae under-studied. Efforts improve sampling extraction specificity reference databases crucial capture these ecologically important future surveys. In rapidly diversifying field, synthetises procedures can guide users towards best practice.

Language: Английский

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

Annual Review of Marine Science, Journal Year: 2021, Volume and Issue: 14(1), P. 161 - 185

Published: Aug. 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.

Language: Английский

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Conservation and the Genomics of Populations

Oxford University Press eBooks, Journal Year: 2022, Volume and Issue: unknown

Published: Feb. 10, 2022

Abstract Loss of biodiversity is among the greatest problems facing world today. Conservation and Genomics Populations gives a comprehensive overview essential background, concepts, tools needed to understand how genetic information can be used conserve species threatened with extinction, manage ecological or commercial importance. New molecular techniques, statistical methods, computer programs, principles, methods are becoming increasingly useful in conservation biological diversity. Using balance data theory, coupled basic applied research examples, this book examines phenotypic variation natural populations, principles mechanisms evolutionary change, interpretation from these conservation. The includes examples plants, animals, microbes wild captive populations. This third edition has been thoroughly revised include advances genomics contains new chapters on population genomics, monitoring, genetics practice, as well sections climate emerging diseases, metagenomics, more. More than one-third references were published after previous edition. Each 24 Appendix end Guest Box written by an expert who provides example presented chapter their own work. for advanced undergraduate graduate students genetics, resource management, biology, professional biologists policy-makers working wildlife habitat management agencies. Much will also interest nonprofessionals curious about role

Language: Английский

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Toward quantitative metabarcoding

Ecology, Journal Year: 2022, Volume and Issue: 104(2)

Published: Nov. 2, 2022

Amplicon-sequence data from environmental DNA (eDNA) and microbiome studies provide important information for ecology, conservation, management, health. At present, amplicon-sequencing studies-known also as metabarcoding studies, in which the primary consist of targeted, amplified fragments sequenced many taxa a mixture-struggle to link genetic observations underlying biology quantitative way, but applications require about or systems under scrutiny. As proliferate it becomes more develop ways make them ensure that their conclusions are adequately supported. Here we previously disparate sets techniques making such quantitative, showing polymerase chain reaction mechanism explains observed patterns amplicon general way. By modeling process through amplicon-sequence arise, rather than transforming post hoc, show how estimate starting proportions mixture taxa. We illustrate calibrate model using mock communities apply approach simulated series empirical examples. Our opens door improve use wide range public health, related fields.

Language: Английский

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The current state of eDNA research in freshwater ecosystems: are we shifting from the developmental phase to standard application in biomonitoring?

Hydrobiologia, Journal Year: 2022, Volume and Issue: 850(6), P. 1263 - 1282

Published: May 12, 2022

Abstract Environmental DNA (eDNA) has seen a massive increase in application freshwater systems with concurrent growth protocol developments and drive to gain better understanding of the ‘ecology’ eDNA. This raises question whether we are currently still an early, developmental phase eDNA-based assessments or already transitioning into more applied stage for biomonitoring. I conducted systematic literature review on 381 eDNA-focused studies targeting macro-organisms over last 5 years, assessing study goals, methods, target taxa design aspects. The results show biomonitoring-focused throughout while fraction investigating eDNA decreased. metabarcoding significantly increased applying qPCRs tentatively declined. A geographic inequality was observed concerning numbers goals biased towards global North. Descriptive increased, but in-field conventional methods combined revealed no trend. These shift application-focused work also reveal this field be developing. In transitional phase, practitioners need ensure consistency data comparability long-term monitoring programmes.

Language: Английский

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Applications of environmental DNA (eDNA) to detect subterranean and aquatic invasive species: A critical review on the challenges and limitations of eDNA metabarcoding

Environmental Advances, Journal Year: 2023, Volume and Issue: 12, P. 100370 - 100370

Published: April 19, 2023

The world is struggling to solve a devastating biodiversity loss that not only affects the extinction of treasured species and irreplaceable genetic variation, but also jeopardizes food production, health, safety people. All initiatives aimed conserve rely heavily on monitoring both populations get accurate spatial patterns overall population assessments. Conventional techniques, such as visual surveys counting individuals, are problematic due challenges in identifying cryptic or immature life stages. Environmental DNA (eDNA) relatively new technology has potential be faster, non-invasive, cost-effective tool for biodiversity, conservation, management practices. eDNA been extracted from materials ancient present, its applications range identification individual study entire ecosystems. In past few years, there substantial increase usage research pertaining ecological preservation conservation. However, several technological problems still need solved. To reduce number false positives and/or negatives produced by current technologies, it necessary improve optimize calibration validation at every stage procedure. There significant greater information about physical constraints use, well synthesis, state, expected lifespan, modes movement. Due widespread use research, essential assess extent breadth these studies. this article, we critically reviewed primary subterranean aquatic invasive species. Through review, readers can better understand limitations metabarcoding.

Language: Английский

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Drone-assisted collection of environmental DNA from tree branches for biodiversity monitoring

Science Robotics, Journal Year: 2023, Volume and Issue: 8(74)

Published: Jan. 18, 2023

The protection and restoration of the biosphere is crucial for human resilience well-being, but scarcity data on status distribution biodiversity puts these efforts at risk. DNA released into environment by organisms, i.e., environmental (eDNA), can be used to monitor in a scalable manner if equipped with appropriate tool. However, collection eDNA terrestrial environments remains challenge because many potential surfaces sources that need surveyed their limited accessibility. Here, we propose survey sampling outer branches tree canopies an aerial robot. drone combines force-sensing cage haptic-based control strategy establish maintain contact upper surface branches. Surface then collected using adhesive integrated drone. We show autonomously land variety stiffnesses between 1 103 newton/meter without prior knowledge structural stiffness robustness linear angular misalignments. Validation natural demonstrates our method successful detecting animal species, including arthropods vertebrates. Combining robotics from unreachable aboveground substrates offer solution broad-scale monitoring biodiversity.

Language: Английский

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