Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects

Biodiversity and Conservation, Год журнала: 2020, Номер 29(7), С. 2089 - 2121

Опубликована: Апрель 8, 2020

Язык: Английский

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Soil microbial network complexity predicts ecosystem function along elevation gradients on the Tibetan Plateau

Soil Biology and Biochemistry, Год журнала: 2022, Номер 172, С. 108766 - 108766

Опубликована: Июнь 25, 2022

Язык: Английский

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Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring

Molecular Ecology, Год журнала: 2020, Номер 29(22), С. 4258 - 4264

Опубликована: Сен. 23, 2020

The last decade brought a spectacular development of so-called environmental (e)DNA studies. In general, "environmental DNA" is defined as DNA isolated from samples, in contrast to genomic that extracted directly specimens. However, the variety different sources eDNA and range taxonomic groups are targeted by studies large, which has led some discussion about breadth concept. particular, there recent trend restrict use term "eDNA" macro-organisms, not physically present samples. this paper, we argue such distinction may be ideal, because signal can come organisms across whole tree life. Consequently, advocate should used its generic sense, originally defined, encompassing all including microbial, meiofaunal macrobial taxa. We first suggest specifying origin sample, water eDNA, sediment or soil eDNA. A second specification would then define group through polymerase chain reaction amplification, fish invertebrate bacterial This terminology does also require assumptions specific state sampled (intracellular extracellular). hope will help better scope studies, especially for managers, who them reference routine biomonitoring bioassessment.

Язык: Английский

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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 shedding and decay rates from diverse animal forms and thermal regimes

Environmental DNA, Год журнала: 2020, Номер 3(2), С. 492 - 514

Опубликована: Сен. 29, 2020

Abstract Environmental DNA (eDNA) analysis from water samples is a promising new method to identify both targeted species and whole communities of aquatic organisms. However, the current literature regarding eDNA shedding rates primarily focuses on fish most decay rate constants are reported for warm sunlit waters. Here, we conducted experiments investigate how differs between animal forms long can persist in waters varying temperature light conditions. We designed quantitative PCR assays one (mummichog, Fundulus heteroclitus ), crustacean (grass shrimp, Palaemon spp.), two scyphomedusae (moon jelly, Aurelia aurita nettle, Chrysaora spp.) estimate rates. found that were highly variable all organisms, but grass shrimp had lowest rate. quantified at 6, 15, 23°C mummichog larger higher temperatures, while those did not show clear dependence. also higher‐order models with tails fit data better than first‐order log‐linear models, suggesting temporal variability Results indicate different shed types eDNA, impacting These findings fill critical knowledge gaps variation across under range realistic marine will be useful interpreting field studies utilize ocean habitats otherwise difficult access.

Язык: Английский

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

The Science of The Total Environment, Год журнала: 2023, Номер 873, С. 162322 - 162322

Опубликована: Фев. 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.

Язык: Английский

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A practical guide to DNA-based methods for biodiversity assessment

Pensoft Publishers eBooks, Год журнала: 2021, Номер unknown

Опубликована: Дек. 2, 2021

DNA-based methods for species detection and identification have revolutionised our ability to assess biodiversity in terrestrial, freshwater marine ecosystems. Starting from the seminal study that used eDNA detect invasive american bullfrogs France (Gentile Francesco Ficetola et al. 2008)), research conducted over last decade has demonstrated power of these approaches surveying a wide range groups. Early applications included use monitor Asian Carp USA (Jerde 2013). Following heavy scrutiny, method was eventually adopted, is still employed today by United States Geological Survey (USGS). A flurry followed, with tests designed many threatened including New zealand mudsnails (Goldberg 2013), crayfish (Geerts 2018), gammarids (R. Blackman 2017), great crested newts (Biggs 2015). The newt test been regulatory monitoring UK since 2014. During same time period, there proliferation studies high-throughput sequencing describe whole communities organisms mixed environmental samples, using an approach termed DNA metabarcoding (Taberlet 2012).

Язык: Английский

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Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

Molecular Ecology, Год журнала: 2022, Номер 31(20), С. 5132 - 5164

Опубликована: Авг. 16, 2022

Abstract Vast global declines of freshwater and marine fish diversity population abundance pose serious threats to both ecosystem sustainability human livelihoods. Environmental DNA (eDNA)‐based biomonitoring provides robust, efficient, cost‐effective assessment species occurrences trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks facilitate conservation fisheries management. However, the many technical considerations rapid developments underway eDNA arena can overwhelm researchers practitioners new field. Here, we systematically analysed 416 studies summarize research terms investigated targets, aims, study systems, reviewed applications, rationales, methodological considerations, limitations methods with an emphasis on research. We highlighted how technology may advance our knowledge behaviour, distributions, genetics, community structures, ecological interactions. also synthesized current several important concerns, including qualitative quantitative power has recover biodiversity abundance, spatial temporal representations respect its sources. To applications implementing techniques, recent literature was summarized generate guidelines effective sampling lentic, lotic, habitats. Finally, identified gaps limitations, pointed out newly emerging avenues eDNA. As optimization standardization improve, should revolutionize monitoring promote management that transcends geographic boundaries.

Язык: Английский

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Genomics for monitoring and understanding species responses to global climate change

Nature Reviews Genetics, Год журнала: 2023, Номер 25(3), С. 165 - 183

Опубликована: Окт. 20, 2023

All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish species' potential adapt future environments. Understanding monitoring how organisms respond human-driven change is therefore major priority for conservation rapidly changing environment. Recent developments genomic, transcriptomic epigenomic technologies enabling unprecedented insights into evolutionary processes molecular bases adaptation. This Review summarizes methods that apply integrate omics tools experimentally investigate, monitor predict species communities wild cope with change, which by genetically adapting new conditions, through range shifts or phenotypic plasticity. We identify advantages limitations each method discuss research avenues would improve our understanding responses highlighting need holistic, multi-omics approaches ecosystem during Species can shifting their these responses.

Язык: Английский

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Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes

Environmental DNA, Год журнала: 2020, Номер 3(1), С. 142 - 156

Опубликована: Окт. 2, 2020

Abstract Environmental DNA (eDNA) analysis is a revolutionary method to monitor marine biodiversity from animal traces. Examining the capacity of eDNA provide accurate measures in species‐rich ecosystems such as coral reefs prerequisite for their application long‐term monitoring. Here, we surveyed two Colombian tropical reefs, island Providencia and Gayraca Bay near Santa Marta, using underwater visual census (UVC) methods. We collected large quantity surface water (30 L per filter) above applied metabarcoding protocol three different primer sets targeting 12S mitochondrial DNA, which are specific vertebrates Actinopterygii Elasmobranchii. By assigning sequences species public reference database, detected presence 107 85 fish species, 106 92 genera, 73 57 families Bay, respectively. Of identified eDNA, 32.7% (Providencia) 18.8% (Gayraca) were also found UVCs. further congruence genus richness abundance between UVC approaches but not Bay. Mismatches had phylogenetic ecological signal, with detecting broader diversity more effectively smaller pelagic those deeper habitats. Altogether, can be used fast broad surveys applicable tropics, improved coverage database required before this new could serve an effective complement traditional

Язык: Английский

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