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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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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Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions

Molecular Ecology Resources, Год журнала: 2022, Номер 22(7), С. 2640 - 2650

Опубликована: Май 29, 2022

Abstract Although the use and development of molecular biomonitoring tools based on environmental nucleic acids (eDNA eRNA; collectively known as eNAs) have gained broad interest for quantification biodiversity in natural ecosystems, studies investigating impact site‐specific physicochemical parameters eNA‐based detection methods (particularly eRNA) remain scarce. Here, we used a controlled laboratory microcosm experiment to comparatively assess degradation eDNA eRNA across an acid–base gradient following complete removal progenitor organism ( Daphnia pulex ). Using water samples collected over 30‐day period, copy numbers were quantified using droplet digital PCR (ddPCR) assay targeting mitochondrial cytochrome c oxidase subunit I (COI) gene D. . We found that decayed more rapidly than at all pH conditions tested, with detectability—predicted by exponential decay model—for up 57 h (eRNA; neutral pH) 143 days (eDNA; acidic post organismal removal. Decay rates significantly higher alkaline conditions, while did not differ among levels. Collectively, our findings provide basis predictive framework assessing persistence dynamics range ecologically relevant establish potential be spatially temporally sensitive (as it is detectable levels), may inform future sampling strategies aquatic habitats.

Язык: Английский

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Environmental RNA can distinguish life stages in amphibian populations

Molecular Ecology Resources, Год журнала: 2023, Номер 24(4)

Опубликована: Авг. 18, 2023

Abstract Applications of environmental DNA (eDNA) analysis methods for biomonitoring have grown exponentially over the last decade and provide a wealth new information on distribution species. However, eDNA limited application estimating population‐level metrics. Environmental RNA (eRNA) has potential to address ecological questions by gathering population demographic from media but may be challenging detect analyze. We developed gene‐specific eRNA assays targeting keratin‐associated genes in two focal species, American bullfrogs ( Lithobates catesbeianus ) tiger salamanders Ambystoma mavortium answer an important question amphibian management: whether species detections represent breeding populations versus transitory adults. performed extensive laboratory validation with amphibians housed across development stages, where we collected 95 127 samples salamanders, respectively. Both were highly specific larval stage amplified high sensitivity (90% bullfrog 88.4% salamander samples). then applied our validated multiple natural systems. When larvae present, found 74.1% overall detection field 70.8% 48.5% ponds A. macrodactylum californiense larvae, correlating rates. only adults did not larvae‐specific ponds, despite Although much work is ahead optimizing assay design, sampling filtering methods, demonstrate that can successfully used discern life stages direct ecology conservation management.

Язык: Английский

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Harnessing decay rates for coastal marine biosecurity applications: A review of environmental DNA and RNA fate

Environmental DNA, Год журнала: 2023, Номер 5(5), С. 960 - 972

Опубликована: Март 30, 2023

Abstract Marine nonindigenous species (NIS) are spreading at an alarming rate internationally through anthropogenic activities such as shipping and aquaculture, affecting local biodiversity negatively impacting the ecosystem human well‐being. Countries international organizations have recognized this global threat begun implementing biosecurity management programs to ensure early detection, effective surveillance, mitigation of marine NIS spread. Molecular techniques based on environmental DNA RNA (eDNA/eRNA), collectively referred nucleic acids (eNAs), become a popular noninvasive tool for detecting monitoring locally globally. However, uncertainties about eNAs detection probabilities location source population impede broad uptake in programs. It's been hypothesized that most these can be explained by studying molecules' dynamics within environment distribution models. To contribute further knowledge development area, our study reviews data from 20 recent reports degradation mechanisms fate environment. We classified critical factors influencing eNAs' persistence should considered practitioners, outlining complex interaction between processes particular conditions. help guide parameterization models, review also summarizes standardizes decay rates eDNA/eRNA literature. Finally, manuscript outlines guidelines calculate accurate build appropriate “fit‐for‐purpose” tools improved target detectability greater resolution assessing biodiversity.

Язык: Английский

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Pathogens and disease vectors/hosts monitoring in aquatic environments: Potential of using eDNA/eRNA based approach

The Science of The Total Environment, Год журнала: 2021, Номер 796, С. 148810 - 148810

Опубликована: Июль 1, 2021

Язык: Английский

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Plant–animal interactions in the era of environmental DNA (eDNA)—A review

Environmental DNA, Год журнала: 2022, Номер 4(5), С. 987 - 999

Опубликована: Май 21, 2022

Abstract Plant–animal interactions (PAI) represent major channels of energy transfer through ecosystems, where both positive and antagonistic simultaneously contribute to ecosystem functioning. Monitoring PAI therefore increases the understanding environmental health, integrity, functioning, studying complex accurate, cost‐effective sampling can aid in management detrimental anthropogenic impacts. Environmental DNA (eDNA)‐based monitoring represents an increasingly common, nondestructive approach for biodiversity monitoring, which could help elucidate PAI. Here, we aim provide overall discussion on potential using eDNA study We assessed existing literature this subject from 2009 2021 a freely accessible web search tool. The was conducted by keywords involving PAI, including species‐specific metabarcoding approaches, recovering 43 studies. summarized advantages current limitations such outline research priorities improve future eDNA‐based methods analysis. Among studies identified measure as pollination, herbivory, mutualistic, parasitic relationships, they have often higher taxonomic diversity several direct comparisons with DNA‐based gut/bulk conventional survey methods. Research needs include following: better influencing factors detection involved (e.g., degradation, origin, types), methodological standardization (sampling primer development), more inclusive sequence reference databases. If these are addressed, it will significant impact enable eDNA. In future, implementation particularly benefit scalability biomonitoring surveys that imperative health assessments.

Язык: Английский

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Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water

Molecular Ecology Resources, Год журнала: 2022, Номер 22(7), С. 2471 - 2493

Опубликована: Апрель 4, 2022

Elusive aquatic wildlife, such as endangered sea turtles, are difficult to monitor and conserve. As novel molecular genetic technologies develop, it is possible adapt optimize them for wildlife conservation. One technology environmental (e)DNA - the detection of DNA shed from organisms into their surrounding environments. We developed species-specific green (Chelonia mydas) loggerhead (Caretta caretta) turtle probe-based qPCR assays, which can detect quantify eDNA in controlled (captive tank water sand samples) free ranging (oceanic samples nesting beach sand) settings. complemented traditional in-water monitoring by enabling even when turtles were not visually observed. Furthermore, we report that high throughput shotgun sequencing enabled population studies pathogen monitoring, demonstrating noninvasive techniques viable efficient alternatives biological sampling (e.g., biopsies blood draws). Genetic information was obtained many hours after events, without having observe or interact with target individual. This greatly reduces stress experienced mothers emerging hatchlings, avoids sacrificing eggs analysis. The pathogens indicates significant potential increased disease capacity viral variant surveillance. Together, these results demonstrate approaches ultimately help understand conserve threatened species turtles.

Язык: Английский

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Environmental DNA-Based Methods in Biodiversity Monitoring of Protected Areas: Application Range, Limitations, and Needs

Diversity, Год журнала: 2022, Номер 14(6), С. 463 - 463

Опубликована: Июнь 9, 2022

Novel methods for species detection based on collection of environmental DNA (eDNA) are not only important in biodiversity assessment a scientific context, but also increasingly being applied conservation practice. The eDNA-based have significant potential regular use status assessments and actions protected areas (PAs) other effective area-based measures (OECMs) worldwide. Species from samples, such as water, sediment, soil, air, or organic material, has broad application scope with precise, comprehensive, rapid identification. Here, we provide an overview the range monitoring PAs, evaluate which this technology already been implemented nature conservation, examine challenges that can hamper further real world Based outcomes two projects, practical experience, current literature focusing their application, conclude promising novel approaches strong supplement methods, some cases even substitutes conventional used PAs. This advancement is expected to affect decision-making efforts PAs OECMs.

Язык: Английский

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Environmental RNA outperforms eDNA metabarcoding in assessing impact of marine pollution: A chromium-spiked mesocosm test

Chemosphere, Год журнала: 2022, Номер 298, С. 134239 - 134239

Опубликована: Март 12, 2022

Язык: Английский

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