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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The Application of eDNA for Monitoring Aquatic Non-Indigenous Species: Practical and Policy Considerations

Diversity, Journal Year: 2023, Volume and Issue: 15(5), P. 631 - 631

Published: May 6, 2023

Aquatic non-indigenous species (NIS) threaten biodiversity, ecosystem functions, and the economy worldwide. Monitoring NIS is of immediate concern to identify newly arriving species, assess efficacy mitigation measures, report long-term indicators introduction, spread, impacts. The challenges associated with conventional methods specimen collection morphological identification have led development alternative methods, such as DNA-based which could offer rapid cost-effective detection NIS. Depending on whether a few (targeted monitoring) or many (passive are being monitored, environmental DNA (eDNA) can infer presence-absence relative abundances, enabling informed decisions actions be made based patterns detection. Compared more eDNA tools increase levels sensitivity for rare elusive even noticeable some taxa when using targeted monitoring. use not only minimizes onus taxonomic expertise reduces resource demands but also sensitive cost-efficient in detecting NIS, thus proving its value an early warning tool. As nucleic acid (DNA/RNA) advance rapidly detection, there must balance between method sensitivity, logistical requirements, costs, factored into future management decisions. While complementary reviews available, our aim emphasize importance incorporating surveys highlight available opportunities this field.

Language: Английский

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Assessment of responses of cultured benthic foraminiferal communities to copper pollution through environmental RNA metabarcoding analysis

Environmental Toxicology and Chemistry, Journal Year: 2025, Volume and Issue: 44(1), P. 159 - 168

Published: Jan. 1, 2025

Copper (Cu) is an essential trace element and can accumulate in sedimentary environments. However, beyond a certain concentration threshold, Cu pose toxicity risks to biota. Benthic foraminifera are widely distributed exhibit characteristics such as high biodiversity, short life cycle, good preservation potential, pollutant sensitivity, making them bioindicators. In this study, we investigated the responses of benthic foraminiferal communities various concentrations through environmental RNA metabarcoding under controlled laboratory conditions. Some genera-Glandulina, Pyrgo, Quinqueloculina, Sorites, Vellaria-exhibited sensitivity concentrations. Other genera-Ammonia, Operculina, Reophax, Bolivina, Glabratella, Miliammina, Parasorites-displayed tolerance Moreover, levels led reduced living abundance interspecific interactions, albeit without inducing test deformities. Our findings provide novel efficient approach for exploring heavy metal pollution.

Language: Английский

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Comparing eDNA and eRNA Sampling Methodologies From Pond Environments

Aquatic Conservation Marine and Freshwater Ecosystems, Journal Year: 2025, Volume and Issue: 35(2)

Published: Feb. 1, 2025

ABSTRACT Molecular traces are increasingly being applied to assess the presence of species and communities. Studies on environmental DNA (eDNA) have, a large extent, become common practice in detection, but less studies have compared biodiversity estimations with more temporary RNA (eRNA). This study compares metabarcoding results from pond water obtained both molecule types by sequencing V4 region 18S rRNA marker. Water was collected two depths, 20 80 cm, filtered sequentially through filter porosities, 0.45 0.22 μm. Each cut half before fixation either 96% ETOH or RNAlater. The showed no differences between fixatives for molecule. Overall, estimates eDNA significantly overperformed eRNA, likely due higher concentrations terrestrial sources. Comparisons depths variation only, increasing levels found at upper layer. Both pore sizes captured distinctive compositions taxa, where about 30% diversity uniquely identified second, finer filter. Taken together, these findings imply that choice molecular marker, depth size affects pond.

Language: Английский

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A review of eDNA technology in avian monitoring: Current status, challenges and future perspectives

Avian Research, Journal Year: 2025, Volume and Issue: unknown, P. 100235 - 100235

Published: March 1, 2025

Language: Английский

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Environmental RNA as a Tool for Marine Community Biodiversity Assessments

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: Oct. 22, 2022

Abstract Microscopic organisms are often overlooked in traditional diversity assessments due to the difficulty of identifying them based on morphology. Metabarcoding is a method for rapidly where Environmental DNA (eDNA) used as template. However, legacy problematically detected from no longer environment during sampling. RNA (eRNA), which only produced by living organisms, can also be collected environmental samples and metabarcoding. The aim this study was determine differences community composition between eRNA eDNA templates Using mesocosms containing field-collected communities an estuary, were co-extracted sediment, libraries prepared two loci (18S COI), sequenced using Illumina MiSeq. Results show higher number unique sequences both markers α-diversity compared eDNA. Significant all β-diversity metrics detected. This first demonstrate with estuarine system illustrates broad applications tool assessing benthic diversity, particularly conservation management applications.

Language: Английский

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Assessment of the ecological quality status of the Sepetiba Bay (SE Brazil): When metabarcoding meets morphology on foraminifera

Marine Environmental Research, Journal Year: 2024, Volume and Issue: 195, P. 106340 - 106340

Published: Jan. 9, 2024

Language: Английский

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Benthic foraminifera as proxies for the environmental quality assessment of the Kuwait Bay (Kuwait, Arabian Gulf): Morphological and metabarcoding approaches

The Science of The Total Environment, Journal Year: 2022, Volume and Issue: 833, P. 155093 - 155093

Published: April 11, 2022

The rapid urbanization and industrialization of Kuwait the consequent effluent discharges into marine environments have resulted in a degradation water sediment quality coastal ecosystems such as Bay. This study investigates ecological response benthic foraminifera (protists) to environmental stress traditional morphological approach was compared innovative DNA (eDNA) metabarcoding evaluate status (EcoQS). Forty-six surface samples were collected from selected stations To detect pollution gradient, parameters (e.g., salinity, pH, dissolved oxygen) grain-size, trace metals, total organic carbon, petroleum hydrocarbons) measured at each station. Although foraminiferal assemblages different molecular datasets, species turnover congruent statistically significant. Diversity-based biotic indices derived both approaches, reflect gradient (i.e., metal contaminations) lowest values EcoQS bad poor) are found innermost part Sulaibikhat Bay Ras Kazmah), while higher occur outer bay. constitutes first attempt apply assess within Arabian Gulf presents its advantages conventional approach.

Language: Английский

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Environmental DNA metabarcoding serves as a promising method for aquatic species monitoring and management: A review focused on its workflow, applications, challenges and prospects

Marine Pollution Bulletin, Journal Year: 2023, Volume and Issue: 194, P. 115430 - 115430

Published: Aug. 28, 2023

Language: Английский

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Through the eDNA looking glass: Responses of fjord benthic foraminiferal communities to contrasting environmental conditions

Journal of Eukaryotic Microbiology, Journal Year: 2023, Volume and Issue: 70(4)

Published: March 27, 2023

The health of coastal marine environments is severely declining with global changes. Proxies, such as those based on microeukaryote communities, can record biodiversity and ecosystem responses. However, conventional studies rely microscopic observations limited taxonomic range size fraction, missing putatively ecologically informative community components. Here, we tested molecular tools to survey foraminiferal in a fjord system (Sweden) spatial temporal scales: Alpha beta diversity responses natural anthropogenic environmental trends were assessed variability DNA (eDNA) compared morphology-based data. identification eDNA-obtained units was aided by single-cell barcoding. Our study revealed wide diversity, including typical morphospecies recognized the fjords, so-far unrecognized taxa. extraction method impacted composition outputs significantly. extractions 10 g sediment more reliably represented present than 0.5-g samples and, thus, are preferred for assessments this region. Alpha- 10-g extracts correlated bottom-water salinity similar morpho-assemblage Sub-annual resolved only partially, indicating damped sensitivity communities short timescales using established metabarcoding techniques. Systematically addressing current limitations may strongly improve future assessments.

Language: Английский

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