A review on the applications and recent advances in environmental DNA (eDNA) metagenomics

Garlapati, Deviram; Charankumar, B.; Ramu, Karri; Perumal, Mugunthan; Murthy, M.V. Ramana

doi:10.1007/s11157-019-09501-4

Cited by 102 publications

(81 citation statements)

References 132 publications

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“…In China, there is still a lot of unsurveyed biodiversity, from rainforests to deserts, where both taxonomists and evolutionary biologists could conduct investigations via DNA barcoding. This technology may also be applied to studies on macroevolution, interactions and food webs, environmental monitoring (Valentini et al, 2009;Garlapati et al, 2019). To maximize the value of DNA barcoding data, the people who collect it must collaborate with ecologists and evolutionary biologists (Joly et al, 2013;Cristescu, 2014) to expand the usefulness of barcode data.…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Sixteen Years of DNA Barcoding in China: What Has Been Done? What Can Be Done?

Yang

Zhang

2020

Front. Ecol. Evol.

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Over the past 16 years, more than half (59.68%) of research papers in China on DNA barcoding have been published in Chinese rather than English. Using the records in the BOLD (Barcode of Life Data) system, we found Chinese scientists have contributed nearly 120,000 DNA barcodes for more than 16,000 species as of September 2019, with barcoded species distributed throughout China. Based on 2,624 articles and 494 dissertations published during the last 16 years, we reviewed the basic statistics of these studies as well as the type of articles contributed by Chinese scientists, the preference of taxonomic groups, the characteristic of barcoding studies in China, the current limitations, and potential future directions as well. We found that most barcode data pertain primarily to plants and animals. Most work in China has focused on verification of the authenticity of species used in traditional Chinese medicine, while other applications have paid more attention to food safety, inspection and quarantine, and the control of pests and invasive species. In methodology and technology, a number of new DNA barcoding methods have been developed by Chinese scientists. However, there are several significant limitations to research into DNA barcoding in China in general, such as the lack of leadership in pioneering international projects, the absence of an open bioinformatics infrastructure, and the fact that some Chinese journals do not clearly require data transparency and availability for DNA barcodes, impeding the further development of barcode libraries and research in China. In the future, Chinese scientists should build authoritative online libraries, while aiming for theoretical innovations for both concepts and methodology of DNA barcoding.

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Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Sixteen Years of DNA Barcoding in China: What Has Been Done? What Can Be Done?

Yang

Zhang

2020

Front. Ecol. Evol.

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“…Genomic technologies, if adequately developed and applied, can also revolutionize our ability to detect invasive species [44]; early detection may enable prevention of their establishment. For example, eDNA can detect a species presence without capture or direct observation, and is currently employed to study invasions in freshwater environments [45][46][47].…”

Section: Insight For Monitoring and Early Detectionmentioning

confidence: 99%

“…For example, improvement of detection and monitoring of invasives and illegal trade is an urgent priority. However, current eDNA methods can suffer from uncertainties in species identification (especially in marine environments), presenting a risk of false positives, and could have weak statistical power (leading to overconfidence when no detections are recorded) [22,44]. This highlights the need for more high-quality reference genomes of invasive species of concern, as eDNA technologies are likely to become a major focus in invasive species management [48].…”

Section: The Applicability and Readiness Of Genomic And Biotechnologimentioning

confidence: 99%

“…Intervention tools are well established in model species for biomedical and functional genomic research (i.e., fruit flies, zebrafish, mice), but are also advancing for agricultural species. For application to wildlife conservation, these require development and innovation, but are achievable short-term, with laboratory examples of success already established for some terrestrial species (e.g., transgenic chestnut trees immune to fungal blight [95], successful gene drive trials in mosquitoes [44]). The real barrier to intervention is having enough knowledge to construct phased-approaches that advance from the lab to the field effectively and safely and that obtain the intended benefits of intervention while avoiding unintended consequences.…”

Section: Figure 2 Comparing Actual Marine Animal Biodiversity To Seqmentioning

confidence: 99%

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Transforming Ocean Conservation: Applying the Genetic Rescue Toolkit

Novak¹,

Fraser

Maloney³

2020

Genes

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Although oceans provide critical ecosystem services and support the most abundant populations on earth, the extent of damage impacting oceans and the diversity of strategies to protect them is disconcertingly, and disproportionately, understudied. While conventional modes of conservation have made strides in mitigating impacts of human activities on ocean ecosystems, those strategies alone cannot completely stem the tide of mounting threats. Biotechnology and genomic research should be harnessed and developed within conservation frameworks to foster the persistence of viable ocean ecosystems. This document distills the results of a targeted survey, the Ocean Genomics Horizon Scan, which assessed opportunities to bring novel genetic rescue tools to marine conservation. From this Horizon Scan, we have identified how novel approaches from synthetic biology and genomics can alleviate major marine threats. While ethical frameworks for biotechnological interventions are necessary for effective and responsible practice, here we primarily assessed technological and social factors directly affecting technical development and deployment of biotechnology interventions for marine conservation. Genetic insight can greatly enhance established conservation methods, but the severity of many threats may demand genomic intervention. While intervention is controversial, for many marine areas the cost of inaction is too high to allow controversy to be a barrier to conserving viable ecosystems. Here, we offer a set of recommendations for engagement and program development to deploy genetic rescue safely and responsibly.

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“…Research on molecular and bioinformatic aspects of eDNA analyses has massively expanded within the last few years [Alberdi et al, 2017;Beng and Corlett, 2020;Calderón-Sanou et al, 2019;Deiner et al, 2017;Ficetola et al, 2016;Garlapati et al, 2019;Leray et al, 2019]. Much less focus, however, has been attributed to the "ecology of eDNA", namely "its origin, state, transport, and fate within the environment" [Barnes and Turner, 2015], and how these factors influence its detection [Barnes and Turner, 2015;Harrison et al, 2019].…”

Section: Introductionmentioning

confidence: 99%

How to design optimal eDNA sampling strategies for biomonitoring in river networks

Carraro

Stauffer

Altermatt

2020

Preprint

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The current biodiversity crisis calls for appropriate and timely methods to assess state and change of biodiversity. In this respect, environmental DNA (eDNA) is a highly promising tool, especially for aquatic ecosystems. While initial eDNA studies assessed biodiversity at a few sites, technology now allows analyses of samples from many points at a time. However, the selection of these sites has been mostly motivated on an ad-hoc basis, and it is unclear where to position sampling sites in a river network to most effectively sample biodiversity. To this end, hydrology-based models might offer a unique guidance on where to sample eDNA to reconstruct the spatial patterns of taxon density based on eDNA data collected across a watershed.Here, we performed computer simulations to identify best-practice criteria for the choice of positioning of eDNA sampling sites in river networks. To do so, we combined a hydrology-based eDNA transport model with a virtual river network reproducing the scaling features of real rivers. In particular, we conducted simulations investigating scenarios of different number and location of eDNA sampling sites in a riverine network, different spatial taxon distributions, and different eDNA measurement errors.We identified best practices for sampling site selection for taxa that have a scattered versus an even distribution across the network. We observed that, due to hydrological controls, non-uniform patterns of eDNA concentration arise even if the taxon distribution is uniform and decay is neglected. We also found that uncertainties in eDNA concentration estimates do not necessarily hamper model predictions. Knowledge of eDNA decay rates improves model predictions, highlighting the need for empirical estimates of these rates under relevant environmental conditions. Our simulations help define strategies for the design of eDNA sampling campaigns in river networks, and can guide the sampling effort of field ecologists and environmental authorities.

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A review on the applications and recent advances in environmental DNA (eDNA) metagenomics

Cited by 102 publications

References 132 publications

Sixteen Years of DNA Barcoding in China: What Has Been Done? What Can Be Done?

Sixteen Years of DNA Barcoding in China: What Has Been Done? What Can Be Done?

Transforming Ocean Conservation: Applying the Genetic Rescue Toolkit

How to design optimal eDNA sampling strategies for biomonitoring in river networks

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