Advances and prospects of environmental DNA in neotropical rainforests

Zinger, Lucie; Donald, Julian; Brosse, Sébastien; González, Mailyn; Iribar, Amaia; Leroy, Céline; Murienne, Jérôme; Orivel, Jérôme; Schimann, Heidy; Taberlet, Pierre; Lopes, Carla Martins

doi:10.1016/bs.aecr.2020.01.001

Cited by 40 publications

(47 citation statements)

References 218 publications

(263 reference statements)

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“…4 , 5 ). Our findings complement and lend further support for the promise of using eDNA metabarcoding as a tool for measuring and monitoring biodiversity 99 – 102 .…”

Section: Discussionsupporting

confidence: 69%

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Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems

Ladin

Ferrell

Dums

et al. 2021

Sci Rep

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We investigated the nascent application and efficacy of sampling and sequencing environmental DNA (eDNA) in terrestrial environments using rainwater that filters through the forest canopy and understory vegetation (i.e., throughfall). We demonstrate the utility and potential of this method for measuring microbial communities and forest biodiversity. We collected pure rainwater (open sky) and throughfall, successfully extracted DNA, and generated over 5000 unique amplicon sequence variants. We found that several taxa including Mycoplasma sp., Spirosoma sp., Roseomonas sp., and Lactococcus sp. were present only in throughfall samples. Spiroplasma sp., Methylobacterium sp., Massilia sp., Pantoea sp., and Sphingomonas sp. were found in both types of samples, but more abundantly in throughfall than in rainwater. Throughfall samples contained Gammaproteobacteria that have been previously found to be plant-associated, and may contribute to important functional roles. We illustrate how this novel method can be used for measuring microbial biodiversity in forest ecosystems, foreshadowing the utility for quantifying both prokaryotic and eukaryotic lifeforms. Leveraging these methods will enhance our ability to detect extant species, describe new species, and improve our overall understanding of ecological community dynamics in forest ecosystems.

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“…4 , 5 ). Our findings complement and lend further support for the promise of using eDNA metabarcoding as a tool for measuring and monitoring biodiversity 99 – 102 .…”

Section: Discussionsupporting

confidence: 69%

“…However, using eDNA metabarcoding as an ecological monitoring tool comes with some inherent challenges and potential pitfalls 102 , 115 . Depending on the particular application, eDNA metabarcoding may not provide the ideal data to allow for developing and testing certain hypotheses.…”

Section: Discussionmentioning

confidence: 99%

Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems

Ladin

Ferrell

Dums

et al. 2021

Sci Rep

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“…eDNA is one of the most emerging critical biological resources in the field of ecotoxicology [ 11 ]. Sequencing and bioinformatic analysis of eDNA samples have been extensively used to comprehensively investigate changes in the ecosystem and use it as a barometer of ecological health [ 10 , 12 ]. Therefore, here we briefly discuss it.…”

Section: Edna and Environmental Impact Assessmentmentioning

confidence: 99%

Environmental DNA and RNA as Records of Human Exposome, Including Biotic/Abiotic Exposures and Its Implications in the Assessment of the Role of Environment in Chronic Diseases

Thakur

Roy

2020

IJMS

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Most of environment-related diseases often result from multiple exposures of abiotic and/or biotic stressors across various life stages. The application of environmental DNA/RNA (eDNA/eRNA) to advance ecological understanding has been very successfully used. However, the eminent extension of eDNA/eRNA-based approaches to estimate human exposure to biotic and/or abiotic environmental stressors to understand the environmental causes of chronic diseases has yet to start. Here, we introduce the potential of eDNA/eRNA for bio-monitoring of human exposome and health effects in the real environmental or occupational settings. This review is the first of its kind to discuss how eDNA/eRNA-based approaches can be applied for assessing the human exposome. eDNA-based exposome assessment is expected to rely on our ability to capture the genome- and epigenome-wide signatures left behind by individuals in the indoor and outdoor physical spaces through shedding, excreting, etc. Records of eDNA/eRNA exposome may reflect the early appearance, persistence, and presence of biotic and/or abiotic-exposure-mediated modifications in these nucleic acid molecules. Functional genome- and epigenome-wide mapping of eDNA offer great promise to help elucidate the human exposome. Assessment of longitudinal exposure to physical, biological, and chemical agents present in the environment through eDNA/eRNA may enable the building of an integrative causal dynamic stochastic model to estimate environmental causes of human health deficits. This model is expected to incorporate key biological pathways and gene networks linking individuals, their geographic locations, and random multi-hits of environmental factors. Development and validation of monitoring of eDNA/eRNA exposome should seriously be considered to introduce into safety and risk assessment and as surrogates of chronic exposure to environmental stressors. Here we highlight that eDNA/eRNA reflecting longitudinal exposure of both biotic and abiotic environmental stressors may serve as records of human exposome and discuss its application as molecular tools for understanding the toxicogenomics basis of environment-related health deficits.

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“…In fact, the species list obtained with one eDNA sampling session was often comparable to cumulative traditional sampling sessions and historical records (Civade et al 2016;Hänfling et al 2016;Nakagawa et al 2018;Pont et al 2018;Cantera et al 2019). Due to its sampling efficiency to reconstruct whole aquatic communities, eDNA methods are expected to revolutionize survey methods for ecological research and biodiversity monitoring on aquatic ecosystems (Rees et al 2014(Rees et al , 2015Keck et al 2017;Zinger et al 2020). This is particularly true for large rivers where sampling the fauna can be very difficult, as it is time consuming, costly and limited to specific habitats (Pont et al 2018).…”

Section: Introductionmentioning

confidence: 99%

“…The above-mentioned studies reached this aim because they targeted species or communities with well-known spatial distributions. However, one of the main advantages of eDNA is to provide biodiversity inventories that cannot be performed by traditional methods, as in remote and highly diverse tropical freshwater ecosystems (Cilleros et al 2018;Zinger et al 2020). Here, we propose a methodological framework to characterize the extent of eDNA spatial signal to detect community structure independently from the known distribution of the species.…”

Section: Introductionmentioning

confidence: 99%

Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach

Cantera

Decotte

Déjean

et al. 2020

Preprint

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Environmental DNA (eDNA) is gaining a growing popularity among scientists but its applicability to biodiversity research and management remain limited in river systems by the lack of knowledge about the spatial extent of the downstream transport of eDNA. Up to now, attempts to measure eDNA detection distance compared known species distributions to eDNA results, limiting therefore studies to a few intensively studied rivers. Here we developed a framework to measure the detection distance of eDNA in rivers based on the comparison of faunas across an increasing range of spatial extents, making it independent from knowledge on species distributions. We hypothesized that under short detection distance the similarity between fish faunas should peak between nearby sites, whereas under long detection distance each site should cumulate species from a large upstream area. Applying this framework to the fish fauna of two large and species rich Neotropical river basins (Maroni and Oyapock), we show that fish eDNA detection distance did not exceed a few kilometers. eDNA hence provided inventories of local species communities. Those results were validated by retrieving the distance decay of species similarity, a general pattern in ecology based on the decline of local species community similarity with spatial distance between them. We finally compared species distribution derived from eDNA to the known distribution of the species based on capture data, and this comparison also confirmed a global match between methods, testifying for a short distance of detection of the fauna by eDNA.

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Advances and prospects of environmental DNA in neotropical rainforests

Cited by 40 publications

References 218 publications

Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems

Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems

Environmental DNA and RNA as Records of Human Exposome, Including Biotic/Abiotic Exposures and Its Implications in the Assessment of the Role of Environment in Chronic Diseases

Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach

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