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

Molecular Ecology, Journal Year: 2020, Volume and Issue: 29(22), P. 4258 - 4264

Published: Sept. 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.

Language: Английский

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Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap

Molecular Ecology, Journal Year: 2020, Volume and Issue: 30(13), P. 2937 - 2958

Published: May 16, 2020

Abstract A decade after environmental scientists integrated high‐throughput sequencing technologies in their toolbox, the genomics‐based monitoring of anthropogenic impacts on biodiversity and functioning ecosystems is yet to be implemented by regulatory frameworks. Despite broadly acknowledged potential genomics this end, technical limitations conceptual issues still stand way its broad application end‐users. In addition, multiplicity implementation strategies may contribute a perception that routine methodology premature or “in development”, hence restraining regulators from binding these tools into legal Here, we review recent implementations methods, applied biomonitoring ecosystems. By taking general overview, without narrowing our perspective particular habitats groups organisms, paper aims compare, discuss strengths four for monitoring: (a) Taxonomy‐based analyses focused identification known bioindicators described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; (d) Functional (metagenomics metatranscriptomics). We emphasise utility three latter integrate meiofauna microorganisms are not traditionally utilised because difficult taxonomic identification. Finally, propose roadmap programmes leverage analytical advancements, while pointing out current future research needs.

Language: Английский

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Toward sustainable environmental quality: Priority research questions for Europe

Environmental Toxicology and Chemistry, Journal Year: 2018, Volume and Issue: 37(9), P. 2281 - 2295

Published: July 19, 2018

Abstract The United Nations’ Sustainable Development Goals have been established to end poverty, protect the planet, and ensure prosperity for all. Delivery of will require a healthy productive environment. An understanding impacts chemicals which can negatively impact environmental health is therefore essential delivery Goals. However, current research on regulation in environment tend take simplistic view do not account complexity real world, inhibits way we manage chemicals. There an urgent need step change study communicate control natural To this requires major questions be identified so that resources are focused really matter. We present findings horizon‐scanning exercise identify priorities European science community around Using key approach, 22 priority. These covered overarching about should most concerned where, global megatrends, protection goals, sustainability chemicals; development parameterization assessment management frameworks; mechanisms maximize research. provide first‐step path forward research, regulatory, business communities better assess Environ Toxicol Chem 2018;37:2281–2295. © 2018 Authors. Environmental Toxicology Chemistry published by Wiley Periodicals, Inc. behalf SETAC.

Language: Английский

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

Reviews in Environmental Science and Bio/Technology, Journal Year: 2019, Volume and Issue: 18(3), P. 389 - 411

Published: July 29, 2019

Language: Английский

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Redistribution of intracellular and extracellular free & adsorbed antibiotic resistance genes through a wastewater treatment plant by an enhanced extracellular DNA extraction method with magnetic beads

Environment International, Journal Year: 2019, Volume and Issue: 131, P. 104986 - 104986

Published: July 9, 2019

Due to the limitations of current extraction methods, extracellular DNA (eDNA) is rarely discerned from intracellular (iDNA) despite having unique contributions antibiotic resistance genes (ARGs) propagation. Furthermore, eDNA may be free (f-eDNA) or adsorbed suspended solids, including cells (a-eDNA), which affects ARG persistence and transmissivity. We developed a novel method using magnetic beads separate iDNA, a-eDNA, f-eDNA assess how these physical states ARGs change across wastewater treatment plant. This efficiently extracted (>85.3%) with higher recovery than methods such as alcohol precipitation, CTAB-based extraction, kits (<10%). Biological UV disinfection decreased concentration (iARGs) (a-eARGs), causing an increase released (f-eARGs). More were discharged through wasted biosolids in effluent; iARGs a-eARGs are prevalent ((73.9 ± 22.5) % (23.4 15.3) total respectively), while f-eARGs effluent ((90.3 16.5) %). Bacterial community analysis showed significant correlations between specific genera (e.g., Aeromonas, Pseudomonas Acinetobacter strongly correlated multidrug-resistance gene blaTEM). system discharge receiving environments, however, increased eARG concentrations present effluent, contribute environmental resistome.

Language: Английский

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Improved freshwater macroinvertebrate detection from environmental DNA through minimized nontarget amplification

Environmental DNA, Journal Year: 2020, Volume and Issue: 3(1), P. 261 - 276

Published: Dec. 21, 2020

Abstract DNA metabarcoding of freshwater communities typically relies on PCR amplification a fragment the mitochondrial cytochrome c oxidase I (COI) gene with degenerate primers. The advantage COI is its taxonomic resolution and availability an extensive reference database. However, when universal primers are used environmental (eDNA) isolated from water, benthic invertebrate read OTU numbers “watered down,” that is, under represented, compared to whole specimen “bulk samples” due greater co‐amplification abundant nontarget taxa (e.g., fungi, algae, bacteria). Because stream prime importance for regulatory biomonitoring, more effective ways capture their diversity via eDNA water important. In this study, we aimed improve assessment by minimizing amplification. Therefore, generated data using BF2/BR2 samples collected throughout 15 months German Long‐Term Ecological Research site (Rhine‐Main‐Observatory, Kinzig River) identify most taxa. Based these data, designed new reverse primer (EPTDr2n) 3’‐specificity toward validated specificity in silico together forward fwhF2 available GenBank BOLD. We then performed situ tests 20 River samples. found percentage target reads was much higher combination two pairs, fwhF2/fwhR2n (99.6% versus 25.89% 39.04%, respectively). Likewise, number detected species substantially (305 113 185) exceeded 153 identified expert taxonomists at nearby sites across decades sampling. While few taxa, such as flatworms, were not detected, show optimized avoids bias thus significantly improves detection eDNA.

Language: Английский

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Human activities' fingerprint on multitrophic biodiversity and ecosystem functions across a major river catchment in China

Global Change Biology, Journal Year: 2020, Volume and Issue: 26(12), P. 6867 - 6879

Published: Sept. 16, 2020

Abstract Human‐induced global change dramatically alters individual aspects of river biodiversity, such as taxonomic, phylogenetic or functional diversity, and is predicted to lead losses associated ecosystem functions. Understanding these dependencies are critical human well‐being. Until now, however, most studies have only looked either at organismal groups single functions, little known on the effect activities multitrophic biodiversity multifunctionality in riverine ecosystem. Here we profiled from bacteria invertebrates based environmental DNA (hereafter, ‘eDNA’) samples across a major catchment China, analysed their with multiple especially linked C/N/P‐cycling. Firstly, found spatial cross‐taxon congruence pattern communities' structure network Shaying river, which was related strong filtering due land use. Secondly, use explained decline multifaceted but increased redundancy Thirdly, function relationships an integrative level showed concave‐up (non‐saturating) shape. Finally, structural equation modeling suggested that affects functions through biodiversity‐mediated pathways, including loss altered community interdependence groups. Our study highlights value complete inclusive assessment for integrated land‐use management ecosystems.

Language: Английский

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Strategies for sample labelling and library preparation in DNA metabarcoding studies

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 22(4), P. 1231 - 1246

Published: Sept. 22, 2021

Abstract Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to profile biota in basic and applied biodiversity research because its targeted nature that allows sequencing genetic markers many parallel. To achieve this, PCR amplification carried out with primers designed target a taxonomically informative marker within taxonomic group, sample‐specific nucleotide identifiers are added the amplicons prior sequencing. The latter enables assignment sequences back they originated from. Nucleotide can be during metabarcoding “library preparation”, is, when prepared for Different strategies this labelling exist. All have advantages, challenges limitations, some which lead misleading results, worst case compromise fidelity data. Given range questions addressed using metabarcoding, ensuring data generation robust fit chosen purpose critically important practitioners seeking employ assessments. Here, we present an overview three main workflows library preparation studies on Illumina platforms; one‐step PCR, two‐step tagged PCR. Further, distill key considerations researchers select appropriate strategy their specific study. Ultimately, by gaining insights into consequences different workflows, hope further consolidate power as tool assess across applications.

Language: Английский

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Uncovering the complete biodiversity structure in spatial networks: the example of riverine systems

Oikos, Journal Year: 2020, Volume and Issue: 129(5), P. 607 - 618

Published: Jan. 13, 2020

Uncovering biodiversity as an inherent feature of ecosystems and understanding its effects on ecosystem processes is one the most central goals ecology. Studying organisms’ occurrence patterns in natural has spurred discovery foundational ecological rules, such species–area relationship, general scientific interest. Recent global changes add relevance urgency to diversity organisms, their respective roles processes. While information properties abiotic environmental conditions are now available at unprecedented, highly‐resolved spatial temporal scales, fundamental variable – itself still often studied a local perspective, generally not wide taxonomic breadth, high scale coverage. This limiting capacity impact ecology field science. In this forum article, we propose that complete assessments should be inclusive across functional groups, space, time better understand emergent properties, functioning. We use riverine case example because they among biodiverse worldwide, but also highly threatened, in‐depth these systems critically needed. Furthermore, structure requires multiscale perspective consideration autocorrelation structures commonly ignored biodiversity–ecosystem functioning studies. show how recent methodological advances DNA (eDNA) provide novel opportunities uncover broad link it processes, with potential revolutionize sciences. then outline roadmap for using technique assess manner. Our proposed approach will help get associated scales relevant landscape managers.

Language: Английский

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Holistic pelagic biodiversity monitoring of the Black Sea via eDNA metabarcoding approach: From bacteria to marine mammals

Environment International, Journal Year: 2019, Volume and Issue: 135, P. 105307 - 105307

Published: Dec. 24, 2019

As the largest semi-closed marine ecosystem in world, Black Sea has been heavily affected by human activities for a long time. Describing biodiversity of multi-trophic biota pelagic zone and identifying dominant environmental factors are prerequisites protecting sustainability ecosystems. However, up to now, taxonomic distributional information about is not clear. Here, we employed Tree-of-Life metabarcoding analyze eight communities Sea, investigated their biogeographical distribution, further analyzed influence biological abiotic on large scales. We found that, (1) Over 8900 OTUs were detected which 630 species identified, covering holistic from single-celled (bacteria 5620 141 species; algae 1096 185 protozoa 546 146 species) multicellular organisms (invertebrate metazoans 150 34 fishes 1369 76 mammals 39 5 species). (2) Higher trophic (fishes mammals) distributed more evenly space than lower (microorganisms, invertebrates). For organisms, vertical stratification was obvious horizontal (vertical p < 0.02, 0.05). (3) The bottom algae) food web significantly distribution composition others through interactions (Mantel (4) At level factors, effect local sorting 15% higher that mass dispersal effect. first time, this study monitored profiled provided technological advances preliminary knowledge ongoing protection efforts.

Language: Английский

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