scholarly journals Recent advances in environmental DNA‐based biodiversity assessment and conservation

2021 ◽  
Vol 27 (10) ◽  
pp. 1876-1879
Author(s):  
Jun Yang ◽  
Xiaowei Zhang ◽  
Xiaowei Jin ◽  
Mathew Seymour ◽  
Catherine Richter ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Biodiversity Assessment ◽  
Recent Advances

Extracellular DNA in environmental samples: Occurrence, extraction, quantification, and impact on microbial biodiversity assessment

2021 ◽  
Author(s):  
Sakcham Bairoliya ◽  
Jonas Koh Zhi Xiang ◽  
Bin Cao
Keyword(s):  
Dna Sequencing ◽  
Microbial Communities ◽  
Dna Extraction ◽  
Environmental Samples ◽  
Environmental Dna ◽  
Extracellular Dna ◽  
Biodiversity Assessment ◽  
Microbial Biodiversity ◽  
Technical Details ◽  
The Impact

Environmental DNA, i.e., DNA directly extracted from environmental samples, has been applied to understand microbial communities in the environments and to monitor contemporary biodiversity in the conservation context. Environmental DNA often contains both intracellular DNA (iDNA) and extracellular DNA (eDNA). eDNA can persist in the environment and complicate environmental DNA sequencing-based analyses of microbial communities and biodiversity. Although several studies acknowledged the impact of eDNA on DNA-based profiling of environmental communities, eDNA is still being neglected or ignored in most studies dealing with environmental samples. In this article, we summarize key findings on eDNA in environmental samples and discuss the methods used to extract and quantify eDNA as well as the importance of eDNA on the interpretation of experimental results. We then suggest several factors to consider when designing experiments and analyzing data to negate or determine the contribution of eDNA to environmental DNA-based community analyses. This field of research will be driven forward by: (i) carefully designing environmental DNA extraction pipelines by taking into consideration technical details in methods for eDNA extraction/removal and membrane-based filtration and concentration; (ii) quantifying eDNA in extracted environmental DNA using multiple methods including qPCR and fluorescent DNA binding dyes; (iii) carefully interpretating effect of eDNA on DNA-based community analyses at different taxonomic levels; and (iv) when possible, removing eDNA from environmental samples for DNA-based community analyses.

scholarly journals An urban Blitz with a twist: rapid biodiversity assessment using aquatic environmental DNA

2020 ◽  
Author(s):  
Kamil Hupało ◽  
Markus Majaneva ◽  
Molly Victoria Czachur ◽  
Lucas Sire ◽  
Daniel Marquina ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Biodiversity Assessment ◽  
Rapid Biodiversity Assessment

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

2019 ◽  
Vol 18 (3) ◽  
pp. 389-411 ◽  
Author(s):  
Deviram Garlapati ◽  
B. Charankumar ◽  
K. Ramu ◽  
P. Madeswaran ◽  
M. V. Ramana Murthy
Keyword(s):  
Environmental Dna ◽  
Recent Advances

scholarly journals Alpine freshwater fish biodiversity assessment: an intercalibration test for metabarcoding method set up

2021 ◽  
Vol 4 ◽  
Author(s):  
Giulia Riccioni ◽  
Isabelle Domaizon ◽  
Andrea Gandolfi ◽  
Massimo Pindo ◽  
Marine Vautier ◽  
...  
Keyword(s):  
Freshwater Fish ◽  
Population Decline ◽  
Environmental Dna ◽  
Well Being ◽  
Taxonomic Resolution ◽  
Anthropogenic Pressure ◽  
Biodiversity Assessment ◽  
Good Efficiency ◽  
Essential Information ◽  
Fish Biodiversity

Environmental DNA (eDNA) based methods (Fig. 1) are proving to be a promising tool for freshwater fish biodiversity assessment in Europe within the Water Framework Directive (WFD, 2000/60/EC) especially for large rivers and lakes where current fish monitoring techniques have known shortcomings. Freshwater fish are actively involved in aquatic ecosystems functioning and diversity, contributing to the health, well-being and economy in every geographic realm. Unfortunately, many freshwater fish are experiencing critical population decline with risk of local or global extinction because of intense anthropogenic pressure. Within the EU project Eco-AlpsWater, advanced high throughput sequencing (HTS) techniques are used to improve the traditional WFD monitoring approaches by using environmental DNA (eDNA) collected in Alpine waterbodies. To evaluate the performance of the metabarcoding approach specifically designed to measure freshwater fish biodiversity in Alpine lakes and rivers, an intercalibration test was performed. This exercise forecasted the use of mock samples containing either tissue-extracted DNA of different target species or water collected from aquaculture tanks to mimic real environmental water sampling and processing. Moreover, three water samples collected in Lake Bourget (France) were used to compare the efficiency of taxonomic assignments in natural and mock community samples. Our results highlighted a good efficiency of the molecular laboratory protocols for HTS and a good amplification success of the selected primers, providing essential information concerning the taxonomic resolution of the 12S mitochondrial marker. As further confirmation, different concentration of species DNA in the mock samples were well represented by the relative read abundance. This preliminary test confirmed the applicability of eDNA metabarcoding analyses for the biomonitoring of freshwater fish inhabiting Alpine and perialpine lakes and rivers.

scholarly journals Environmental DNA: history of studies, current and perspective applications in fundamental and applied research

2020 ◽  
Vol 18 (4) ◽  
pp. 493-509
Author(s):  
Daria V. Pinakhina ◽  
Elena M. Chekunova
Keyword(s):  
Applied Research ◽  
Environmental Dna ◽  
Review Article ◽  
Biodiversity Assessment ◽  
Major Research ◽  
Research Directions ◽  
History Of ◽  
Key Issues

This review article is dedicated to a relatively young, actively developing approach to biodiversity assessment analysis of environmental DNA (or eDNA). Current views on the nature of eDNA, a brief overview of the history of this approach and methods of eDNA analysis are presented. Major research directions, utilizing eDNA techniques, and perspectives of their application to the study of biodiversity are described. Key issues in development of eDNA approach, its advantages and drawbacks are outlined.

scholarly journals New 12S metabarcoding primers for enhanced Neotropical freshwater fish biodiversity assessment

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
David T. Milan ◽  
Izabela S. Mendes ◽  
Júnio S. Damasceno ◽  
Daniel F. Teixeira ◽  
Naiara G. Sales ◽  
...  
Keyword(s):  
Fish Species ◽  
Species Delimitation ◽  
Fish Fauna ◽  
Environmental Dna ◽  
Threshold Value ◽  
Full Length ◽  
Taxonomic Resolution ◽  
Reference Database ◽  
Biodiversity Assessment ◽  
Neotropical Fish

Abstract The megadiverse Neotropical fish fauna lacks a comprehensive and reliable DNA reference database, which hampers precise species identification and DNA based biodiversity assessment in the region. Here, we developed a mitochondrial 12S ribosomal DNA reference database for 67 fish species, representing 54 genera, 25 families, and six major Neotropical orders. We aimed to develop mini-barcode markers (i.e. amplicons with less than 200 bp) suitable for DNA metabarcoding by evaluating the taxonomic resolution of full-length and mini-barcodes and to determine a threshold value for fish species delimitation using 12S. Evaluation of the target amplicons demonstrated that both full-length library (565 bp) and mini-barcodes (193 bp) contain enough taxonomic resolution to differentiate all 67 fish species. For species delimitation, interspecific genetic distance threshold values of 0.4% and 0.55% were defined using full-length and mini-barcodes, respectively. A custom reference database and specific mini-barcode markers are important assets for ecoregion scale DNA based biodiversity assessments (such as environmental DNA) that can help with the complex task of conserving the megadiverse Neotropical ichthyofauna.

scholarly journals Spider webs as eDNA tool for biodiversity assessment of life’s domains

2020 ◽  
Author(s):  
Matjaž Gregorič ◽  
Denis Kutnjak ◽  
Katarina Bačnik ◽  
Cene Gostinčar ◽  
Anja Pecman ◽  
...  
Keyword(s):  
Spatial Information ◽  
Wide Spectrum ◽  
Environmental Dna ◽  
Amplicon Sequencing ◽  
Biodiversity Assessment ◽  
Biodiversity Monitoring ◽  
Spider Webs ◽  
Spider Web ◽  
Domains Of Life ◽  
Temporal And Spatial

AbstractThe concept of environmental DNA (eDNA) utilizes nucleic acids of organisms directly from the environment. Recent breakthrough studies have successfully detected a wide spectrum of prokaryotic and eukaryotic eDNA from a variety of environments, ranging from ancient to modern, and from terrestrial to aquatic. These numerous sources promise to establish eDNA as a tool for diverse scientific settings. Here, we propose and establish spider webs as a source of eDNA with far reaching implications. First, we conducted a field study to track specific arthropod targets from different spider webs. We then employed high-throughput amplicon sequencing of taxonomic barcodes to investigate the utility of spider web eDNA for biodiversity monitoring of animals, fungi and bacteria. Our results show that genetic remains on spider webs allow the detection of even the smallest target organisms. We also demonstrate that eDNA from spider webs is useful in research of community compositions in different domains of life, with potentially highly detailed temporal and spatial information.

scholarly journals Estimating fish alpha- and beta-diversity along a small stream with environmental DNA metabarcoding

2018 ◽  
Vol 2 ◽  
pp. e24262 ◽  
Author(s):  
Yiyuan Li ◽  
Nathan T. Evans ◽  
Mark A. Renshaw ◽  
Christopher L. Jerde ◽  
Brett P. Olds ◽  
...  
Keyword(s):  
Species Turnover ◽  
Environmental Dna ◽  
Physical Distance ◽  
Similar Species ◽  
Biodiversity Assessment ◽  
Stream Length ◽  
Small Stream ◽  
Alpha And Beta Diversity ◽  
Β Diversity ◽  
Α Diversity

Environmental DNA (eDNA) metabarcoding has been increasingly applied to biodiversity surveys in stream ecosystems. In stream networks, the accuracy of eDNA-based biodiversity assessment depends on whether the upstream eDNA influx affects downstream detection. Biodiversity assessment in low-discharge streams should be less influenced by eDNA transport than in high-discharge streams. We estimated α- and β-diversity of the fish community from eDNA samples collected in a small Michigan (USA) stream from its headwaters to its confluence with a larger river. We found that α-diversity increased from upstream to downstream and, as predicted, we found a significant positive correlation between β-diversity and physical distance (stream length) between locations indicating species turnover along the longitudinal stream gradient. Sample replicates and different genetic markers showed similar species composition, supporting the consistency of the eDNA metabarcoding approach to estimate α- and β-diversity of fishes in low-discharge streams.

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