scholarly journals Complexity matters: Evaluating the impact of bioinformatics parameters on eukaryotic MOTU delimitation and taxonomy assignment

2021 ◽  
Vol 4 ◽  
Author(s):  
Holly Bik
Keyword(s):  
Recent Work ◽  
Marine Sediment ◽  
Dna Sequences ◽  
Environmental Dna ◽  
Microbial Eukaryotes ◽  
Dna Metabarcoding ◽  
Animal Phyla ◽  
Global Biodiversity ◽  
Intragenomic Variation ◽  
The Impact

Microbial metazoans (e.g. nematodes, copepods, tardigrades and other 'minor' animal phyla < 1mm in size) are ubiquitous and abundant across most ecosystems on earth. In marine sediment habitats, microbial metazoa exhibit high biodiversity but suffer from poor taxonomy and an ongoing lack of reference DNA sequences in public databases. Environmental DNA metabarcoding thus represents an increasingly critical tool for rapidly assessing the global biodiversity and phylogeographic patterns of such neglected metazoan groups. However, there are significant bioinformatics hurdles facing the study of microbial eukaryotes. Most software pipelines and databases have been designed and optimized for smaller (e.g. bacteria/archaea) or larger (e.g. vertebrate) taxa, and emphasize "standard" metabarcoding loci such as COI which are not useful for groups such as nematodes which lack universal COI primer binding regions. In addition, the sparsity of public reference barcodes for microbial metazoa often precludes accurate taxonomy assignments for unknown MOTUs in metabarcoding datasets. Here, I will present recent work focused on the refinement of bionformatics workflows for microbial metazoan groups, including efforts to account for intragenomic variation observed in rRNA loci, discrepancies in results across OTU vs. ASV generation pipelines, and biases in sequence-based taxonomhy assignment methods.

scholarly journals Monitoring fish communities through environmental DNA metabarcoding in the fish pass system of the second largest hydropower plant in the world

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Giorgi Dal Pont ◽  
Camila Duarte Ritter ◽  
Andre Olivotto Agostinis ◽  
Paula Valeska Stica ◽  
Aline Horodesky ◽  
...  
Keyword(s):  
Fish Communities ◽  
Environmental Dna ◽  
Hydropower Plant ◽  
Southeastern Brazil ◽  
Fish Diversity ◽  
Pass System ◽  
Fish Pass ◽  
Dna Metabarcoding ◽  
The World ◽  
The Impact

AbstractThe Itaipu Hydroelectric Power Plant is the second largest in the world in power generation. The artificial barrier created by its dam imposes an obstacle for fish migration. Thus, in 2002, a fish pass system, named Piracema Channel, was built to allow fish to access areas upstream of the reservoir. We tested the potential of environmental DNA metabarcoding to monitor the impact of both the dam and associated fish pass system in the Paraná River fish communities and to compare it with traditional monitoring methods. Using a fragment of the 12S gene, we characterized richness and community composition based on amplicon sequence variants, operational taxonomic units, and zero-radius OTUs. We combined GenBank and in-house data for taxonomic assignment. We found that different bioinformatics approaches showed similar results. Also, we found a decrease in fish diversity from 2019 to 2020 probably due to the recent extreme drought experienced in southeastern Brazil. The highest alpha diversity was recorded in the mouth of the fish pass system, located in a protected valley with the highest environmental heterogeneity. Despite the clear indication that the reference databases need to be continuously improved, our results demonstrate the analytical efficiency of the metabarcoding to monitor fish species.

scholarly journals DNA Metabarcoding Reveals Broad Presence of Plant Pathogenic Oomycetes in Soil From Internationally Traded Plants

2021 ◽  
Vol 12 ◽  
Author(s):  
Simeon Rossmann ◽  
Erik Lysøe ◽  
Monica Skogen ◽  
Venche Talgø ◽  
May Bente Brurberg
Keyword(s):  
Dna Sequences ◽  
Assessment Tool ◽  
Disease Outbreaks ◽  
Environmental Dna ◽  
Its Region ◽  
Rhizospheric Soil ◽  
Enrichment Method ◽  
Detection And Identification ◽  
Dna Metabarcoding ◽  
Abundant Genus

Plants with roots and soil clumps transported over long distances in plant trading can harbor plant pathogenic oomycetes, facilitating disease outbreaks that threaten ecosystems, biodiversity, and food security. Tools to detect the presence of such oomycetes with a sufficiently high throughput and broad scope are currently not part of international phytosanitary testing regimes. In this work, DNA metabarcoding targeting the internal transcribed spacer (ITS) region was employed to broadly detect and identify oomycetes present in soil from internationally shipped plants. This method was compared to traditional isolation-based detection and identification after an enrichment step. DNA metabarcoding showed widespread presence of potentially plant pathogenic Phytophthora and Pythium species in internationally transported rhizospheric soil with Pythium being the overall most abundant genus observed. Baiting, a commonly employed enrichment method for Phytophthora species, led to an increase of golden-brown algae in the soil samples, but did not increase the relative or absolute abundance of potentially plant pathogenic oomycetes. Metabarcoding of rhizospheric soil yielded DNA sequences corresponding to oomycete isolates obtained after enrichment and identified them correctly but did not always detect the isolated oomycetes in the same samples. This work provides a proof of concept and outlines necessary improvements for the use of environmental DNA (eDNA) and metabarcoding as a standalone phytosanitary assessment tool for broad detection and identification of plant pathogenic oomycetes.

scholarly journals Let me see your iD: Impacts of Environmental Stressors on Aquatic Ecosystems Assessed by (e)DNA Metabarcoding

2018 ◽  
Vol 2 ◽  
pp. e25983
Author(s):  
Romana Salis ◽  
Arne Beermann ◽  
Jan Macher ◽  
Christoph Matthaei ◽  
Jeremy Piggott ◽  
...  
Keyword(s):  
Case Studies ◽  
Aquatic Ecosystems ◽  
Environmental Dna ◽  
Quantitative Information ◽  
Freshwater Ecosystems ◽  
Environmental Stressors ◽  
Macroinvertebrate Communities ◽  
Ecological Requirements ◽  
Dna Metabarcoding ◽  
The Impact

Traditionally, taxonomic characterisation of organisms has relied on their morphology; however, molecular methods are increasingly used to monitor and assess biodiversity and ecosystem health. Approaches such as DNA amplicon diversity assessments are a particularly useful tool when morphology-based taxonomy is difficult or taxa are morphologically ambiguous, for example for freshwater bacteria and fungi as well as many freshwater invertebrate species. DNA metabarcoding provides the ability to distinguish cryptic taxa (which can differ markedly in their ecological requirements and tolerances) and in addition it can provide valuable insights into the genetic and ecological diversity of taxa and ecosystems. While DNA metabarcoding has been used mostly on tissue of sampled specimens, recent years have seen an increased use of metabarcoding on environmental DNA samples: DNA extracted not from sampled specimens, but from the surrounding soil or water. However, the ability of metabarcoding of specimens and metabarcoding of environmental DNA (eDNA) to assess biodiversity and the impact of anthropogenic stressors on freshwater ecosystems is largely understudied. In this talk, several studies that document the advantages and still open challenges of (e)DNA metabarcoding for assessing impacts of environmental stressors on aquatic ecosystems will be presented. These studies, performed in Europe and New Zealand, integrate impacts across different biotic groups, i.e. look at stressor effects on bacterial, protist, fungal and macroinvertebrate communities. Specifically, we use various case studies from freshwater ecosystems to address the following questions: whether eDNA samples, which can be relatively quickly obtained from the water, can act as reliable proxies for catchment-level stressor impacts by comparing these to DNA obtained from local bulk samples, and whether DNA metabarcoding data can also provide quantitative information rather than only presence-absence data. In view of the case studies presented, a perspective on the urgent next steps that need to be taken in order to include genetic tools in routine biomonitoring will be derived and linked to the vision of the international network DNAqua-Net.

COMPARATIVE STUDY BETWEEN FISH COLLECTION BY NATIONAL CENSUS ON RIVER ENVIRONMENT AND ENVIRONMENTAL DNA METABARCODING

2018 ◽  
Vol 74 (5) ◽  
pp. I_415-I_420 ◽  
Author(s):  
Yoshihisa AKAMATSU ◽  
Takayoshi TSUZUKI ◽  
Ryota YOKOYAMA ◽  
Yayoi FUNAHASHI ◽  
Munehiro OHTA ◽  
...  
Keyword(s):  
Comparative Study ◽  
Environmental Dna ◽  
Dna Metabarcoding ◽  
Fish Collection

Environmental DNA for functional diversity

2018 ◽  
Author(s):  
Pierre Taberlet ◽  
Aurélie Bonin ◽  
Lucie Zinger ◽  
Eric Coissac
Keyword(s):  
Functional Groups ◽  
Functional Diversity ◽  
Environmental Dna ◽  
Soil Organisms ◽  
Meaningful Information ◽  
Dna Metabarcoding ◽  
Pros And Cons ◽  
Target Community

Chapter 10 “Environmental DNA for functional diversity” discusses the potential of environmental DNA to assess functional diversity. It first focuses on DNA metabarcoding and discusses the extent to which this approach can be used and/or optimized to retrieve meaningful information on the functions of the target community. This knowledge usually involves coarsely defined functional groups (e.g., woody, leguminous, graminoid plants; shredders or decomposer soil organisms; pathogenicity or decomposition role of certain microorganisms). Chapter 10 then introduces metagenomics and metatranscriptomics approaches, their advantages, but also the challenges and solutions to appropriately sampling, sequencing these complex DNA/RNA populations. Chapter 10 finally presents several strategies and software to analyze metagenomes/metatranscriptomes, and discusses their pros and cons.

Environmental DNA

2018 ◽  
Author(s):  
Pierre Taberlet ◽  
Aurélie Bonin ◽  
Lucie Zinger ◽  
Eric Coissac
Keyword(s):  
Graduate Students ◽  
Feeding Habits ◽  
Environmental Dna ◽  
Research Field ◽  
Background Information ◽  
Ecological Processes ◽  
Biodiversity Research ◽  
Dna Metabarcoding ◽  
Standard Information

Environmental DNA (eDNA), i.e. DNA released in the environment by any living form, represents a formidable opportunity to gather high-throughput and standard information on the distribution or feeding habits of species. It has therefore great potential for applications in ecology and biodiversity management. However, this research field is fast-moving, involves different areas of expertise and currently lacks standard approaches, which calls for an up-to-date and comprehensive synthesis. Environmental DNA for biodiversity research and monitoring covers current methods based on eDNA, with a particular focus on “eDNA metabarcoding”. Intended for scientists and managers, it provides the background information to allow the design of sound experiments. It revisits all steps necessary to produce high-quality metabarcoding data such as sampling, metabarcode design, optimization of PCR and sequencing protocols, as well as analysis of large sequencing datasets. All these different steps are presented by discussing the potential and current challenges of eDNA-based approaches to infer parameters on biodiversity or ecological processes. The last chapters of this book review how DNA metabarcoding has been used so far to unravel novel patterns of diversity in space and time, to detect particular species, and to answer new ecological questions in various ecosystems and for various organisms. Environmental DNA for biodiversity research and monitoring constitutes an essential reading for all graduate students, researchers and practitioners who do not have a strong background in molecular genetics and who are willing to use eDNA approaches in ecology and biomonitoring.

Estimating aquatic plant diversity and distribution in rivers from Jingjinji Region, China, using environmental DNA metabarcoding and a traditional survey method

2021 ◽  
pp. 111348
Author(s):  
Fenfen Ji ◽  
Liang Yan ◽  
Saihong Yan ◽  
Tianlong Qin ◽  
Jianzhong Shen ◽  
...  
Keyword(s):  
Plant Diversity ◽  
Aquatic Plant ◽  
Environmental Dna ◽  
Survey Method ◽  
Dna Metabarcoding

Systematic benchmark of ancient DNA read mapping

2021 ◽  
Author(s):  
Adrien Oliva ◽  
Raymond Tobler ◽  
Alan Cooper ◽  
Bastien Llamas ◽  
Yassine Souilmi
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Population Genetic ◽  
Reference Genome ◽  
Population Data ◽  
Human Populations ◽  
Current Standard ◽  
Read Mapping ◽  
Reference Bias ◽  
The Impact

Abstract The current standard practice for assembling individual genomes involves mapping millions of short DNA sequences (also known as DNA ‘reads’) against a pre-constructed reference genome. Mapping vast amounts of short reads in a timely manner is a computationally challenging task that inevitably produces artefacts, including biases against alleles not found in the reference genome. This reference bias and other mapping artefacts are expected to be exacerbated in ancient DNA (aDNA) studies, which rely on the analysis of low quantities of damaged and very short DNA fragments (~30–80 bp). Nevertheless, the current gold-standard mapping strategies for aDNA studies have effectively remained unchanged for nearly a decade, during which time new software has emerged. In this study, we used simulated aDNA reads from three different human populations to benchmark the performance of 30 distinct mapping strategies implemented across four different read mapping software—BWA-aln, BWA-mem, NovoAlign and Bowtie2—and quantified the impact of reference bias in downstream population genetic analyses. We show that specific NovoAlign, BWA-aln and BWA-mem parameterizations achieve high mapping precision with low levels of reference bias, particularly after filtering out reads with low mapping qualities. However, unbiased NovoAlign results required the use of an IUPAC reference genome. While relevant only to aDNA projects where reference population data are available, the benefit of using an IUPAC reference demonstrates the value of incorporating population genetic information into the aDNA mapping process, echoing recent results based on graph genome representations.

scholarly journals Environmental DNA preserved in marine sediment for detecting jellyfish blooms after a tsunami

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mizuki Ogata ◽  
Reiji Masuda ◽  
Hiroya Harino ◽  
Masayuki K. Sakata ◽  
Makoto Hatakeyama ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Oil Spills ◽  
Sediment Cores ◽  
Environmental Dna ◽  
Target Species ◽  
Tank Experiment ◽  
Polycyclic Aromatic ◽  
Flow Through ◽  
High Concentrations ◽  
One Year

AbstractEnvironmental DNA (eDNA) can be a powerful tool for detecting the distribution and abundance of target species. This study aimed to test the longevity of eDNA in marine sediment through a tank experiment and to use this information to reconstruct past faunal occurrence. In the tank experiment, juvenile jack mackerel (Trachurus japonicus) were kept in flow-through tanks with marine sediment for two weeks. Water and sediment samples from the tanks were collected after the removal of fish. In the field trial, sediment cores were collected in Moune Bay, northeast Japan, where unusual blooms of jellyfish (Aurelia sp.) occurred after a tsunami. The samples were analyzed by layers to detect the eDNA of jellyfish. The tank experiment revealed that after fish were removed, eDNA was not present in the water the next day, or subsequently, whereas eDNA was detectable in the sediment for 12 months. In the sediment core samples, jellyfish eDNA was detected at high concentrations above the layer with the highest content of polycyclic aromatic hydrocarbons, reflecting tsunami-induced oil spills. Thus, marine sediment eDNA preserves a record of target species for at least one year and can be used to reconstruct past faunal occurrence.

Environmental DNA metabarcoding as a useful tool for evaluating terrestrial mammal diversity in tropical forests

2021 ◽  
Author(s):  
José Luis Mena ◽  
Hiromi Yagui ◽  
Vania Tejeda ◽  
Emilio Bonifaz ◽  
Eva Bellemain ◽  
...  
Keyword(s):  
Tropical Forests ◽  
Environmental Dna ◽  
Terrestrial Mammal ◽  
Dna Metabarcoding ◽  
Mammal Diversity
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