scholarly journals Biodiversity assessments in the 21st century: the potential of insect traps to complement environmental samples for estimating eukaryotic and prokaryotic diversity using high-throughput DNA metabarcoding

Genome ◽  
2019 ◽  
Vol 62 (3) ◽  
pp. 147-159 ◽  
Author(s):  
Camila D. Ritter ◽  
Sibylle Häggqvist ◽  
Dave Karlsson ◽  
Ilari E. Sääksjärvi ◽  
A. Muthama Muasya ◽  
...  
Keyword(s):  
Species Identification ◽  
Environmental Dna ◽  
Cost Effective ◽  
Taxonomic Composition ◽  
Soil Samples ◽  
Morphological Studies ◽  
Prokaryotic Diversity ◽  
Dna Metabarcoding ◽  
Morphological Species ◽  
Ecosystem Interactions

The rapid loss of biodiversity, coupled with difficulties in species identification, call for innovative approaches to assess biodiversity. Insects make up a substantial proportion of extant diversity and play fundamental roles in any given ecosystem. To complement morphological species identification, new techniques such as metabarcoding make it possible to quantify insect diversity and insect–ecosystem interactions through DNA sequencing. Here we examine the potential of bulk insect samples (i.e., containing many non-sorted specimens) to assess prokaryote and eukaryote biodiversity and to complement the taxonomic coverage of soil samples. We sampled 25 sites on three continents and in various ecosystems, collecting insects with SLAM traps (Brazil) and Malaise traps (South Africa and Sweden). We then compared our diversity estimates with the results obtained with biodiversity data from soil samples from the same localities. We found a largely different taxonomic composition between the soil and insect samples, testifying to the potential of bulk insect samples to complement soil samples. Finally, we found that non-destructive DNA extraction protocols, which preserve insect specimens for morphological studies, constitute a promising choice for cost-effective biodiversity assessments. We propose that the sampling and sequencing of insect samples should become a standard complement for biodiversity studies based on environmental DNA.

scholarly journals The power of metabarcoding: Can we improve bioassessment and biodiversity surveys of stream macroinvertebrate communities?

2021 ◽  
Vol 5 ◽  
Author(s):  
Jarno Turunen ◽  
Heikki Mykrä ◽  
Vasco Elbrecht ◽  
Dirk Steinke ◽  
Thomas Braukmann ◽  
...  
Keyword(s):  
Species Identification ◽  
Cost Effective ◽  
Morphological Identification ◽  
Macroinvertebrate Communities ◽  
Dna Metabarcoding ◽  
Stream Macroinvertebrate ◽  
Data Deficient ◽  
Morphological Species ◽  
High Level ◽  
The Impact

Most stream bioassessment and biodiversity surveys are currently based on morphological identification of communities. However, DNA metabarcoding is emerging as a fast and cost-effective alternative for species identification. We compared both methods in a survey of benthic macroinvertebrate communities across 36 stream sites in northern Finland. We identified 291 taxa of which 62% were identified only by DNA metabarcoding. DNA metabarcoding produced extensive species level inventories for groups (Oligochaeta, Chironomidae, Simuliidae, Limoniidae and Limnephilidae), for which morphological identification was not feasible due to the high level of expertise needed. Metabarcoding also provided more insightful taxonomic information on the occurrence of three red-listed vulnerable or data deficient species, the discovery of two likely cryptic and potentially new species to Finland and species information of insect genera at an early larval stage that could not be separated morphologically. However, it systematically failed to reliably detect the occurrence of gastropods that were easily identified morphologically. The impact of mining on community structure could only be shown using DNA metabarcoding data which suggests that the finer taxonomic detail can improve detection of subtle impacts. Both methods generally exhibited similar strength of community-environment relationships, but DNA metabarcoding showed better performance with presence/absence data than with relative DNA sequence abundances. Our results suggest that DNA metabarcoding holds a promise for future anthropogenic impact assessments, although, in our case, the performance did not improve much from the morphological species identification. The key advantage of DNA metabarcoding lies in efficient biodiversity surveys, taxonomical studies and applications in conservation biology.

scholarly journals Characterizing parasitic nematode faunas in faeces and soil using DNA metabarcoding

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Marie Louise Davey ◽  
Kjersti Selstad Utaaker ◽  
Frode Fossøy
Keyword(s):  
Parasitic Nematode ◽  
Cost Effective ◽  
Gastrointestinal Nematodes ◽  
Soil Samples ◽  
Taxonomic Resolution ◽  
Parasitic Nematodes ◽  
Morphological Identification ◽  
Detection Rates ◽  
Non Invasive ◽  
Dna Metabarcoding

Abstract Background Gastrointestinal parasitic nematodes can impact fecundity, development, behaviour, and survival in wild vertebrate populations. Conventional monitoring of gastrointestinal parasitic nematodes in wild populations involves morphological identification of eggs, larvae, and adults from faeces or intestinal samples. Adult worms are typically required for species-level identification, meaning intestinal material from dead animals is needed to characterize the nematode community with high taxonomic resolution. DNA metabarcoding of environmental samples is increasingly used for time- and cost-effective, high-throughput biodiversity monitoring of small-bodied organisms, including parasite communities. Here, we evaluate the potential of DNA metabarcoding of faeces and soil samples for non-invasive monitoring of gastrointestinal parasitic nematode communities in a wild ruminant population. Methods Faeces and intestines were collected from a population of wild reindeer, and soil was collected both from areas showing signs of animal congregation, as well as areas with no signs of animal activity. Gastrointestinal parasitic nematode faunas were characterized using traditional morphological methods that involve flotation and sedimentation steps to concentrate nematode biomass, as well as using DNA metabarcoding. DNA metabarcoding was conducted on bulk samples, in addition to samples having undergone sedimentation and flotation treatments. Results DNA metabarcoding and morphological approaches were largely congruent, recovering similar nematode faunas from all samples. However, metabarcoding provided higher-resolution taxonomic data than morphological identification in both faeces and soil samples. Although concentration of nematode biomass by sedimentation or flotation prior to DNA metabarcoding reduced non-target amplification and increased the diversity of sequence variants recovered from each sample, the pretreatments did not improve species detection rates in soil and faeces samples. Conclusions DNA metabarcoding of bulk faeces samples is a non-invasive, time- and cost-effective method for assessing parasitic nematode populations that provides data with comparable taxonomic resolution to morphological methods that depend on parasitological investigations of dead animals. The successful detection of parasitic gastrointestinal nematodes from soils demonstrates the utility of this approach for mapping distribution and occurrences of the free-living stages of gastrointestinal parasitic nematodes. Graphical abstract

scholarly journals Considerations for metabarcoding-based port biological baseline surveys aimed at marine non-indigenous species monitoring and risk-assessments

2019 ◽  
Author(s):  
Anaïs Rey ◽  
Oihane C. Basurko ◽  
Naiara Rodriguez-Ezpeleta
Keyword(s):  
Environmental Dna ◽  
Cost Effective ◽  
Taxonomic Composition ◽  
Risk Assessments ◽  
List Type ◽  
Indigenous Species ◽  
Promising Alternative ◽  
International Convention ◽  
Outer Estuary ◽  
Non Indigenous Species

AbstractMonitoring introduction and spread of non-indigenous species via maritime transport and performing risk assessments require port biological baseline surveys. Yet, the comprehensiveness of these surveys is often compromised by the large number of habitats present in a port, the seasonal variability and the time-consuming morphological approach used for taxonomic identification. Metabarcoding represents a promising alternative for rapid comprehensive port biological baseline surveys, but its application in this context requires further assessments.We applied metabarcoding (based on barcodes of the Cytochrome c oxidase subunit I and of the 18S ribosomal RNA gene) to 192 port samples collected i) from diverse habitats (water column – including environmental DNA and zooplankton, sediment and fouling structures), ii) at different sites (from inner to outer estuary), and iii) during the four seasons of the year.By comparing the biodiversity metrics derived from each sample group, we show that each sampling method resulted in a distinct community profile and that environmental DNA alone cannot substitute for organismal sampling, and that, although sampling at different seasons and locations resulted in higher observed biodiversity, operational results can be obtained by sampling selected locations and seasons.By assessing the taxonomic composition of the samples, we show that metabarcoding data allowed the detection of previously recorded non-indigenous species as well as to reveal presence of new ones, even if in low abundance.Synthesis and application. Our comprehensive assessment of metabarcoding for port biological baseline surveys sets the basics for cost-effective, standardized and comprehensive monitoring of non-indigenous species and for performing risk assessments in ports. This development will contribute to the implementation of the recently entered into force International Convention for the Control and Management of Ships’ Ballast Water and Sediments.

scholarly journals Soil Metabarcoding Offers a New Tool for the Investigation and Hunting of Truffles in Northern Thailand

2021 ◽  
Vol 7 (4) ◽  
pp. 293
Author(s):  
Nakarin Suwannarach ◽  
Jaturong Kumla ◽  
Ammarin In-on ◽  
Saisamorn Lumyong
Keyword(s):  
Morphological Characteristics ◽  
Environmental Dna ◽  
Soil Samples ◽  
Northern Thailand ◽  
Its1 Region ◽  
Dna Metabarcoding ◽  
New Locations ◽  
Molecular Phylogenetic ◽  
Management And Conservation ◽  
Tuber Species

Truffles (Tuber spp.) are well-known as edible ectomycorrhizal mushrooms, and some species are one of the most expensive foods in the world. During the fruiting process, truffles produce hypogeous ascocarps; a trained pig or dog is needed to locate the ascocarps under the ground. Truffles in northern Thailand have been recorded in association with Betulaalnoides and Carpinus poilanei. In this study, we investigated the soil mycobiota diversity of soil samples from both of these truffle host plants in native forests using environmental DNA metabarcoding to target the internal transcribed spacer 1 (ITS1) region of the rDNA gene for the purposes of investigation of truffle diversity and locating truffles during the non-fruiting phase. In this study, a total of 38 soil samples were collected from different locations. Of these, truffles had been found at three of these locations. Subsequently, a total of 1341 putative taxonomic units (OTUs) were obtained. The overall fungal community was dominated by phylum-level sequences assigned to Ascomycota (57.63%), Basidiomycota (37.26%), Blastocladiomycota (0.007%), Chytridiomycota (0.21%), Glomeromycota (0.01%), Kickxellomycota (0.01%), Mortierellomycota (2.08%), Mucoromycota (0.24%), Rozellomycota (0.01%), Zoopagomycota (0.003%), and unidentified (2.54%). The results revealed that six OTUs were determined to be representative and belonged to the genus Tuber. OTU162, OTU187, OTU447, and OTU530 belonged to T. thailandicum, T. lannaense, T. bomiense, and T. magnatum, whereas OTU105 and OTU720 were acknowledged as unrecognized Tuber species. From 38 locations, OTUs of truffles were found in 33 locations (including three previously known truffle locations). Thus, 30 collection sites were considered new locations for T. thailandicum, T. bomiense, and other unrecognized Tuber species. Interestingly, at 16 new locations, mature ascocarps of truffles that were undergoing the fruiting phase were located underground. All 16 truffle samples were identified as T. thailandicum based on morphological characteristics and molecular phylogenetic analysis. However, ascocarps of other truffle species were not found at the new OTUs representative locations. The knowledge gained from this study can be used to lead researchers to a better understanding of the occurrence of truffles using soil mycobiota diversity investigation. The outcomes of this study will be particularly beneficial with respect to the search and hunt for truffles without the need for trained animals. In addition, the findings of this study will be useful for the management and conservation of truffle habitats in northern Thailand.

scholarly journals Revisiting the effect of PCR replication and sequencing depth on biodiversity metrics in environmental DNA metabarcoding

2021 ◽  
Author(s):  
Sabrina Shirazi ◽  
Rachel Meyer ◽  
Beth Shapiro
Keyword(s):  
Environmental Dna ◽  
Data Interpretation ◽  
Soil Samples ◽  
Data Sets ◽  
Average Depth ◽  
Rare Taxa ◽  
Β Diversity ◽  
Large Numbers ◽  
Dna Metabarcoding ◽  
Methodological Approaches

Environmental DNA (eDNA) metabarcoding is a common tool for measuring and cataloguing biodiversity, yet standard methodological approaches to generate metabarcoding data sets have yet to emerge, in part due to challenges understanding the biological and technical biases that affect eDNA profiles. Here, we explore how two experimental choices – depth of sequencing of PCR amplicon libraries and the number of PCR replicates – influence estimates of α and β diversity. We extracted DNA from six soil samples from three ecologically distinct locations, performed 24 PCR replicates from each using two common metabarcodes, and sequenced each to an average depth of 83,898 reads. We found PCR replicates are consistent in composition and relative abundance of abundant taxa, allowing differentiation of samples and sites. However, rare taxa were unique to one or a few replicates, suggesting that even large numbers of experimental replicates may be insufficient to catalogue biodiversity fully. We recommend that to differentiate sites, separately sequencing only a minimum of two PCR replicates to a depth that allows 1,000 reads identified to taxa, is sufficient to differentiate sites. We also conclude that metabarcoding is impractical for exhaustive taxonomic inventory and, because rare taxa are not amplified consistently, taxonomic tallies that rely on consensus among replicates artificially lower richness estimates. These findings provide new considerations for eDNA experimental design and data interpretation.

scholarly journals Environmental DNA metabarcoding as an effective and rapid tool for fish monitoring in canals:

2018 ◽  
Author(s):  
Allan D McDevitt ◽  
Naiara Guimaraes Sales ◽  
Samuel S Browett ◽  
Abbie Sparnenn ◽  
Stefano Mariani ◽  
...  
Keyword(s):  
Fish Assemblages ◽  
Fish Communities ◽  
Environmental Dna ◽  
Cost Effective ◽  
Aquatic Habitats ◽  
Dna Metabarcoding ◽  
Canal Systems ◽  
Rapid Tool ◽  
Fish Monitoring

Environmental DNA (eDNA) metabarcoding has revolutionized biomonitoring of aquatic habitats. Man-made canal systems are among the least-studied environments in terms of biodiversity in Britain. Here we focus on a case study along an English canal comparing eDNA metabarcoding with two types of electrofishing techniques (wade-and-reach and boom-boat). In addition to corroborating data obtained by electrofishing, eDNA provided a wider snapshot of fish assemblages. Given the semi-lotic nature of canals, we encourage the use of eDNA as a fast and cost-effective tool to detect and monitor whole fish communities.

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.

scholarly journals Development of Quantum Dot (QD) Based Color Converters for Multicolor Display

Nanomaterials ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1089
Author(s):  
Muhammad T. Sajjad ◽  
Ashu K. Bansal ◽  
Francesco Antolini ◽  
Eduard Preis ◽  
Lenuta Stroea ◽  
...  
Keyword(s):  
Polymer Matrix ◽  
Cost Effective ◽  
Final Size ◽  
Force Microscopy ◽  
Morphological Studies ◽  
Color Displays ◽  
Transmission Electron ◽  
Different Temperatures ◽  
Color Conversion ◽  
Temperature Time

Many displays involve the use of color conversion layers. QDs are attractive candidates as color converters because of their easy processability, tuneable optical properties, high photoluminescence quantum yield, and good stability. Here, we show that emissive QDs with narrow emission range can be made in-situ in a polymer matrix, with properties useful for color conversion. This was achieved by blending the blue-emitting pyridine based polymer with a cadmium selenide precursor and baking their films at different temperatures. To achieve efficient color conversion, blend ratio and baking temperature/time were varied. We found that thermal decomposition of the precursor leads to highly emissive QDs whose final size and emission can be controlled using baking temperature/time. The formation of the QDs inside the polymer matrix was confirmed through morphological studies using atomic force microscopy (AFM) and transmission electron microscopy (TEM). Hence, our approach provides a cost-effective route to making highly emissive color converters for multi-color displays.

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