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 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 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 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.

A Non-Intrusive Pipeline Leak Detection Service Using Pressure-Wave Analysis

2018 ◽  
Author(s):  
Srinivasan Jagannathan ◽  
Neil Stewart ◽  
Graham Jack
Keyword(s):  
Pressure Wave ◽  
Cost Effective ◽  
Leak Detection ◽  
Environmental Damage ◽  
Detailed Knowledge ◽  
Effective Manner ◽  
The Moment ◽  
Pressurized Fluids ◽  
High Level ◽  
The Impact

Product losses from pipelines, whether attributed to acts of man or nature, amount to operator losses of approximately USD 133 billion annually [1], not even considering costs associated with remediation, environmental damage, and reputational harm. When an incident occurs, pipeline operators need to minimize the event by quickly and accurately locating and quantifying the pipeline loss and its cause. Having this detailed knowledge enables determination of the best method for dealing with possible issues while helping minimize remediation costs, pipeline downtime, and the impact of the work on surrounding infrastructure. Currently, most systems for pipeline leak detection are limited to either listening methods, which require being online and monitoring both pipeline ends at the moment the leak occurs, or intrusive methods that require the insertion of a pig into the pipeline. Both of these techniques are restricted in usage because access should be available to both ends of the pipeline. Additionally, for the intrusive method, the pipeline should be piggable and, for the listening method, the instrumentation should be able to communicate with a central data processing point placed at both pipeline ends as they rely on travel time difference between signals received at either end of the pipeline. The method this paper describes is a proven, nonintrusive technology that can be used by pipeline operators to identify losses quickly and safely with a repeatable and verified high level of accuracy. It monitors the signature response of a generated fluid hammer and resulting pressure wave transiting within the pipeline and analyzes the reflected signature wave and pressure data to extrapolate both the location and magnitude of the loss with all pipeline parameters taken into account. The method enables operators to detect, locate, and quantify the loss of pipeline inventory in a safe and cost-effective manner without having to stop production, beyond the temporary closing of a mainline valve, or risk tools or personnel, due to exposure to pressurized fluids, before performing any intervention at the leak site.

scholarly journals Watered-down biodiversity? A comparison of metabarcoding results from DNA extracted from matched water and bulk tissue biomonitoring samples

2019 ◽  
Author(s):  
Mehrdad Hajibabaei ◽  
Teresita M. Porter ◽  
Chloe V. Robinson ◽  
Donald J. Baird ◽  
Shadi Shokralla ◽  
...  
Keyword(s):  
Water Samples ◽  
Cost Effective ◽  
Benthic Invertebrate ◽  
Biological Information ◽  
Morphological Identification ◽  
Sample Type ◽  
Cost Effective Method ◽  
Dna Metabarcoding ◽  
Wetland Complex ◽  
Benthic Invertebrate Communities

AbstractBiomonitoring programs have evolved beyond the sole use of morphological identification to determine the composition of invertebrate species assemblages in an array of ecosystems. The application of DNA metabarcoding in freshwater systems for assessing benthic invertebrate communities is now being employed to generate biological information for environmental monitoring and assessment. A possible shift from the extraction of DNA from net-collected bulk benthic samples to its extraction directly from water samples for metabarcoding has generated considerable interest based on the assumption that taxon detectability is comparable when using either method. To test this, we studied paired water and benthos samples from a taxon-rich wetland complex, to investigate differences in the detection of taxa from each sample type. We demonstrate that metabarcoding of DNA extracted directly from water samples is a poor surrogate for DNA extracted from bulk benthic samples, focusing on key bioindicator groups. Our results continue to support the use of bulk benthic samples as a basis for metabarcoding-based biomonitoring, with nearly three times greater total richness in benthic samples compared to water samples. We also demonstrated that few arthropod taxa are shared between collection methods, with a notable lack of key bioindicator EPTO taxa in the water samples. Although species coverage in water could likely be improved through increased sample replication and/or increased sequencing depth, benthic samples remain the most representative, cost-effective method of generating aquatic compositional information via metabarcoding.

ПРАГМАТИЧНИЙ ПОТЕНЦІАЛ НАТИВНОЇ РЕКЛАМИ: ФОРМИ, ТРЕНДИ (НА ПРИКЛАДІ НАТИВНОГО КОНТЕНТУ В СОЦІАЛЬНІЙ МЕРЕЖІ FACEBOOK ЩОДО БРЕНДА ФАКУЛЬТЕТУ ЖУРНАЛІСТИКИ ЗНУ)

2020 ◽  
pp. 113
Author(s):  
V. Kovpak ◽  
N. Trotsenko
Keyword(s):  
Social Network ◽  
Professional Training ◽  
Educational Process ◽  
Communication Strategy ◽  
Student Centered ◽  
Teacher Student ◽  
The Social ◽  
National University ◽  
High Level ◽  
The Impact

<div><p><em>The article analyzes the peculiarities of the format of native advertising in the media space, its pragmatic potential (in particular, on the example of native content in the social network Facebook by the brand of the journalism department of ZNU), highlights the types and trends of native advertising. The following research methods were used to achieve the purpose of intelligence: descriptive (content content, including various examples), comparative (content presentation options) and typological (types, trends of native advertising, in particular, cross-media as an opportunity to submit content in different formats (video, audio, photos, text, infographics, etc.)), content analysis method using Internet services (using Popsters service). And the native code for analytics was the page of the journalism department of Zaporizhzhya National University on the social network Facebook. After all, the brand of the journalism department of Zaporozhye National University in 2019 celebrates its 15th anniversary. The brand vector is its value component and professional training with balanced distribution of theoretical and practical blocks (seven practices), student-centered (democratic interaction and high-level teacher-student dialogue) and integration into Ukrainian and world educational process (participation in grant programs).</em></p></div><p><em>And advertising on social networks is also a kind of native content, which does not appear in special blocks, and is organically inscribed on one page or another and unobtrusively offers, just remembering the product as if «to the word». Popsters service functionality, which evaluates an account (or linked accounts of one person) for 35 parameters, but the main three areas: reach or influence, or how many users evaluate, comment on the recording; true reach – the number of people affected; network score – an assessment of the audience’s response to the impact, or how far the network information diverges (how many share information on this page).</em></p><p><strong><em>Key words:</em></strong><em> nativeness, native advertising, branded content, special project, communication strategy.</em></p>

Regulatory and sustainability initiatives lead to improved polyaminopolyamide epichlorohydrin (PAE) wet-strength resins and paper products

TAPPI Journal ◽  
2018 ◽  
Vol 17 (09) ◽  
pp. 519-532 ◽  
Author(s):  
Mark Crisp ◽  
Richard Riehle
Keyword(s):  
Health And Safety ◽  
Cost Effective ◽  
Worker Safety ◽  
Regulatory Requirements ◽  
Wet Strength ◽  
The Past ◽  
Consumer Safety ◽  
Federal Institute ◽  
Sustainability Initiatives ◽  
The Impact

Polyaminopolyamide-epichlorohydrin (PAE) resins are the predominant commercial products used to manufacture wet-strengthened paper products for grades requiring wet-strength permanence. Since their development in the late 1950s, the first generation (G1) resins have proven to be one of the most cost-effective technologies available to provide wet strength to paper. Throughout the past three decades, regulatory directives and sustainability initiatives from various organizations have driven the development of cleaner and safer PAE resins and paper products. Early efforts in this area focused on improving worker safety and reducing the impact of PAE resins on the environment. These efforts led to the development of resins containing significantly reduced levels of 1,3-dichloro-2-propanol (1,3-DCP) and 3-monochloropropane-1,2-diol (3-MCPD), potentially carcinogenic byproducts formed during the manufacturing process of PAE resins. As the levels of these byproducts decreased, the environmental, health, and safety (EH&S) profile of PAE resins and paper products improved. Recent initiatives from major retailers are focusing on product ingredient transparency and quality, thus encouraging the development of safer product formulations while maintaining performance. PAE resin research over the past 20 years has been directed toward regulatory requirements to improve consumer safety and minimize exposure to potentially carcinogenic materials found in various paper products. One of the best known regulatory requirements is the recommendations of the German Federal Institute for Risk Assessment (BfR), which defines the levels of 1,3-DCP and 3-MCPD that can be extracted by water from various food contact grades of paper. These criteria led to the development of third generation (G3) products that contain very low levels of 1,3-DCP (typically <10 parts per million in the as-received/delivered resin). This paper outlines the PAE resin chemical contributors to adsorbable organic halogens and 3-MCPD in paper and provides recommendations for the use of each PAE resin product generation (G1, G1.5, G2, G2.5, and G3).

THE IMPACT OF UKRAINE'S EXCISE DUTY POLICY ON THE TRANSFORMATION PROCESSES OF THE TOBACCO MARKET

2020 ◽  
Vol 2020 (10) ◽  
pp. 19-33
Author(s):  
Nadiia NOVYTSKA ◽  
◽  
Inna KHLIEBNIKOVA ◽  
Keyword(s):  
Structural Changes ◽  
Tax Avoidance ◽  
Transformation Process ◽  
State Regulation ◽  
Tobacco Products ◽  
Excise Duty ◽  
Increasing Demand ◽  
High Level ◽  
The Impact ◽  
Transformation Processes

The market of tobacco products in Ukraine is one of the most dynamic and competitive. It develops under the influence of certain factors that cause structural changes, therefore, the aim of the article is to conduct a comprehensive analysis of transformation processes in the market of tobacco and their alternatives in Ukraine and identify the factors that cause them. The high level of tax burden and the proliferation of alternative products with a potentially lower risk to human health, including heating tobacco products and e-cigarettes, are key factors in the market’s transformation process. Their presence leads to an increase in illicit turnover of tobacco products, which accounts for 6.37% of the market, and the gradual replacement of cigarettes with alternative products, which account for 12.95%. The presence on the market of products that are not taxed or taxed at lower rates is one of the reasons for the reduction of excise duty revenues. According to the results of 2019, the planned indicators of revenues were not met by 23.5%. Other reasons for non-fulfillment of excise duty revenues include: declining dynamics of the tobacco products market; reduction in the number of smokers; reorientation of «cheap whites» cigarette flows from Ukraine to neighboring countries; tax avoidance. Prospects for further research are identified, namely the need to develop measures for state regulation and optimization of excise duty taxation of tobacco products and their alternatives, taking into account the risks to public health and increasing demand of illegal products.

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