scholarly journals Airborne environmental DNA for terrestrial vertebrate community monitoring

2021 ◽  
Author(s):  
Christina Lynggaard ◽  
Mads Frost Bertelsen ◽  
Casper V. Jensen ◽  
Matthew S. Johnson ◽  
Tobias Guldberg Froslev ◽  
...  
Keyword(s):  
Large Scale ◽  
Environmental Dna ◽  
Cost Effective ◽  
Monitoring Methods ◽  
Natural Ecosystems ◽  
Terrestrial Vertebrate ◽  
Detection Failure ◽  
Routine Monitoring ◽  
Community Monitoring ◽  
Wide Range

Assessing and studying the distribution, ecology, diversity and movements of species is key in understanding environmental and anthropogenic effects on natural ecosystems. Although environmental DNA is rapidly becoming the tool of choice to assess biodiversity there are few eDNA sample types that effectively capture terrestrial vertebrate diversity and those that do can be laborious to collect, require special permits and contain PCR inhibitory substances, which can lead to detection failure. Thus there is an urgent need for novel environmental DNA approaches for efficient and cost-effective large-scale routine monitoring of terrestrial vertebrate diversity. Here we show that DNA metabarcoding of airborne environmental DNA filtered from air can be used to detect a wide range of local vertebrate taxa. We filtered air at three localities in Copenhagen Zoo, detecting mammal, bird, amphibian and reptile species present in the zoo or its immediate surroundings. Our study demonstrates that airDNA has the capacity to complement and extend existing terrestrial vertebrate monitoring methods and could form the cornerstone of programs to assess and monitor terrestrial communities, for example in future global next generation biomonitoring frameworks.

scholarly journals Advancing the use of molecular methods for routine freshwater macroinvertebrate biomonitoring – the need for calibration experiments

2019 ◽  
Vol 3 ◽  
Author(s):  
Rosetta Blackman ◽  
Elvira Mächler ◽  
Florian Altermatt ◽  
Amanda Arnold ◽  
Pedro Beja ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Molecular Methods ◽  
Macroinvertebrate Communities ◽  
Monitoring Methods ◽  
Molecular Monitoring ◽  
Routine Application ◽  
Routine Monitoring ◽  
Wide Range ◽  
The Status ◽  
Dna 2

Over the last decade, steady advancements have been made in the use of DNA-based methods for detection of species in a wide range of ecosystems. This progress has culminated in molecular monitoring methods being employed for the detection of several species for enforceable management purposes of endangered, invasive, and illegally harvested species worldwide. However, the routine application of DNA-based methods to monitor whole communities (typically a metabarcoding approach) in order to assess the status of ecosystems continues to be limited. In aquatic ecosystems, the limited use is particularly true for macroinvertebrate communities. As part of the DNAqua-Net consortium, a structured discussion was initiated with the aim to identify potential molecular methods for freshwater macroinvertebrate community assessment and identify important knowledge gaps for their routine application. We focus on three complementary DNA sources that can be metabarcoded: 1) DNA from homogenised samples (bulk DNA), 2) DNA extracted from sample preservative (fixative DNA), and 3) environmental DNA (eDNA) from water or sediment. We provide a brief overview of metabarcoding macroinvertebrate communities from each DNA source and identify challenges for their application to routine monitoring. To advance the utilisation of DNA-based monitoring for macroinvertebrates, we propose an experimental design template for a series of methodological calibration tests. The template compares sources of DNA with the goal of identifying the effects of molecular processing steps on precision and accuracy. Furthermore, the same samples will be morphologically analysed, which will enable the benchmarking of molecular to traditional processing approaches. In doing so we hope to highlight pathways for the development of DNA-based methods for the monitoring of freshwater macroinvertebrates.

Enterprise Crowdsourcing Platform to Improve HR Workflow

2020 ◽  
Vol 9 (5) ◽  
pp. 5-8 ◽  
Author(s):  
G. Zuev
Keyword(s):  
Large Scale ◽  
Best Practice ◽  
Cost Effective ◽  
Hr Management ◽  
Practical Project ◽  
Effective Manner ◽  
Wide Range ◽  
Hr Managers ◽  
Short Time ◽  
Small Parts

Crowdsourcing technologies may solve a wide range of business issues: improve efficiency of HR management, increase customer loyalty and maximize economic efficiency of whole enterprise. The recent years best practice has shown how crowdsourcing is gaining particular relevance of human resource management, allowing HR managers to resolve organization relevant problems in quick and cost-effective manner. Important advantage of crowdsourcing сomes from his main ability: decomposition of tasks into small parts and the ability to perform it’s remotely, via Internet. Thanks to this, not only large corporations, but also small and medium-sized businesses can execute a large-scale projects in a short time. This article discusses the main approaches and principles of practical project management via crowdsourcing platforms, using as the example “Beorg Smart Vision” solution.

scholarly journals Airborne environmental DNA for terrestrial vertebrate community monitoring

2022 ◽  
Author(s):  
Christina Lynggaard ◽  
Mads Frost Bertelsen ◽  
Casper V. Jensen ◽  
Matthew S. Johnson ◽  
Tobias Guldberg Frøslev ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Terrestrial Vertebrate ◽  
Community Monitoring

scholarly journals Impresión 3D como Herramienta Didáctica para la Enseñanza de Algunos Conceptos de Ingeniería y Diseño

Ingeniería ◽  
2018 ◽  
Vol 23 (1) ◽  
pp. 70 ◽  
Author(s):  
Edwin Blasnilo Rua Ramirez ◽  
Fernando Jimenez Diaz ◽  
German Andres Gutierrez Arias ◽  
Nelson Iván Villamizar
Keyword(s):  
Teaching And Learning ◽  
Mechanical Engineering ◽  
Large Scale ◽  
Low Cost ◽  
Cost Effective ◽  
3D Printer ◽  
Course Grades ◽  
Wide Range ◽  
Technical Specifications ◽  
Future Work

Context: 3D printing can be used for a wide range of tasks such as the design and testing of prototypes and finished products in a shorter time. In mechanical engineering, prototype designs are continuously generated in academic class activities and final coursework projects by students and teachers. However, students show limitations while understanding the abstract concepts represented with such designs.Method: Firstly, a large scale 3D printer with improved technical specifications compared to traditional market options and similar price, was fabricated. By means of free software and hardware tools and easy-to-obtain alternative manufacturing materials, it was possible to decrease its manufacturing and operating costs. Then a set of study cases utilising the 3D printer in three different subject classes were designed and tested with two cohorts of students of Mechanical Engineering programme.Results: It was feasible to fabricate a cost-effective and practical 3D printer for constructing prototypes and pieces that benefit teaching and learning concepts in engineering and design areas. The experiments carried out in three subjects of engineering courses with second-year students, showed a similar trend of improving the average course grades, as it was observed in two cohorts in different terms.Conclusions: This type of low cost 3D printer obtained academic advantages as a didactic tool for the learning process in engineering and design subjects. Future work will consider applying this tool to other courses and subjects to further evaluate its convenience and effectivity.

scholarly journals A large-scale ecological assessment of Swiss rivers using environmental DNA for the monitoring of macroinvertebrates 

2021 ◽  
Vol 4 ◽  
Author(s):  
Jeanine Brantschen ◽  
Rosetta Blackman ◽  
Jean-Claude Walser ◽  
Florian Altermatt
Keyword(s):  
Random Forest ◽  
Community Composition ◽  
Large Scale ◽  
Anthropogenic Activities ◽  
Ecological Status ◽  
Environmental Dna ◽  
Biotic Index ◽  
Reference Database ◽  
Macroinvertebrate Communities ◽  
Monitoring Methods

Anthropogenic activities are changing the state of ecosystems worldwide, affecting community composition and often resulting in loss of biodiversity. Riverine ecosystems are among the most impacted ecosystems. Recording their current state with regular biomonitoring is important to assess the future trajectory of biodiversity. However, traditional monitoring methods for ecological assessments are costly and time-intense. Here, we compare environmental DNA (eDNA) to traditional kick-net sampling in a standardized framework of surface water quality assessment. We use surveys of macroinvertebrate communities to assess biodiversity and the biological state of riverine systems. Both methods were employed to monitor aquatic macroinvertebrate indicator groups at 92 sites across major Swiss river catchments. The eDNA data were taxonomically assigned using a customised reference database. All zero-radius Operational Taxonomic Units (zOTUs) mapping to one of the 142 traditionally used indicator taxon levels were used for subsequent diversity analyses (n = 205). At the site level, eDNA detected less indicator taxa than the kick-net method and alpha diversity correlated only weakly between the methods. However, the methods showed a strong congruence in the overall community composition (gamma diversity), as the same indicator groups were commonly detected. In order to set the community composition in relation to the biotic index, the ecological states of the sampling sites were predicted by a random forest approach. Using all zOTUs mapping to macroinvertebrate indicator groups (n = 693) as predictive features, the random forest models successfully predicted the ecological status of the sampled sites. The majority of the predictions (71%) resulted in the same classification like the kick-net based scores. Thus, the sampling of eDNA enabled the detection of indicator communities and provided valuable classifications of the ecological state, when combined with machine learning. Overall, eDNA based sampling has the potential to complement traditional surveys of macroinvertebrate communities in routine large-scale assessments in a non-invasive and scalable approach.

scholarly journals A validated protocol for fish farm monitoring using environmental DNA

2021 ◽  
Vol 4 ◽  
Author(s):  
Xavier Pochon ◽  
Susie Wood ◽  
Javier Atalah ◽  
Lauren Fletcher ◽  
Olivier Laroche ◽  
...  
Keyword(s):  
New Zealand ◽  
Assessment Tool ◽  
Environmental Dna ◽  
Fish Farming ◽  
Cost Effective ◽  
Low Flow ◽  
Biotic Index ◽  
Fish Farms ◽  
Physico Chemical ◽  
Wide Range

Sea-based fish farms are associated with strong benthic enrichment gradients and routine monitoring is usually required by regulation. Internationally a wide range of approaches exist for measuring the degree of benthic deterioration around fish farming activities, ranging from simple visual or odour assessments to the calculation of secondary indices that combine multiple biological and/or physico-chemical metrics (e.g., AZTI Marine Biotic Index; Invertebrate Species Index; Norwegian Quality Index; Infauna Trophic Index). In New Zealand, the health of marine benthic ecosystems around coastal salmon farms is currently measured using an Enrichment State (ES) index. This index incorporates physico-chemical (redox, organic matter, sulphates, etc.) and benthic macrofaunal measurements, which requires taxonomic expertise, is time consuming and expensive. Supported by a range of private/government agencies and industry partners, we have developed and tested the robustness of bacterial, eukaryotic, and multi-trophic Metabarcoding Biotic Indices (b-MBI, e-MBI, and mt-MBI, respectively) using a molecular Eco-Group approach. The indices were calculated via automatic computer pipelines using data collected over a period of nine years from a range of high- and low-flow salmon farms (12 farms and 60 stations) from three distinct regions in New Zealand. The MBIs were compared against the established ES index. All MBIs yielded strong and highly significant relationships with the ES index. The strongest relationships (R2 > 0.9) were obtained with the b-MBI. A refinement of the b-MBI (2019-2020) was supported by highly prolific microbes throughout the ES spectrum, and in particular in the upper end of the organic enrichment scale where traditional benthic indices tend to fail. This resulted in ES values of both (molecular-based versus morphology-based) indices to follow a near one-to-one relationship, performing consistently across water flow environments and considered sub-regions. Station-averaged results were also used to compare regulated compliance outcomes between the two indices, based on the current key compliance criteria for farms within each flow regime. Of the 67 seabed monitoring stations that were subsequently classified as compliant or non‑compliant, 62 stations had identical compliance outcomes (i.e. 92% of instances). Furthermore, the b-MBI showed consistently narrower (~50%) confidence interval bands when compared to the traditional ES index. The b-MBI offers unprecedented precision for determining subtle changes along enrichment gradients, constituting a valuable asset for triggering timely management responses and improving compliance. The protocols developed in this project enable rapid, standardised, and cost-effective eDNA isolation and extraction, followed by automatic b-MBI calculation. The affordability and versatility of the b-MBI tool suggests that it could be immediately integrated into current monitoring strategies as the primary benthic assessment tool for assessing benthic impacts of salmon farms in New Zealand.

scholarly journals Microalgal Biomass Generation via Electroflotation: A Cost-Effective Dewatering Technology

2020 ◽  
Vol 10 (24) ◽  
pp. 9053
Author(s):  
Jaison Jeevanandam ◽  
Mohd Razif Harun ◽  
Sie Yon Lau ◽  
Divine D. Sewu ◽  
Michael K. Danquah
Keyword(s):  
Large Scale ◽  
Cost Effective ◽  
Electrode System ◽  
Consumer Products ◽  
Separation Processes ◽  
Microalgal Biomass ◽  
Microalgae Culture ◽  
Wide Range ◽  
Agricultural Industries ◽  
Cell Densities

Microalgae are an excellent source of bioactive compounds for the production of a wide range of vital consumer products in the biofuel, pharmaceutical, food, cosmetics, and agricultural industries, in addition to huge upstream benefits relating to carbon dioxide biosequestration and wastewater treatment. However, energy-efficient, cost-effective, and scalable microalgal technologies for commercial-scale applications are limited, and this has significantly impacted the full-scale implementation of microalgal biosystems for bioproduct development, phycoremediation, and biorefinery applications. Microalgae culture dewatering continues to be a major challenge to large-scale biomass generation, and this is primarily due to the low cell densities of microalgal cultures and the small hydrodynamic size of microalgal cells. With such biophysical characteristics, energy-intensive solid–liquid separation processes such as centrifugation and filtration are generally used for continuous generation of biomass in large-scale settings, making dewatering a major contributor to the microalgae bioprocess economics. This article analyzes the potential of electroflotation as a cost-effective dewatering process that can be integrated into microalgae bioprocesses for continuous biomass production. Electroflotation hinges on the generation of fine bubbles at the surface of an electrode system to entrain microalgal particulates to the surface. A modification of electroflotation, which combines electrocoagulation to catalyze the coalescence of microalgae cells before gaseous entrainment, is also discussed. A technoeconomic appraisal of the prospects of electroflotation compared with other dewatering technologies is presented.

scholarly journals GAPeDNA: Assessing and mapping global species gaps in genetic databases for metabarcoding studies

2021 ◽  
Vol 4 ◽  
Author(s):  
Virginie Marques ◽  
Tristan Milhau ◽  
Camille Albouy ◽  
Tony Dejean ◽  
Stéphanie Manel ◽  
...  
Keyword(s):  
Threatened Species ◽  
Large Scale ◽  
Conservation Status ◽  
Environmental Dna ◽  
Bulk Sample ◽  
Data Availability ◽  
Reference Database ◽  
Flexible Tool ◽  
Initial Application ◽  
Wide Range

Environmental DNA metabarcoding has recently emerged as a non-invasive tool for aquatic biodiversity inventories, frequently surpassing traditional methods for detecting a wide range of taxa in most habitats. One of the major limitations currently impairing the large-scale application of DNA-based inventories, such as eDNA or bulk-sample analysis is the lack of species sequences available in public genetic databases. These gaps are still largely unknown spatially and taxonomically for most regions of the world, which can hinder targeted future sequencing efforts. We propose GAPeDNA, a user-friendly web-interface (Fig. 1) that provides a global overview of genetic database completeness for a given taxon across space and conservation status. As an initial application, we synthetized data from regional checklists for marine and freshwater fishes along with their IUCN conservation status to provide global maps of species coverage using the European Nucleotide Archive public reference database for 19 metabarcoding primers. This tool automatizes the scanning of gaps in these databases to guide future sequencing efforts and support the deployment of DNA-based inventories at larger scale. It is flexible and can be expanded to other taxa and primers upon data availability. Using our global fish case study, we show that gaps increase toward the tropics where species diversity and the number of threatened species were the highest. It highlights priority areas for fish sequencing like the Congo, the Mekong and the Mississippi freshwater basins which host more than 60 non-sequenced threatened fish species. For marine fishes, the Caribbean and East Africa host up to 42 non-sequenced threatened species. As an open-acces, updatable and flexible tool, GAPeDNA can be used to evaluate the completeness of sequence reference libraries of various markers and for any taxonomic group.

scholarly journals Inference of Chromosome-Length Haplotypes Using Genomic Data of Three or a Few More Single Gametes

2020 ◽  
Vol 37 (12) ◽  
pp. 3684-3698 ◽  
Author(s):  
Ruidong Li ◽  
Han Qu ◽  
Jinfeng Chen ◽  
Shibo Wang ◽  
John M Chater ◽  
...  
Keyword(s):  
Large Scale ◽  
Low Cost ◽  
Genomic Data ◽  
Cost Effective ◽  
R Package ◽  
Chromosome Length ◽  
Sequencing Data ◽  
Experimental Phasing ◽  
Wide Range ◽  
Haplotype Data

Abstract Compared with genomic data of individual markers, haplotype data provide higher resolution for DNA variants, advancing our knowledge in genetics and evolution. Although many computational and experimental phasing methods have been developed for analyzing diploid genomes, it remains challenging to reconstruct chromosome-scale haplotypes at low cost, which constrains the utility of this valuable genetic resource. Gamete cells, the natural packaging of haploid complements, are ideal materials for phasing entire chromosomes because the majority of the haplotypic allele combinations has been preserved. Therefore, compared with the current diploid-based phasing methods, using haploid genomic data of single gametes may substantially reduce the complexity in inferring the donor’s chromosomal haplotypes. In this study, we developed the first easy-to-use R package, Hapi, for inferring chromosome-length haplotypes of individual diploid genomes with only a few gametes. Hapi outperformed other phasing methods when analyzing both simulated and real single gamete cell sequencing data sets. The results also suggested that chromosome-scale haplotypes may be inferred by using as few as three gametes, which has pushed the boundary to its possible limit. The single gamete cell sequencing technology allied with the cost-effective Hapi method will make large-scale haplotype-based genetic studies feasible and affordable, promoting the use of haplotype data in a wide range of research.

Are there general laws in parasite ecology?

Parasitology ◽  
2007 ◽  
Vol 134 (6) ◽  
pp. 763-776 ◽  
Author(s):  
R. POULIN
Keyword(s):  
Large Scale ◽  
Population Level ◽  
Parasite Community ◽  
Scientific Discipline ◽  
Natural Ecosystems ◽  
Parasite Ecology ◽  
Wide Range ◽  
Abundance And Diversity ◽  
Living Organisms ◽  
Host Parasite

SUMMARYAs a scientific discipline matures, its theoretical underpinnings tend to consolidate around a few general laws that explain a wide range of phenomena, and from which can be derived further testable predictions. It is one of the goals of science to uncover the general principles that produce recurring patterns in nature. Although this has happened in many areas of physics and chemistry, ecology is yet to take this important step. Ecological systems are intrinsically complex, but this does not necessarily mean that everything about them is unpredictable or chaotic. Ecologists, whose grand aim is to understand the interactions that govern the distribution, abundance and diversity of living organisms at different scales, have uncovered several regular patterns, i.e. widely observable statistical tendencies, in the abundance or diversity of organisms in natural ecosystems. Some of these patterns, however, are contingent, i.e. they are only true under particular circumstances; nevertheless, the broad generality of many patterns hints at the existence of universal principles. What about parasite ecology: is it also characterized by recurring patterns and general principles? Evidence for repeatable empirical patterns in parasite ecology is reviewed here, in search of patterns that are consistently detectable across taxa or geographical areas. The coverage ranges from the population level all the way to large-scale patterns of parasite diversity and abundance (or biomass) and patterns in the structure of host-parasite interaction networks. Although general laws seem to apply to these extreme scales of studies, most patterns observed at the intermediate scale, i.e. the parasite community level, appear highly contingent and far from universal. The general laws uncovered to date are proving valuable, as they offer glimpses of the underlying processes shaping parasite ecology and diversity.

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