Dataset Information

Environmental DNA: A New Low-Cost Monitoring Tool for Pathogens in Salmonid Aquaculture.

ABSTRACT: Environmental DNA (eDNA) metabarcoding is a relatively new monitoring tool featuring in an increasing number of applications such as the facilitation of the accurate and cost effective detection of species in environmental samples. eDNA monitoring is likely to have a major impact on the ability of salmonid aquaculture industry producers and their regulators to detect the presence and abundance of pathogens and other biological threats in the surrounding environment. However, for eDNA metabarcoding to develop into a useful bio-monitoring tool it is necessary to (a) validate that sequence datasets derived from amplification of metabarcoding markers reflect the true species' identity, (b) test the sensitivity under different abundance levels and environmental noise and (c) establish a low-cost sequencing method to enable the bulk processing of field samples. In this study, we employed an elaborate experimental design whereby different combinations of five biological agents were crossed at three abundance levels and exposed to sterile pre-filtered and unfiltered seawater, prior to coarse filtering and then eDNA ultrafiltration of the resultant material. We then benchmarked the low-cost, scalable, Ion Torrent sequencing method against the current gold-standard Illumina platform for eDNA surveys in aquaculture. Based on amplicon-seq of the 18S SSU rDNA v9 region, we were able to identify two parasites (Lepeophtheirus salmonis and Paramoeba perurans) to species level, whereas the microalgae species Prymnesium parvum, Pseudo-nitzschia seriata, and P. delicatissima could be assigned correctly only to the genus level. Illumina and Ion Torrent provided near identical results in terms of community composition in our samples, whereas Ion Torrent was more sensitive in detecting species richness when the medium was unfiltered seawater. Both methods were able to reflect the difference in relative abundance between treatments in 4 out of 5 species when samples were exposed to the unfiltered seawater, despite the significant amount of background noise from both bacteria and eukaryotes. Our findings indicate that eDNA metabarcoding offers significant potential in the monitoring of species harmful to aquaculture and for this purpose, the low-cost Ion Torrent sequencing is as accurate as Illumina in determining differences in their relative abundance between samples.

SUBMITTER: Peters L

PROVIDER: S-EPMC6292926 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Environmental DNA: A New Low-Cost Monitoring Tool for Pathogens in Salmonid Aquaculture.

Peters Lucy L Spatharis Sofie S Dario Maria Augusta MA Dwyer Toni T Roca Inaki J T IJT Kintner Anna A Kanstad-Hanssen Øyvind Ø Llewellyn Martin S MS Praebel Kim K

Frontiers in microbiology 20181207

Environmental DNA (eDNA) metabarcoding is a relatively new monitoring tool featuring in an increasing number of applications such as the facilitation of the accurate and cost effective detection of species in environmental samples. eDNA monitoring is likely to have a major impact on the ability of salmonid aquaculture industry producers and their regulators to detect the presence and abundance of pathogens and other biological threats in the surrounding environment. However, for eDNA metabarcodi ...[more]

PMID: 30581425

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Project description:Environmental DNA (eDNA) metabarcoding has been increasingly used to monitor the community assemblages of a wide variety of organisms. Here, we test the efficacy of eDNA metabarcoding to assess the composition of Iberian freshwater fishes, one of the most endangered groups of vertebrates in Spain. For this purpose, we sampled 12 sampling sites throughout one of Spain's largest basins, the Duero, which is home to approximately 70% of the genera and 30% of the primary freshwater fish in Spain. We sampled these sampling sites in the summer by using electrofishing, a traditional sampling method, and eDNA metabarcoding of river water samples using the mitochondrial 12S rRNA gene (12S) as a marker. We also resampled four of these sampling sites in autumn by eDNA. We compared the results obtained through eDNA metabarcoding with those of electrofishing surveys (ones conducted for the present study and past ones) and assessed the suitability of 12S as an eDNA metabarcoding marker for this group of freshwater fishes. We found that the 12S fragment, analysed for 25 Iberian species, showed sufficient taxonomic resolution to be useful for eDNA approaches, and even showed population-level differences in the studied populations across the tissue samples for Achondrostoma arcasii. In most cases, a greater number of species was detected through eDNA metabarcoding than through electrofishing. Based on our results, eDNA metabarcoding is a powerful tool to study the freshwater fish composition in the Iberian Peninsula and to unmask cryptic diversity. However, we highlight the need to generate a local genetic database for 12S gene for such studies and to interpret the results with caution when studying only mitochondrial DNA. Finally, our survey shows that the high detection sensitivity of eDNA metabarcoding and the non-invasiveness of this method allows it to act as a detection system for species of low abundance, such as early invasive species or species in population decline, two key aspects of conservation management of Spanish freshwater fishes.

Project description:BackgroundHigh-quality cardiopulmonary resuscitation (CPR) remains essential to improve the outcome of patients in sudden cardiorespiratory arrest. Feedback on performance is a crucial component of the learning processes associated with simulation and has been shown to improve CPR quality during simulated cardiac arrest on mannequins. This study aims to evaluate skills acquisition using a new low-cost feedback device for CPR self-training when compared to standard training methods.MethodsThirty-nine pregraduated medical and biomedical engineering students were recruited for a longitudinal double-blinded randomized control study. For training Basic Life Support skills, the control group used a standard task-trainer and received feedback from an instructor. The intervention group used the same standard task-trainer, instrumented with the CPR Personal Trainer that provided automated performance feedback (with no instructor) on compression-related parameters. Students' knowledge and skills were assessed before and after training, through a theoretical knowledge test and 2 minutes of CPR practical performance.ResultsThe theoretical tests showed an improvement both in the intervention and in the control group. For each compression-related parameters (hands position, recoil, rate, and depth), significant increase in scores is observed, between the pre- and the post-test, in both groups. The intervention and control groups presented identical mean differences for the total score (0.72 vs 0.72), with no statistical difference (P?=?0.754).ConclusionsThe proposed tool proved to be effective in the acquisition of compression-related skills, with similar outcomes as the traditional instructor-based method, corroborating the hypothesis that a low-cost tool with feedback for CPR self-training can provide an alternative or a complementary extension to traditional training methods. The system can also be considered cost-efficient as it reduces the permanent presence of an instructor for the chest compressions training, promoting regular training outside formal training courses.

Dataset Information

Environmental DNA: A New Low-Cost Monitoring Tool for Pathogens in Salmonid Aquaculture.

Publications

Environmental DNA: A New Low-Cost Monitoring Tool for Pathogens in Salmonid Aquaculture.

Similar Datasets

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