Enumeration potential of environmental DNA for Pacific salmon stock assessments DOI Creative Commons
Geoffrey Su, Michael J. Allison,

Jordan Beblow

et al.

Environmental DNA, Journal Year: 2023, Volume and Issue: 6(1)

Published: Dec. 29, 2023

Abstract The field of environmental DNA (eDNA) has advanced over the past decade, with multiple approaches available for a variety sampling media and species. While using eDNA purpose simply detecting species is becoming routine process, utility to estimate abundance not well understood. Here, we quantify salmon upstream fish counting fence along river velocity, together, use these values determine correlation between number passing by daily rates in water before, during, after spawning season four Pacific salmonids ( Oncorhynchus gorbuscha , O. kisutch tshawytscha nerka ; pink, coho, chinook, sockeye, respectively). Throughout season, approximately 182,000 were counted through fence, which >98% pink salmon. Pink exhibited strong human counts (effect size = 0.65, SE 0.040) present study day‐to‐day variation unimodal profile rising falling counts. However, observed much lower numbers weaker levels higher during pre‐migratory period than migratory chinook. Thus, runs less ~1000 adults ~100, juvenile and/or prior seasons signal appears be indistinguishable from adult our system. large run, appeared reflect local space time, essentially tracking within days site.

Language: Английский

Bioaerosols in Agriculture: A Comprehensive Approach for Sustainable Crop Health and Environmental Balance DOI Creative Commons
Njomza Gashi, Zsombor Szőke, Péter Fauszt

et al.

Agronomy, Journal Year: 2025, Volume and Issue: 15(5), P. 1003 - 1003

Published: April 22, 2025

Bioaerosols have risen as pivotal constituents of airborne particles. Closely intertwined with the agricultural domain, these particles exert a significant influence on crops through dissemination various microorganisms that modulate crop growth dynamics, adaptive responses to environmental stimuli, and nutritional profile products. As main vector, are at forefront in transmission plant pathogens. Therefore, this review explains factors influencing their composition settings spreading. Furthermore, it elucidates complex bioaerosol-based communication networks, including bacteria–bacteria, bacteria–plant, plant–plant interactions, mediated by specialized volatile organic compounds (VOCs) released plants bacterial (BVCs) produced bacteria. These play crucial role synchronizing stress facilitating processes. They serve pathway for regulating behavior both microorganisms. Delving into origin dispersion, we assess key methods collection analysis while also comparing strengths weaknesses sampling techniques. The discussion extends delineating roles such formation biodiversity. Central discourse is an in-depth exploration context, particularly focusing potential utility forecasting pathogen subsequent diseases. This highlights importance applying strategies promotion sustainable practices, thus contributing advancement ecological balance food security, which remains neglected area scientific research.

Language: Английский

Citations

0
Advanced airborne eDNA sampling allows robust spatiotemporal characterisation of vertebrate communities DOI Creative Commons
Kasun H. Bodawatta,

Agnete le Maire Madsen,

Luke E. Holman

et al.

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 13, 2025

Abstract Effective biodiversity survey methods are crucial for monitoring ecosystems threatened by climatic fluctuations and anthropogenic pressures. Here we advance the collection of a novel source data - airborne environmental DNA (eDNA) investigate whether it yields habitat- season-specific signatures terrestrial vertebrate communities. Using portable low budget samplers, sampled eDNA in three protected nature areas across Denmark show that air filters with large surface area widest range particle retention sizes yield detections higher numbers taxa community homogeneity samples. Further, increased airflow rate dry storage − 20°C more diverse consistent Overall, demonstrate robust spatio-temporal dynamics classes, which can be adapted conservation programs to monitor globe.

Language: Английский

Citations

0
Evaluation of Oxford Nanopore Technologies MinION Sequencer as a Novel Short Amplicon Metabarcoding Tool Using Arthropod Mock Sample and Irish Bat Diet Characterisation DOI Creative Commons
James Nolan, Ilze Skujina, Gwenaëlle Hurpy

et al.

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(5)

Published: May 1, 2025

ABSTRACT Biodiversity monitoring using metabarcoding is now widely used as a routine environmental management tool. However, despite the rapid advancement of third‐generation high‐throughput sequencing platforms, there are limited studies assessing most suitable tools and approaches for studies. We tested utility Oxford Nanopore Technologies MinION short‐read amplicon mitochondrial COI mini‐barcodes from known composition arthropod species compared its performance with more commonly Illumina NovaSeq sequencing. The mock assemblage allowed us to optimise bioinformatic filtering pipeline identify long reads. Using this pipeline, we identified host diet by droppings collected five individual Irish brown long‐eared bats ( Plecotus auritus ) roosts. showed that data provided similar taxonomic assignment but only if reference barcode database was accurate comprehensive. P. inferred expected based on previous morphological less depth, higher number biological samples were necessary complete detection MinION. A relatively simple tool such NanoPipe could adequately retrieve both composition. biggest standing challenge format transferability comprehensiveness. This can be guide future nanopore minimise cost effort while optimising results.

Language: Английский

Citations

0
From Water to Land: A Review on the Applications of Environmental DNA and Invertebrate‐Derived DNA for Monitoring Terrestrial and Semi‐Aquatic Mammals DOI
Holly A. Broadhurst, Naiara Guimarães Sales,

Robert Raynor

et al.

Mammal Review, Journal Year: 2025, Volume and Issue: unknown

Published: May 5, 2025

ABSTRACT Terrestrial and semi‐aquatic mammals are facing increasing threats globally, highlighting the need for reliable data on species' occurrence, distribution, abundance effective conservation efforts. However, obtaining robust information over broad spatial temporal scales remains a significant challenge. Environmental DNA (eDNA) invertebrate‐derived (iDNA) applications have emerged as powerful surveying methods, with potential to revolutionise ecological monitoring by improving species detections providing better insights into mammalian distribution diversity. While eDNA relies genetic material shed their surroundings, iDNA leverages from invertebrates that interact mammals. Both approaches offer cost‐effective means obtain records community diversity metrics. This review explores global of e/iDNA terrestrial By comprehensive overview applications, sampling design, challenges, prospects, this serves guide researchers conservationists seeking use evaluating current state identifies challenges milestones be addressed these methods become practical method scale. It highlights further research enhance sensitivity reliability detections, standardisation methodologies, validation through comparison traditional methods. sheds light valuable tools aiding mammal inspiring future advancements in field.

Language: Английский

Citations

0
La reconnaissance des espèces basée sur l’ADN : applications, perspectives et défisen milieu continental terrestre DOI Open Access

H. Le Borgne,

Christophe Bouget

Naturae, Journal Year: 2024, Volume and Issue: 2024(3)

Published: Feb. 12, 2024

Face aux changements globaux actuels, l’enjeu des suivis de la dynamique biodiversité est croissant et entraîne une forte demande d’évaluations rapides détaillées biodiversité. L’identification moléculaire espèces plus en utilisée pour remplacer ou compléter les méthodes surveillance écologique classiques. Le metabarcoding considéré comme un outil d’inventaire, connaissance biologie (prédateurs proies, pollinisateurs, etc.) même découverte l’histoire d’écosystèmes. Il permet générer données sur manière rapide, précise fiable, large éventail d’organismes. Ce type méthodologie particulièrement intéressant observatoires dépourvus l’expertise nécessaire distinguer nombreuses groupes hyper diversifiés insectes ceux difficiles à inventorier. La reconnaissance partir l’ADN d’échantillons environnementaux (ADNe), tels que l’eau, sédiments, le sol, l’air diverses matières organiques, a champ d’application. Par son caractère non invasif destructif, ces approches sont importantes l’évaluation déontologique Les chercheurs intègrent l’ADNe dans leurs études biosurveillance raison sa précision facilité déploiement. Dans ce document, nous donnons aperçu champs d’application basées suivi biodiversité, d’acquisition données, traitement classification espèces, évoquons défis inhérents chacune étapes.

Citations

1
Macrobial airborne environmental DNA analysis: A review of progress, challenges, and recommendations for an emerging application DOI Creative Commons
Mark D. Johnson, Matthew A. Barnes

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(7)

Published: Aug. 8, 2024

In the context of looming global biodiversity loss, effective species detection represents a critical concern for ecological research and management. Environmental DNA (eDNA) analysis, which refers to collection taxonomic identification genetic fragments that are shed from an organism into its surroundings, emerged approximately 15 years ago as sensitive tool detection. Today, one frontiers eDNA concerns analysis material in dust other airborne materials, termed analysis. As study matures, it is appropriate time review foundational emerging studies make up current literature, use reviewed literature summarize, synthesize, forecast major challenges opportunities this advancing front. Specifically, we "ecology eDNA" framework organize our findings across origin, state, transport, fate materials environment, summarize what so far known their interactions with surrounding abiotic biotic factors, including population community ecologies ecosystem processes. Within work identify key challenges, opportunities, future directions associated application development. Lastly, discuss development applications, partnerships, messaging promote growth field. Together, broad potential rate at accelerating field suggest sky's limit science.

Language: Английский

Citations

1
Assessment of Microbial Contamination in Various Processing Rooms Using Culture-Dependent and 16S rRNA Methods in a Commercial Kitchen in Eastern China DOI
Honggang Lai,

Minjun Liu,

Xia Chen

et al.

Food Control, Journal Year: 2024, Volume and Issue: unknown, P. 110931 - 110931

Published: Sept. 1, 2024

Language: Английский

Citations

1
Enumeration potential of environmental DNA for Pacific salmon stock assessments DOI Creative Commons
Geoffrey Su, Michael J. Allison,

Jordan Beblow

et al.

Environmental DNA, Journal Year: 2023, Volume and Issue: 6(1)

Published: Dec. 29, 2023

Abstract The field of environmental DNA (eDNA) has advanced over the past decade, with multiple approaches available for a variety sampling media and species. While using eDNA purpose simply detecting species is becoming routine process, utility to estimate abundance not well understood. Here, we quantify salmon upstream fish counting fence along river velocity, together, use these values determine correlation between number passing by daily rates in water before, during, after spawning season four Pacific salmonids ( Oncorhynchus gorbuscha , O. kisutch tshawytscha nerka ; pink, coho, chinook, sockeye, respectively). Throughout season, approximately 182,000 were counted through fence, which >98% pink salmon. Pink exhibited strong human counts (effect size = 0.65, SE 0.040) present study day‐to‐day variation unimodal profile rising falling counts. However, observed much lower numbers weaker levels higher during pre‐migratory period than migratory chinook. Thus, runs less ~1000 adults ~100, juvenile and/or prior seasons signal appears be indistinguishable from adult our system. large run, appeared reflect local space time, essentially tracking within days site.

Language: Английский

Citations

1