Research horizons for invasive marine species detection with eDNA/eRNA DOI Creative Commons
Simon Jarman, Fran Ackermann, Michael J. Marnane

et al.

Research Square (Research Square), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 4, 2023

Abstract The global marine ecosystem is changing rapidly as the result of biogeochemical cycles and structure being altered by industrial civilization. Invasive species (IMS) are one most damaging regional consequences human activity, easily attributable to specific processes. This makes IMS introduction tractable threats for management with appropriate policies. Once established, a different set policies required either restrict spread, or attempt local eradication. key tool damage mitigation rapid, widely deployable detection. Environmental Nucleic Acids (eNA), combining environmental DNA (eDNA) RNA (eRNA) analyses, have emerged valuable tools sensitive, cost-effective readily detection IMS. Methods eNA still developed through widespread active research community, so identifying limitations current processes will help prioritise eNA-based research. We analysed synthesised opinions expert managers researchers in Australia New Zealand about knowledge gaps needs synthesis was placed context literature on what technologies currently providing an tool; problems exist technology; could be done improve this general approach. Our analyses produced list priorities that chart path towards best possible systems - Utopia.

Language: Английский

Effect of eDNA metabarcoding temporal sampling strategies on detection of coastal biodiversity DOI Creative Commons
Maelle Sevellec, Anaïs Lacoursière‐Roussel, Éric Normandeau

et al.

Frontiers in Marine Science, Journal Year: 2025, Volume and Issue: 12

Published: Feb. 7, 2025

Introduction Environmental DNA (eDNA) metabarcoding of water is increasingly being used to monitor coastal biodiversity shifts. However, we have limited knowledge whether samples collected during discreet temporal periods depict holistic ecosystem changes over longer time spans. Methods Here, show how eDNA community structure varies across repeated sampling events at different scales ranging from years months days an Arctic site, Churchill (Canada), using analyses with four universal primer pairs (two primers in COI and two the 18S rRNA). Results Daily variations were highly dynamic less structured, likely due stochastic nature estuarine ecosystems, but there was a clear annual consistency communities high proportion shared taxa between years. monthly most efficient for capturing biodiversity. Discussion We provide recommendations optimal design based on our observations. The study underscores importance understanding biological physical factors altering detection improve efficiency detecting interpreting long-term changes.

Language: Английский

Citations

0
An innovative approach for marine macro-organism monitoring: methodology and future perspectives of environmental DNA (eDNA) technology DOI
Yun Jiang,

Wencheng Zhao,

Yiyi Zhu

et al.

Marine Biology, Journal Year: 2025, Volume and Issue: 172(3)

Published: March 1, 2025

Language: Английский

Citations

0
Environmental DNA exploring the distribution of Indo-Pacific humpback dolphins and fish diversity from the Pearl River Estuary, China DOI
Bin Sun,

Dingyu Luo,

Nuoyan Huang

et al.

Marine Pollution Bulletin, Journal Year: 2025, Volume and Issue: 216, P. 118026 - 118026

Published: April 24, 2025

Language: Английский

Citations

0
Critical considerations for communicating environmental DNA science DOI Creative Commons
Eric D. Stein, Christopher L. Jerde, Elizabeth Andruszkiewicz Allan

et al.

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

Published: Sept. 1, 2023

Abstract The economic and methodological efficiencies of environmental DNA (eDNA) based survey approaches provide an unprecedented opportunity to assess monitor aquatic environments. However, instances inadequate communication from the scientific community about confidence levels, knowledge gaps, reliability, appropriate parameters eDNA‐based methods have hindered their uptake in monitoring programs and, some cases, has created misperceptions or doubts management community. To help remedy this situation, scientists convened a session at Second National Marine eDNA Workshop discuss strategies for improving communications with managers. These include articulating readiness different applications, highlighting strengths limitations tools various applications use communicating uncertainties associated specified uses transparently, avoiding exaggeration exploratory preliminary findings. Several key messages regarding implementation, limitations, relationship existing were prioritized. be inclusive diverse managers, practitioners, researchers, we other workshop participants propose development workflow plans, using RACI (Responsible, Accountable, Consulted, Informed) charts clarify roles all pertinent individuals parties minimize chance miscommunications. We also developing decision support such as Structured Decision‐Making (SDM) balance benefits sampling inherent uncertainty, scale articulate technological specific applications. will increase clarity consistency our understanding utility methods, improve transparency, foster common vision confidently applying approaches, enhance benefit assessment

Language: Английский

Citations

8
Investigation of the water environmental DNA/RNA profile for non‐invasive biomonitoring of the fish pathogen Aeromonas salmonicida subsp. salmonicida and detection of immune responses in rainbow trout (Oncorhynchus mykiss) DOI Creative Commons
Moonika Haahr Marana, Hannah Malene Jensen, Debes H. Christiansen

et al.

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(4)

Published: July 1, 2024

Abstract Aquaculture industries face challenges in fish production, primarily due to disease occurrence. Clinical manifestations of these diseases often indicate a considerable advancement the pathological process. Infected experience morbidity, leading compromised welfare and substantial economic losses for production facilities. Therefore, prophylaxis early detection pathogens could allow facility managers intervene or treat before clinical signs occur. For first time, environmental DNA/RNA (collectively eNA) was used detect salmonid pathogen Aeromonas salmonicida subsp. water hosting rainbow trout ( Oncorhynchus mykiss ). This took place under controlled experimental conditions, occurrence outcome mortality. The concentration bacteria determined by using standard curve. To determine window possible intervention, bacterial measured from an stage throughout when became moribund. Furthermore, acute phase protein, serum amyloid A produced trout, detected found be up‐regulated 4 days post challenge. It thereby shown that it is strong immune responses non‐invasive manner. eNA can as tool infection becomes severe. will facilitate interventions limit increase fish, which becoming requirement more sustainable ethical animal production.

Language: Английский

Citations

2
Taxonomic and functional metagenomic assessment of a dolichospermum bloom in a large and deep lake south of the Alps DOI Creative Commons
Nico Salmaso, Leonardo Cerasino, Massimo Pindo

et al.

FEMS Microbiology Ecology, Journal Year: 2024, Volume and Issue: 100(10)

Published: Sept. 3, 2024

Abstract Untargeted genetic approaches can be used to explore the high metabolic versatility of cyanobacteria. In this context, a comprehensive metagenomic shotgun analysis was performed on population Dolichospermum lemmermannii collected during surface bloom in Lake Garda summer 2020. Using phylogenomic approach, almost complete metagenome-assembled genome obtained from allowed clarify taxonomic position species within genus and contributed frame taxonomy ADA group (Anabaena/Dolichospermum/Aphanizomenon). addition common functional traits represented central metabolism photosynthetic cyanobacteria, annotation uncovered some distinctive adaptive that helped define factors promote maintain bloom-forming heterocytous nitrogen-fixing Nostocales oligotrophic lakes. addition, clusters were identified potentially encode several secondary metabolites previously unknown populations evolving southern Alpine district. These included geosmin, anabaenopetins, other bioactive compounds. The results expanded knowledge competitive drive algal blooms provided guidance for more targeted analyses cyanobacterial with implications human health water resource use.

Language: Английский

Citations

2
rCRUX: A rapid and versatile tool for generating metabarcoding reference libraries in R DOI Creative Commons
Emily Curd,

Luna Gal,

Ramón Gallego

et al.

Environmental DNA, Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 29, 2023

The sequencing revolution requires accurate taxonomic classification of DNA sequences. Key to making assignments are curated, comprehensive reference barcode databases. However, the generation and curation such databases has remained challenging given large continuously growing volumes both sequence data novel targets. Monitoring research applications require a greater diversity specialized gene regions targeted taxa then currently curated by professional staff. Thus there is need for an easy implement computational tool that can generate metabarcoding libraries any bespoke locus. We address this reimagining CRUX from Anacapa Toolkit present rCRUX package in R which, like it's predecessor, relies on homology PCR primer compatibility instead keyword-searches avoid limitations user-defined metadata. typical workflow involves searching plausible seed amplicons (

Language: Английский

Citations

4
Research horizons for invasive marine species detection with eDNA/eRNA DOI Creative Commons
Simon Jarman, Fran Ackermann, Michael J. Marnane

et al.

Biological Invasions, Journal Year: 2024, Volume and Issue: 26(11), P. 3715 - 3731

Published: July 24, 2024

Abstract The global marine ecosystem is changing rapidly as the result of biogeochemical cycles and structure being altered by industrial civilization. Invasive species (IMS) are one most damaging regional consequences human activity, easily attributable to specific processes. This makes IMS introduction tractable threats for management appropriate policies. Once established, a different set policies required either restrict spread, or attempt local eradication. key tool damage mitigation rapid, widely deployable detection. Environmental Nucleic Acids (eNA), combining environmental DNA (eDNA) RNA (eRNA) analyses, have emerged valuable tools sensitive, cost-effective readily detection IMS. Methods eNA still developed through widespread active research community, so identifying limitations current processes will help prioritise eNA-based research. We analysed synthesised opinions expert managers researchers in Australia New Zealand about knowledge gaps needs synthesis was placed context with literature on what technologies currently providing an tool; problems exist technology; could be done improve this general approach. Our analyses produced list priorities that chart path towards best possible systems eNA.

Language: Английский

Citations

1
Towards the integration of environmental DNA analysis to profile the upper mesopelagic fish layer in the Northeast Atlantic Ocean DOI Creative Commons
Maddalena Tibone, Thibault Cariou,

Ciarán O’Donnell

et al.

ICES Journal of Marine Science, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 8, 2024

Abstract Interest in mesopelagic fish layers is on the rise due to potential exploitability of their macrofauna; hence, profiling community crucial enable sustainability future fishing practices. In this context, a dedicated survey was carried out September 2022 along Irish shelf break, where (catch) and eDNA metabarcoding analysis using portable high-throughput sequencer were performed investigate upper layer. Catch data showed that targeted consisted mainly young-of-the-year cohort Mueller’s pearlside (Maurolicus muelleri), fish, with little bycatch. reflected high prevalence M. muelleri’s (56%–97% assigned reads), identified species undetected by fishing, least represented differed water samples collected before or after activities. While reflects current limitations each technique, it also shows multidisciplinary approach may provide an increased level resolution for muelleri layer’s ancillary community. Findings from present study provided important insights further refine sample acquisition rapid processing data, which beholds great corroborate methods when ground truthing acoustic approaches assessments.

Language: Английский

Citations

1
Biodiversity of Nematodes from Coral Reef Sediments in the South China Sea Based on eDNA Metabarcoding DOI Creative Commons

Lei An,

Aiyang Wang,

Zhang Zheng

et al.

Diversity, Journal Year: 2024, Volume and Issue: 16(7), P. 362 - 362

Published: June 25, 2024

Coral reef ecosystems in the South China Sea are one of globally important marine biodiversity hotspots. However, there few studies on nematode coral sediments. Here, we assessed sediments using eDNA metabarcoding. Eight sampling stations were set up region north Basin (Xisha and Zhongsha Islands) south it (Nansha Islands), respectively. We also compared analysed community structure different regions, as well effects environmental factors structure. The results showed that a total 503 operational taxonomic units (OTUs) detected 16 sediment samples. nematodes identified belong to two classes, 10 orders, 37 families, 51 genera 61 species, all them Enoplea Chromadorea, except for unidentified taxa, which accounted 97.26% abundance. analyses northern had higher abundance diversity relative southern region. was no significant difference between less affected by geographic location. Similarly, (total nitrogen, phosphorus, copper, zinc, cadmium, lead arsenic) have an effect specific groups but not overall In summary, this study initially reveals composition communities provides reference further in-depth ecosystem.

Language: Английский

Citations

0