Monitoring the Land and Sea: Enhancing Efficiency Through CRISPR-Cas Driven Depletion and Enrichment of Environmental DNA DOI
Anya Kardailsky, Benjamín Durán‐Vinet, Georgia Nester

et al.

The CRISPR Journal, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 30, 2024

Characterizing biodiversity using environmental DNA (eDNA) represents a paradigm shift in our capacity for biomonitoring complex environments, both aquatic and terrestrial. However, eDNA is limited by biases toward certain species the low taxonomic resolution of current metabarcoding approaches. Shotgun metagenomics enables collection whole ecosystem data sequencing all molecules present, allowing characterization identification. Clustered regularly interspaced short palindromic repeats (CRISPR) CRISPR-associated proteins (Cas)-based methods have potential to improve efficiency metagenomic low-abundant target organisms simplify analysis enrichment or nontarget depletion before sequencing. Implementation CRISPR-Cas has been due lack interest support past. This perspective synthesizes approaches study underrepresented taxa advocate further application optimization CRISPR-Cas, holding promise biomonitoring.

Language: Английский

Environmental DNA: The next chapter DOI Creative Commons
Rosetta C. Blackman, Marjorie Couton, François Keck

et al.

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(11)

Published: April 16, 2024

Abstract Molecular tools are an indispensable part of ecology and biodiversity sciences implemented across all biomes. About a decade ago, the use implementation environmental DNA (eDNA) to detect signals extracted from samples opened new avenues research. Initial eDNA research focused on understanding population dynamics target species. Its scope thereafter broadened, uncovering previously unrecorded via metabarcoding in both well‐studied understudied ecosystems taxonomic groups. The application rapidly became established research, field by its own. Here, we revisit key expectations made land‐mark special issue Ecology 2012 frame development six areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour environment (6) reference database development. We pinpoint success eDNA, yet also discuss shortfalls not met, highlighting areas priority identify unexpected developments. In parallel, our retrospective couples screening peer‐reviewed literature with survey users including academics, end‐users commercial providers, which address focus efforts advance eDNA. With rapid ever‐increasing pace technical advances, future looks bright, successful applications best practices must become more interdisciplinary reach full potential. Our retrospect gives towards concretely moving forward.

Language: Английский

Citations

27
A review of data collection methods used to monitor the associations of wild species with marine aquaculture sites DOI Creative Commons
G. English, Michael Lawrence, Christopher W. McKindsey

et al.

Reviews in Aquaculture, Journal Year: 2024, Volume and Issue: 16(3), P. 1160 - 1185

Published: Jan. 25, 2024

Abstract Aquaculture contributes a significant portion of the global aquatic biomass destined for human consumption. Bivalve and marine finfish aquaculture operations require sea‐based farm sites that result in considerable interactions with natural environment. The addition feed waste physical structures (e.g., net pens longline mussel culture) can provide an attractive artificial reef many species studies have shown both positive negative effects on surrounding ecosystem due to wild sites. Assessing these be complex, depending local ecosystem, several monitoring techniques been used accurately determine associations decapods farms. In this review, we assessed main methods monitor aquaculture‐ecosystem interactions. advantages disadvantages each technique are discussed suggestions mitigate shortfalls future outlined. It was evident combining methodologies should prioritised lessen impact identified weaknesses any given approach. Designing complementary approaches may help attain robust data further understand underlying proximate mechanisms.

Language: Английский

Citations

12
Environmental DNA methods for biosecurity and invasion biology in terrestrial ecosystems: Progress, pitfalls, and prospects DOI
Karen L. Bell, Mariana Campos, Benjamin D. Hoffmann

et al.

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 926, P. 171810 - 171810

Published: March 19, 2024

Language: Английский

Citations

12
Environmental DNA (eDNA) removal rates in streams differ by particle size under varying substrate and light conditions DOI Creative Commons
Elise D. Snyder, Jennifer L. Tank, Pedro F. P. Brandão‐Dias

et al.

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 903, P. 166469 - 166469

Published: Aug. 24, 2023

Language: Английский

Citations

22
Environmental DNA and RNA in aquatic community ecology: Toward methodological standardization DOI Creative Commons
Ingrid Vasconcellos Bunholi, Nicole R. Foster, Jordan M. Casey

et al.

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(6), P. 1133 - 1147

Published: Sept. 28, 2023

Abstract Molecular technologies have facilitated the expansion of biodiversity assessments across a broad range organisms and aquatic systems. Environmental DNA (eDNA) environmental RNA (eRNA), collectively referred to as nucleic acids (eNAs), revolutionized monitoring due their noninvasive nature high‐resolution capabilities when compared traditional survey methods. While eNA applications grown exponentially over past decade, methodological inconsistencies hinder reproducibility comparability. To assess current state methodologies in ecology, we conducted systematic review 300 peer‐reviewed studies that ecological communities diverse Of these papers, 291 examine eDNA, four eRNA, five consider both eDNA eRNA. The small number eRNA highlights field is its infancy. looked at, found clear geographic bias, with approximately 50% all occurring six high‐income countries, while less than 10% occur South America Africa. Further, report lack standardization studies, showing high variability water filtration volume, filter material, pore size, extraction method, marker choice, bioinformatic pipelines. We further highlight incomplete reference sequence databases for limit taxonomic assignment inferences. Finally, identify issue community ecology: missing details, which compromise reproducibility, especially newly emerging applications. facilitate systems permit integration monitoring, recommend improvement alongside guidelines encourage transparency.

Language: Английский

Citations

17
New prospects of environmental RNA metabarcoding research in biological diversity, ecotoxicological monitoring, and detection of COVID-19: a critical review DOI
Sakib Tahmid Rishan, Richard J. Kline, Md Saydur Rahman

et al.

Environmental Science and Pollution Research, Journal Year: 2024, Volume and Issue: 31(8), P. 11406 - 11427

Published: Jan. 6, 2024

Language: Английский

Citations

4
Selecting Competent Reverse Transcription Strategies to Maximise Biodiversity Recovery With eRNA Metabarcoding DOI Open Access
Fuwen Wang, Wei Xiong, Xuena Huang

et al.

Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 22, 2025

ABSTRACT Both environmental DNA (eDNA) and RNA (eRNA) have been widely adopted for biodiversity assessment. While eDNA often persists longer in environments, eRNA offers a more current view of biological activities. In metabarcoding, extracted is reverse transcribed into complementary (cDNA) metabarcoding. However, the efficacy various transcription strategies has not evaluated. Here we compared recovery efficiency three strategies: random priming with hexamers, oligo(dT) taxa‐specific using Mifish‐U fish both high‐ low‐biodiversity regions. Our results demonstrate that significantly impact recovery. Random consistently detected highest number taxa low‐ high‐biodiversity areas, performed comparably to hexamers; however, regions, hexamers outperformed oligo(dT), particularly recovering rare taxa. was comparable other high‐abundance taxa, it less effective thus limiting its utility comprehensive These differences are largely due multiple binding sites fewer or absent primers under high degradation. Combining improved recovery, especially low‐abundance species, supporting best practice eukaryotes. For prokaryotes genes lacking polyadenylation, favoured over taxa‐ gene‐specific priming. Collectively, these findings underscore critical importance selecting appropriate significant implications monitoring conservation efforts.

Language: Английский

Citations

0
Biodiversity Monitoring in Remote Marine Environments: Advancing Environmental DNA/RNA Sampling Workflows DOI Creative Commons
Michelle Scriver, Anastasija Zaiko, Xavier Pochon

et al.

Marine Environmental Research, Journal Year: 2025, Volume and Issue: 206, P. 107041 - 107041

Published: Feb. 26, 2025

Language: Английский

Citations

0
Exploring technical improvements for environmental nucleic acids-based biodiversity assessment and management in coastal ecosystems DOI
Fuwen Wang, Wei Xiong,

Yue Liu

et al.

Journal of Environmental Management, Journal Year: 2025, Volume and Issue: 377, P. 124724 - 124724

Published: Feb. 27, 2025

Language: Английский

Citations

0
Fish diversity assessment and semi-quantitative biomass estimation through metabarcoding of environmental DNA DOI Creative Commons
Yassine Kasmi, Ismael Núñez‐Riboni,

Tina Blancke

et al.

Ecological Indicators, Journal Year: 2025, Volume and Issue: 173, P. 113406 - 113406

Published: April 1, 2025

Language: Английский

Citations

0