Evaluation of nanopore sequencing for increasing accessibility of eDNA studies in biodiverse countries DOI Creative Commons
Daniel Gygax,

Susana Giraldo Ramirez,

Moses Chibesa

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 21, 2025

Abstract Biodiversity loss is a global challenge of the 21st century. Environmental DNA (eDNA)-based metabarcoding offers cost- and time-efficient alternative to conventional biodiversity surveys, enabling detection rare, cryptic, elusive species from environmental samples. However, limited access genomic technologies restricts application eDNA in highly biodiverse remote regions low- middle-income countries. Here, we directly compared latest portable nanopore sequencing methods with established Illumina for vertebrate Zambian water We also evaluated cost-effective versus filtration approaches, contrasted comprehensive, computationally intensive taxonomic database search streamlined, manually curated search. Our results show that due recent improvements chemistry optimized basecalling, can recover many detected by sequencing, demonstrating feasibility situ assessment using platforms. We, however, found accurate remains superior quantity detections, eDNA- camera trap-based detections had minimal overlap, suggesting complementary rather than substituting these monitoring technologies. Finally, our findings underscore role completeness assignments, emphasizing need high-quality ecosystem-specific reference databases research.

Language: Английский

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
A review of eDNA technology in avian monitoring: Current status, challenges and future perspectives DOI Creative Commons
Yu Ke, Tong Liu,

Chenglong Han

et al.

Avian Research, Journal Year: 2025, Volume and Issue: unknown, P. 100235 - 100235

Published: March 1, 2025

Language: Английский

Citations

0
eDNA enhances detection efficiency but reveals lower waterbird diversity: A comparison with point counting method DOI Creative Commons

Hongming Shuai,

Xiaoru Liu,

Y. Zhang

et al.

Avian Research, Journal Year: 2025, Volume and Issue: unknown, P. 100236 - 100236

Published: March 1, 2025

Language: Английский

Citations

0
Evaluation of nanopore sequencing for increasing accessibility of eDNA studies in biodiverse countries DOI Creative Commons
Daniel Gygax,

Susana Giraldo Ramirez,

Moses Chibesa

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 21, 2025

Abstract Biodiversity loss is a global challenge of the 21st century. Environmental DNA (eDNA)-based metabarcoding offers cost- and time-efficient alternative to conventional biodiversity surveys, enabling detection rare, cryptic, elusive species from environmental samples. However, limited access genomic technologies restricts application eDNA in highly biodiverse remote regions low- middle-income countries. Here, we directly compared latest portable nanopore sequencing methods with established Illumina for vertebrate Zambian water We also evaluated cost-effective versus filtration approaches, contrasted comprehensive, computationally intensive taxonomic database search streamlined, manually curated search. Our results show that due recent improvements chemistry optimized basecalling, can recover many detected by sequencing, demonstrating feasibility situ assessment using platforms. We, however, found accurate remains superior quantity detections, eDNA- camera trap-based detections had minimal overlap, suggesting complementary rather than substituting these monitoring technologies. Finally, our findings underscore role completeness assignments, emphasizing need high-quality ecosystem-specific reference databases research.

Language: Английский

Citations

0