Cited by Fish environmental RNA sequencing sensitively captures accumulative stress responses through short-term aquarium sampling

Utilizing aquatic environmental DNA to address global biodiversity targets DOI

Florian Altermatt, Marjorie Couton, Luca Carraro

et al.

Published: April 27, 2025

Language: Английский

Citations

Evaluating eDNA and eRNA metabarcoding for aquatic biodiversity assessment: From bacteria to vertebrates DOI

Yan Zhang, Yu Qiu, Kai Liu

et al.

Environmental Science and Ecotechnology, Journal Year: 2024, Volume and Issue: 21, P. 100441 - 100441

Published: June 12, 2024

The monitoring and management of aquatic ecosystems depend on precise estimates biodiversity. Metabarcoding analyses environmental nucleic acids (eNAs), including DNA (eDNA) RNA (eRNA), have garnered attention for their cost-effective non-invasive biomonitoring capabilities. However, the accuracy biodiversity obtained through eNAs can vary among different organismal groups. Here we evaluate performance eDNA eRNA metabarcoding across nine groups, ranging from bacteria to terrestrial vertebrates, in three cross-sections Yangtze River, China. We observe robust complementarity between data. relative detectability was notably influenced by major taxonomic groups sizes, with providing more signals larger organisms. Both exhibited similar cross-sectional longitudinal patterns. organisms declined metabarcoding, possibly due differential release decay or sizes. While underscoring potential large river biomonitoring, emphasize need interpretation versus This highlights importance careful method selection studies.

Language: Английский

Citations

An overlooked source of false positives in eDNA-based biodiversity assessment and management DOI

Wei Xiong, Hugh J. MacIsaac, Aibin Zhan

et al.

Journal of Environmental Management, Journal Year: 2024, Volume and Issue: 358, P. 120949 - 120949

Published: April 23, 2024

Language: Английский

Citations

Overlooked eDNA contamination in human-influenced ecosystems: a call to manage large-scale false positives in biodiversity assessments DOI

Aibin Zhan

Water Biology and Security, Journal Year: 2025, Volume and Issue: unknown, P. 100374 - 100374

Published: Feb. 1, 2025

Language: Английский

Citations

Selecting Competent Reverse Transcription Strategies to Maximise Biodiversity Recovery With eRNA Metabarcoding DOI

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

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

Spatial dispersal of environmental DNA particles in lentic and marine ecosystems: An overview and synthesis DOI

Toshiaki Jo, Hiroaki Murakami, Ryosuke Nakadai

et al.

Ecological Indicators, Journal Year: 2025, Volume and Issue: 174, P. 113469 - 113469

Published: April 15, 2025

Language: Английский

Citations

Validation of fish environmental RNA metabarcoding analysis for ecological surveys by additional traditional field surveys in the Naka River DOI

Kaede Miyata,

Yuta Kusakabe,

Yasuaki Inoue

et al.

Frontiers in Ecology and Evolution, Journal Year: 2025, Volume and Issue: 13

Published: May 8, 2025

Metabarcoding analysis using fish environmental RNA (eRNA) has demonstrated higher performance compared to that DNA (eDNA) in the Naka River Japan. However, results from representative sampling sites were insufficient estimate diversity of organisms entire river. Therefore, we validated evaluation additional traditional field survey (TFS) data. Data seven surveys on fish, covering area near points where eDNA/eRNA metabarcoding analyses conducted, obtained. Ten species newly identified, with nine determined eDNA and eRNA analyses. Performance was evaluated terms both positive predictive value (PPV) sensitivity. Except for specifically detected only estuary, use data increased PPV 26.5% 36.3% 43.6% 57.7% eRNA. After combining multiple surveys, sensitivities 52.4% 67.4% 57.1% 69.8%, respectively. The increase more pronounced than eDNA, indicating does not decrease when datasets are merged. superior suggests is valuable accurately conducting ecological biodiversity assessments may reduce labor required monitoring river by optimizing analysis.

Language: Английский

Citations

Unlocking rivers' hidden diversity and ecological status using DNA metabarcoding in Northwest Spain DOI

Álvaro Fueyo, Omar Sánchez, Carlos Carleos

et al.

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(8)

Published: Aug. 1, 2024

Abstract Rivers are crucial ecosystems supporting biodiversity and human well‐being, yet they face increasing degradation globally. Traditional river biomonitoring methods based on morphological identification of macroinvertebrates present challenges in terms taxonomic resolution scalability. This study explores the application DNA metabarcoding analysis both bulk environmental (eDNA) samples for comprehensive assessment macrozoobenthic biodiversity, detection invasive endangered species, evaluation ecological status northwestern Spain. homogenized water eDNA revealed a mean 100 87 macrozoobenthos species per sample respectively. However, specific composition was significantly different with only 27.3% total being shared. It not possible to identify all OTUs level; 17.43% 49.4% generated could be identified level samples, Additionally, 11 exotic (two first records Iberian Peninsula another three Asturias region) one were detected by molecular tools. Molecular showed significant correlations EQR values (Ecological Quality Ratio) IBMWP index, differences inferred noted, tending indicate higher status. Overall, offers promising approach biomonitoring, providing insights into within single analysis. Further optimization intercalibration required its implementation routine programmes, but scalability multi‐tasking capabilities position it as valuable tool integrated monitoring ecosystems.

Language: Английский

Citations

Fish environmental RNA sequencing sensitively captures accumulative stress responses through short-term aquarium sampling DOI

Kaede Miyata, Yasuaki Inoue,

Masayuki Yamane

et al.

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 959, P. 178182 - 178182

Published: Dec. 23, 2024

Language: Английский

Citations