Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short‐read nanopore sequencing as a potential biomonitoring tool

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(4)

Published: Feb. 28, 2024

Abstract The approach of combining cost‐effective nanopore sequencing and emerging environmental DNA (eDNA) metabarcoding could prove to be a promising tool for biodiversity documentation, especially in Malaysia. Given the substantial funding constraints recent years, relation country's biodiversity, many researchers have been limited conduct restricted research without extended monitoring periods, potentially hindering comprehensive surveys compromise conservation efforts. Therefore, present study aimed evaluate application eDNA on freshwater fish using short reads generated through sequencing. This assessment focused species detection three selected rivers within Endau Rompin Landscape Additionally, compared levels between conventional sampling methods, examined effectiveness primer choice, applied both shotgun approach. We successfully identified total 22 71 with an identification threshold >97% >90%, respectively, MinION platform. detected over 13% more than when method was used. Notably, distinction primers 12S rRNA cytochrome oxidase I insignificant. cost proved effective reduction at 33.4%. With favourable cost‐effectiveness increased detection, complement existing enhance holistic diversity documentation targeted habitats facilitate planning.

Language: Английский

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VertU: universal multilocus primer sets for eDNA metabarcoding of vertebrate diversity, evaluated by both artificial and natural cases

Frontiers in Ecology and Evolution, Journal Year: 2023, Volume and Issue: 11

Published: June 19, 2023

Environmental DNA (eDNA) metabarcoding is a powerful tool for monitoring biodiversity in natural ecosystems. The accuracy of eDNA relies heavily on the PCR primers that amplify target sequences. For vertebrates, most available are designed particular groups. There have been inadequate attempts to design “universal” applicable all vertebrates. Here, we developed three new universal primer sets (V12S-U, V16S-U, and VCOI-U) targeting mitochondrial 12S, 16S, COI genes, respectively. They work vertebrate groups, with amplification length 200-250 bp, facilitating use short-read sequencing platforms. We evaluated compared species detection ability our seven previously published ones through both in-silico experiment tests mock zoo eDNA. success over 90%, showing better performance than sets. also tested water samples environments, detected total 895 OTUs (BLAST identity ≥ 0.95), comprising 182 species, 195 genera, 94 families. Our results indicated utilizing multiple markers can achieve using only single marker, which especially important large biological communities like enable researchers detect presence different groups one survey, simplifies workflow reduces cost. It has potential serve as an alternative/complementary future studies

Language: Английский

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eDNA-based seasonal monitoring reveals fish diversity patterns in mangrove habitats of Guinea-Bissau

Regional Studies in Marine Science, Journal Year: 2025, Volume and Issue: unknown, P. 104013 - 104013

Published: Jan. 1, 2025

Language: Английский

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

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

Published: March 1, 2025

Language: Английский

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Temporal and Spatial Dynamics of the Lotic Fish Communities: A Comparison of Coffee Filter‐Based Passive eDNA Collection Versus Active eDNA Filtering

Environmental DNA, Journal Year: 2025, Volume and Issue: 7(2)

Published: March 1, 2025

ABSTRACT Environmental DNA (eDNA) metabarcoding is a noninvasive and cost‐effective method for fish community monitoring, enabling the determination of both presence/absence species their relative quantity in closed systems. However, integration these novel eDNA‐based methods into current monitoring practices not straightforward require standardization methodological approaches. In this study, we investigated spatial temporal variation assemblages within two lotic systems Croatia. Six sampling stations were located alongside middle section river Sava upstream downstream Zagreb, one location stream Okićnica. We compared traditional field surveys with eDNA methodologies: active filtering passive collection. showed that collection using coffee filters detected composition as effectively filtration, providing comparable results terms local richness assemblages. Generally, our approach greater per site than electrofishing. Each single sample captured an average 18.3 species, from total 30 encountered 78 samples. The sites Zagreb significant differences read abundance comparison to downstream. Nonmetric multidimensional scaling (nMDS) plot based on appeared be structured according type system, clear separation two‐dimensional space between samples Okićnica seasons. A substantial increase during spawning periods certain was observed, emphasizing method's utility unraveling ecological complexities. Altogether, study exemplifies how powerful tool standardized information will valuable environmental management.

Language: Английский

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Validated Environmental DNA Assay for Detection of the Rare Rice's Whale (Balaenoptera ricei)

Environmental DNA, Journal Year: 2025, Volume and Issue: 7(2)

Published: March 1, 2025

ABSTRACT The Rice's whale ( Balaenoptera ricei ) is a critically endangered baleen species that resides year‐round in the Gulf of America (formerly U.S. Mexico). majority sightings occur where seafloor varies between 100 and 400 m depth restricted region northeastern America; however, historical whaling records suggest may have inhabited other areas recent acoustic visual observation data detected their presence northwestern southwestern Mexico. A better understanding distribution movements could aid this species' recovery. In decades, non‐invasive genetic techniques been developed to detect or absence through use environmental DNA (eDNA). We quantitative polymerase chain reaction (qPCR) assay targeting mitochondrial control eDNA shed by whales. rigorous validation process was completed determine assay's sensitivity specificity. final detects low copy numbers target eDNA, highly specific whale, successfully used whale's “flukeprint” samples n = 23). addition, we tested collection methods such as filter pore size ability at different time intervals after surfaced were able long 10 min later. also obtained from Acousonde tags being attached whale. Taken together, these sampling events will help refine improve for many marine mammal species. Future research combining newly with traditional survey our habitat rare

Language: Английский

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A systematic review on environmental DNA (eDNA) Science: An eco-friendly survey method for conservation and restoration of fragile ecosystems

Ecological Indicators, Journal Year: 2025, Volume and Issue: 173, P. 113441 - 113441

Published: April 1, 2025

Language: Английский

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Aquatic eDNA outperforms sedimentary eDNA for the detection of estuarine fish communities in subtropical coastal vegetated ecosystems

Journal of Fish Biology, Journal Year: 2025, Volume and Issue: unknown

Published: April 14, 2025

Abstract In South Africa, mangrove forests and seagrass meadows often co‐occur in estuarine systems combination host rich, endemic biodiversity. There is an urgent need to explore community diversity coastal vegetated ecosystems, given the degrading effects of climate change anthropogenic pressures. Environmental DNA metabarcoding a promising biomonitoring tool African although studies highlight optimise standardise sampling protocols. This study aimed contribute developing protocols by understanding applicability environmental (eDNA) within habitats investigating using two different sample types. Aquatic sedimentary samples from three estuaries along east coast with MiFish metabarcoding, detected 148 operational taxonomic units (OTUs) representing 67 fish genera 50 families, only 16% were resolved species. We observed that aquatic eDNA 97% total diversity, suggesting this efficient comprehensively detect ichthyofaunal diversity. did not communities between mangroves seagrasses our findings underscore importance taking hydrological connectivity into consideration for design. Overall, work reinforces key considerations future focused on fauna estuaries, therefore contributes optimising support

Language: Английский

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A pilot study of fish biodiversity with a highlight of chondrichthyans in Hong Kong waters using environmental DNA metabarcoding

Regional Studies in Marine Science, Journal Year: 2025, Volume and Issue: 86, P. 104194 - 104194

Published: April 28, 2025

Language: Английский

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Environmental DNA enhances comprehension of the spatial and temporal dynamics of fish diversity in a coastal lagoon

Estuarine Coastal and Shelf Science, Journal Year: 2024, Volume and Issue: 304, P. 108824 - 108824

Published: June 3, 2024

Transitional environments have great ecological value and high productivity, many species can benefit from their sheltered conditions food resources. In this study, we performed for the first time a fish-targeted eDNA metabarcoding of 12S rRNA gene at 16 sites broadly covering different water bodies Marano Grado Lagoon (northern Adriatic Sea) in two seasons. The was collected same as beach seine net, allowing direct comparison approaches. With detected 34 species, all functional guilds occurring lagoon. Species regional interest, that uses area nursery feeding ground, diadromous highlighting connectivity between freshwater marine habitats, were found. While some constantly present (e.g. Atherina boyeri, Sparus aurata), others (Squalius cephalus, Platichthys flesus) influenced by salinity (higher lower Marano), which confirmed main driver environment. with traditional methods, identified 18 (11 both approaches), showed is very sensitive detecting most biodiversity lagoon limited sampling effort. Few relevant (Chelon saliens, Knipowitschia panizzae) lacked reference sequences, need to be implemented databases. Our study represents significant advance understanding fish dynamics contributes improvement management strategies these ecologically habitats.

Language: Английский

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