Using eDNA metabarcoding to establish targets for freshwater fish composition following river restoration DOI Creative Commons
Gen Ito, Hiroshi Yamauchi,

Miwa Shigeyoshi

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Май 29, 2022

Abstract Establishing realistic targets for fish community composition is needed to assess the effectiveness of river restoration projects. We used environmental DNA (eDNA) metabarcoding with MiFish primers obtain estimates across 17 sites upstream, downstream and within a mitigation project area (Kaihotsu– Kasumi) located in Shigenobu River system, Ehime Prefecture, Japan. evaluate benefits using eDNA quickly, sensitively, extensively gather data establish existing area, as well potential future short-term, medium-term, long-term species assemblages that could realistically emerge following dispersal into from upstream populations. compare results lists obtained contemporaneous capture surveys historical information. Nonmetric multidimensional scaling plots showed Kaihotsu–Kasumi surrounding reaches were divided three clusters: upper reaches, middle lower estuarine reaches. The Kaihotsu– Kasumi included group containing inflow outflow rivers near area. detected total twenty-six this group, twenty-one native five non-native species. Therefore, these considered suitable short-term target high By comparison, only 14 would have been selected based on literature. One factor increasing resolution our was ability identify presence intraspecific lineages Misgurnus anguillicaudatus (Clades A B), which missed by surveys. These indicate method can provide more comprehensive than surveys, higher monitoring through lineage detection.

Язык: Английский

Applications of environmental DNA (eDNA) to detect subterranean and aquatic invasive species: A critical review on the challenges and limitations of eDNA metabarcoding DOI Creative Commons
Sakib Tahmid Rishan, Richard J. Kline, Md Saydur Rahman

и другие.

Environmental Advances, Год журнала: 2023, Номер 12, С. 100370 - 100370

Опубликована: Апрель 19, 2023

The world is struggling to solve a devastating biodiversity loss that not only affects the extinction of treasured species and irreplaceable genetic variation, but also jeopardizes food production, health, safety people. All initiatives aimed conserve rely heavily on monitoring both populations get accurate spatial patterns overall population assessments. Conventional techniques, such as visual surveys counting individuals, are problematic due challenges in identifying cryptic or immature life stages. Environmental DNA (eDNA) relatively new technology has potential be faster, non-invasive, cost-effective tool for biodiversity, conservation, management practices. eDNA been extracted from materials ancient present, its applications range identification individual study entire ecosystems. In past few years, there substantial increase usage research pertaining ecological preservation conservation. However, several technological problems still need solved. To reduce number false positives and/or negatives produced by current technologies, it necessary improve optimize calibration validation at every stage procedure. There significant greater information about physical constraints use, well synthesis, state, expected lifespan, modes movement. Due widespread use research, essential assess extent breadth these studies. this article, we critically reviewed primary subterranean aquatic invasive species. Through review, readers can better understand limitations metabarcoding.

Язык: Английский

Процитировано

51
Exploitation of environmental DNA (eDNA) for ecotoxicological research: A critical review on eDNA metabarcoding in assessing marine pollution DOI
Sakib Tahmid Rishan, Richard J. Kline, Md Saydur Rahman

и другие.

Chemosphere, Год журнала: 2024, Номер 351, С. 141238 - 141238

Опубликована: Янв. 21, 2024

Язык: Английский

Процитировано

8
Monitoring terrestrial rewilding with environmental DNA metabarcoding: a systematic review of current trends and recommendations DOI Creative Commons

Clare Cowgill,

James Gilbert, Ian Convery

и другие.

Frontiers in Conservation Science, Год журнала: 2025, Номер 5

Опубликована: Янв. 2, 2025

Introduction Rewilding, the facilitation of self-sustaining and resilient ecosystems by restoring natural processes, is an increasingly popular conservation approach potential solution to biodiversity climate crises. Outcomes rewilding can be unpredictable, monitoring essential determine whether are recovering. Metabarcoding, particularly environmental DNA (eDNA), revolutionizing could play important role in understanding impacts but has mostly been applied within aquatic systems. Methods This systematic review focuses on applications eDNA metabarcoding terrestrial monitoring, with additional insights from bulk ingested DNA. We examine publication trends, choice sampling substrate focal taxa, investigate how well performs compared other methods (e.g. camera trapping). Results Terrestrial represented a small proportion total papers, forests most studied system, soil water substrates, vertebrates targeted taxa. Most studies focused measuring species richness, few included analyzes functional diversity. Greater richness was found when using multiple took this approach. Metabarcoding did not consistently outperform terms number vertebrate taxa detected, likely influenced marker, habitat. Discussion Our findings indicate that metabarcoding, eDNA, key rewilding, further ground- truthing needed establish appropriate experimental pipelines for target system interest. Systematic Review Registration https://osf.io/38w9q/?view_only=47fdab224a7a43d298eccbe578f1fcf0 , identifier 38w9q.

Язык: Английский

Процитировано

1
Environmental DNA metabarcoding for fish diversity assessment in a macrotidal estuary: A comparison with established fish survey methods DOI Creative Commons
Thomas I. Gibson, Gary R. Carvalho, Amy Ellison

и другие.

Estuarine Coastal and Shelf Science, Год журнала: 2023, Номер 294, С. 108522 - 108522

Опубликована: Окт. 10, 2023

Fishes are a dominant component of the macrofauna in estuaries and important for assessing health these threatened ecosystems. Several studies have applied environmental DNA (eDNA) metabarcoding to assess biodiversity fishes estuaries. However, none combined measurement physicochemical variables with spatially extensive sampling design across full salinity gradient. This study aimed compare spatial fish assemblage composition detected via eDNA surface water samples conventional fishing gear surveys macrotidal estuary (river Dee, North Wales, UK). In addition, seasons was investigated. autumn 2018, triplicate were taken at 13 stations systematic alongside seine, fyke beam trawl sampling. summer 2019, from eight original collected again upper lower estuary. extracted subjected analysis using an established assay targeting teleost fishes. The key findings that autumn, 17 26 (71%) species caught by gears, which included most abundant species. Overall, greater richness, per 30 samples, than seine or nets (but not trawling). Additionally, there clear correlation between composition, consistent seasons. indicates could enhance existing methods, generating more comprehensive picture estuarine providing additional information ecological inference management actions.

Язык: Английский

Процитировано

14
Evaluation of the Effects of Environmental Factors on Seasonal Variations in Fish Diversity on a Coastal Island in Western Japan DOI Open Access
Nguyen Hong Nhat, Mitsuyo Saito, Mayuko Hamada

и другие.

Environments, Год журнала: 2024, Номер 11(3), С. 60 - 60

Опубликована: Март 20, 2024

Coastal habitats are crucial for supporting ecological processes and serve as vital ecosystems diverse fish species, providing essential functions such feeding, nursery provision, reproductive habitats. Fish communities ecologically important components of coastal affected by multiple environmental factors. Despite their importance, determining the effects factors on seasonal variations in species diversity community dynamics remains a challenge. The advent DNA (eDNA) technology, an environmentally conscious approach, has resulted considerable advancements recent years been progressively adopted marine population monitoring. Here, we used metabarcoding to study structure island, assessed structuring these communities. Our findings revealed rich 72 across 40 families 23 orders seawater surrounding island Seto Inland Sea (SIS), Western Japan. Notably, composition varied significantly between seasons, with temperature, salinity, dissolved inorganic phosphorus (DIP) concentration identified correlated communities’ structures. In conclusion, our provides useful information diversity, suggest that eDNA is valuable technique monitoring areas. These studies oceanic environments.

Язык: Английский

Процитировано

5
Environmental DNA reveals ecologically relevant spatial and temporal variation in fish assemblages between estuaries and seasons DOI Creative Commons
Thomas I. Gibson, Charles Baillie, Rupert A. Collins

и другие.

Ecological Indicators, Год журнала: 2024, Номер 165, С. 112215 - 112215

Опубликована: Июнь 9, 2024

Estuarine ecosystems are threatened by numerous anthropogenic pressures.Fish assemblages a dominant component of estuarine macrofauna and serve as indicators for the health these transitional water ecosystems.Environmental DNA (eDNA) metabarcoding is increasingly used to assess biodiversity fishes in estuaries.However, there need further establish how effective eDNA can be relative conventional fish sampling methods across multiple estuaries seasons.This study compared detected via surface samples contemporary with fishing gears three temperate (UK), during early summer autumn.Most species caught were eDNA.Species richness estimates from two ten times higher than based on fishing, included taxa conservation importance non-native species.The assemblage composition was significantly different seine nets.Importantly, could effectively discriminate between seasons.Fish often not monitored due resource constraints.The dynamic nature may make gear deployment difficult inconsistent.The findings indicate that suited gathering large amounts information biodiversity, at relatively low effort, established methods.Therefore, shows promise an assessment tool structure ecosystem environments, application statutory monitoring.

Язык: Английский

Процитировано

5
From land to sea: Environmental DNA is correlated with long-term water quality indicators in an urbanized estuary DOI Creative Commons
Adam T. Downie, William W. Bennett, Shaun Wilkinson

и другие.

Marine Pollution Bulletin, Год журнала: 2024, Номер 207, С. 116887 - 116887

Опубликована: Авг. 31, 2024

Estuaries provide critical ecosystem services, and yet are increasingly under threat from urbanization. Non-invasive approaches to monitor biodiversity resident or migrating through estuaries is evaluate the holistic health of these ecosystems, often based entirely on water quality. In this study we compared tree life metabarcoding (ToL-metabarcoding) detections with measurements physico-chemical variables (chlorophyll a, turbidity, total nitrogen, phosphorous, dissolved oxygen) at eight sites varying degrees quality in Gold Coast Broadwater Estuary (Queensland, Australia). These were ranked according an adapted Water Quality Index (WQI) score. Here, detected 787 unique taxa, adding 137 new records region, mostly micro-organisms such as bacteria, ciliates, diatoms, dinoflagellates, cryptomonads. Sites lowest WQI characterised by higher lower oxygen, well nitrogen which correlated increased diversity green algae. Similarly, composition taxa was significantly different between variable values for most but less apparent larger vertebrate groups. findings suggest that rapid ToL-metabarcoding detections, particularly order taxonomic groups, can serve valuable indicators flora fauna across associated dynamically shifting estuarine along urbanized coastlines.

Язык: Английский

Процитировано

4
Population Genetic Structure of Marine Fishes DOI Creative Commons
Fidelina González, Patricio Barría, Francisco Ponce‐Gordo

и другие.

IntechOpen eBooks, Год журнала: 2024, Номер unknown

Опубликована: Апрель 18, 2024

Research on population genetics structure of marine fishes is increasing because new technology based DNA sequencing. This knowledge necessary for management and conservation natural in environment. The aim the chapter to discuss about how genetic get from DNA, allows us know dynamic life history species Teleosts (Actinopterigii) Chondrichthyes (Elasmobranchii). analysis taxonomic point view. We hope contribute apply advances wildlife.

Язык: Английский

Процитировано

3
New insights into biologic interpretation of bioinformatic pipelines for fish eDNA metabarcoding: A case study in Pearl River estuary DOI
Zhuoying Li,

Wencheng Zhao,

Yun Jiang

и другие.

Journal of Environmental Management, Год журнала: 2024, Номер 368, С. 122136 - 122136

Опубликована: Авг. 11, 2024

Язык: Английский

Процитировано

3
eDNA-based seasonal monitoring reveals fish diversity patterns in mangrove habitats of Guinea-Bissau DOI
Pieter-Jan Keleman, Jean‐Dominique Durand, Monique Simier

и другие.

Regional Studies in Marine Science, Год журнала: 2025, Номер unknown, С. 104013 - 104013

Опубликована: Янв. 1, 2025

Язык: Английский

Процитировано

0