High frequency environmental DNA metabarcoding provides rapid and effective monitoring of fish community dynamics

Environmental DNA, Год журнала: 2023, Номер 5(6), С. 1623 - 1640

Опубликована: Окт. 28, 2023

Abstract Long‐term monitoring is critical to measure the response of biodiversity patterns and processes human‐mediated environmental pressures. This particularly pertinent in freshwaters, where recent estimates indicated a third all fish species are threatened with extinction, making ongoing biomonitoring essential for conservation management. High frequency annual identifying temporal changes community composition; however, traditional survey methods typically less practical over such timeframes. While (e)DNA measurement represents potentially powerful tool dynamics, studies lacking. To address this deficit, we generated high time‐series dataset entire communities using eDNA metabarcoding, directly assess repeatability sensitivity method detecting population trends. We targeted two differing environments (freshwater vs. intertidal) within Thames catchment, UK, detailed historical records from were available comparison. test how robust data inferring known community, applied hierarchical, nested design encompassing short longer‐term variation data. Our analyses showed that irrespective environment, metabarcoding represented seasonal shifts communities, increased relative read abundance coincided migratory spawning events, including those critically endangered native Anguilla anguilla (European eel). detections across single year included 75% recorded ca. 30‐year dataset, highlighting power detection. findings provide greater insight into utility recovering trends dynamic freshwater systems potential best sampling strategy future surveys.

Язык: Английский

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Environmental DNA analysis of airborne poaceae (grass) pollen reveals taxonomic diversity across seasons and climate zones

Environmental Research, Год журнала: 2023, Номер 247, С. 117983 - 117983

Опубликована: Дек. 30, 2023

Grasses populate most biogeographical zones, and their diversity influences allergic sensitisation to pollen. Previously, the contribution of different Poaceae subfamilies airborne pollen has mostly been inferred from historical herbarium records. We recently applied environmental (e)DNA metabarcoding at one subtropical site revealing that successive grass peaks were derived repeated flowering Chloridoid Panicoid grasses over a season. This study aimed compare spatiotemporal patterns in exposure across seasons climate zones. Airborne concentrations two austral spanning 2017–2019 (Mutdapilly Rocklea, Queensland) temperate (Macquarie Park Richmond, New South Wales) sites, determined with routine volumetric impaction sampler counting by light microscopy. rbcL metabarcode sequences amplified daily samples collected once per week assigned subfamily genus using ribosomal classifier compared Atlas Living Australia sighting eDNA analysis revealed distinct dominance various sites: prevailed both Mutdapilly Macquarie Park, whilst dominated Rocklea site. Overall, sites showed significantly higher proportion than whereas Pooideae sites. Timing Pooid (spring), (late spring autumn), Arundinoid (autumn) related number days mid-winter. Proportions for correlated distributions records between enabled finer taxonomic discernment zones implications understanding adaptation grasslands change, complexity patients respiratory diseases.

Язык: Английский

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Tools for pathogen genetic surveillance: Lessons from the ash dieback invasion of Europe

PLoS Pathogens, Год журнала: 2024, Номер 20(5), С. e1012182 - e1012182

Опубликована: Май 23, 2024

Human movement and climate change are exposing new environments to pathogens increasing the rate of invasions [1].Presently, most studied independently, requiring species-specific expertise, particularly at sampling stage.Genomic surveillance strategies can be applied identify species presence/absence but also within-species diversity, which may not currently capitalised upon.Here, we use ash dieback invasion Europe [2] frame a discussion on significance different types genomic variation biology review application developing microbiome sequencing technologies pathogen surveillance. What is dieback?European (Fraxinus excelsior) prevalent throughout Europe; for example, it third common tree in United Kingdom.Ash keystone with approximately 1,000 associated over 100 obligately/highly [3].The (see [4]), caused by Hymenoscyphus fraxineus, was first identified Estonia, 1992, has since spread west, reaching UK 2012 [2].In its native range East Asia, H. fraxineus saprophyte little effect host, F. mandshurica [5].In Europe, causes crown death least 2 [2].Ash estimated cost economy £7.6 billion 2029 [6].Slow disease symptoms [7], environmental conditions [8], varying resistance [9], propagule pressure [10] make estimating mortality rates difficult.Best estimates suggest 70% 85% [7].Models plant defence against focus genes evolved recognise gene products trigger immunity [11].Reduced susceptibility European appears mediated many meaning that both natural selection breeding programmes have lot work do bring all those together [12].H. within trade infected samplings wind consequently, found 50 km ahead infection front [13].Management diseases these scales difficult, so our attention turns introduction reintroduction.Surveillance measures could important an early or prevent subsequent genetic diversity focussing effort limiting exchanges between reservoirs critically adaptation.

Язык: Английский

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Macrobial airborne environmental DNA analysis: A review of progress, challenges, and recommendations for an emerging application

Molecular Ecology Resources, Год журнала: 2024, Номер 24(7)

Опубликована: Авг. 8, 2024

In the context of looming global biodiversity loss, effective species detection represents a critical concern for ecological research and management. Environmental DNA (eDNA) analysis, which refers to collection taxonomic identification genetic fragments that are shed from an organism into its surroundings, emerged approximately 15 years ago as sensitive tool detection. Today, one frontiers eDNA concerns analysis material in dust other airborne materials, termed analysis. As study matures, it is appropriate time review foundational emerging studies make up current literature, use reviewed literature summarize, synthesize, forecast major challenges opportunities this advancing front. Specifically, we "ecology eDNA" framework organize our findings across origin, state, transport, fate materials environment, summarize what so far known their interactions with surrounding abiotic biotic factors, including population community ecologies ecosystem processes. Within work identify key challenges, opportunities, future directions associated application development. Lastly, discuss development applications, partnerships, messaging promote growth field. Together, broad potential rate at accelerating field suggest sky's limit science.

Язык: Английский

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Airborne eDNA captures three decades of ecosystem biodiversity

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Дек. 11, 2023

Abstract Conserving biodiversity is a global imperative, yet our capacity to quantify and understand species occurrences has been limited. To help address this challenge, we develop novel monitoring approach based on deep sequencing of airborne eDNA. When applied 34-year archive weekly filters from an aerosol sampling station in northern Sweden, methods enabled robust detection over 2,700 genera across all domains life estimates eDNA catchment areas. Reconstructed time series revealed regional declines consistent with contemporary, large-scale transformations forest composition structure. Our results show can reliably monitor underscore the immense latent potential thousands stations deployed worldwide. One-Sentence Summary DNA captured air reveals organisms their long-term trends.

Язык: Английский

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