Quantifying biodiversity using eDNA from water bodies: General principles and recommendations for sampling designs

Environmental DNA, Год журнала: 2023, Номер 5(4), С. 671 - 682

Опубликована: Май 16, 2023

Abstract Reliable and comparable estimates of biodiversity are the foundation for understanding ecological systems informing policy decision‐making, especially in an era massive anthropogenic impacts on biodiversity. Environmental DNA (eDNA) metabarcoding is at forefront technological advances monitoring, last few years have seen major progress solutions to technical challenges from laboratory bioinformatics. Water eDNA has been shown allow fast efficient recovery signals, but rapid pace development meant that some important principles regarding sampling design, which well established traditional inventories, neglected. Using a spatially explicit river flow model, we illustrate how must be adjusted size watercourse increase quality signal recovered. We additionally investigate effect parameters (volume, number sites, sequencing depth) detection probability empirical data set. Based principles, propose aquatic replication volume scaled match organisms' ecosystems' properties provide reliable estimates. present generalizable conceptual equation describing features as function ecosystem monitored, abundance target organisms, procedure. The aim this formalization enhance standardization critical steps design inventory studies using eDNA. More robust standards will generate more eDNA, necessary method's long‐term plausibility comparability.

Язык: Английский

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Destabilizing Effects of Environmental Stressors on Aquatic Communities and Interaction Networks across a Major River Basin

Environmental Science & Technology, Год журнала: 2023, Номер 57(20), С. 7828 - 7839

Опубликована: Май 8, 2023

Human-driven environmental stressors are increasingly threatening species survival and diversity of river systems worldwide. However, it remains unclear how the affect stability changes across aquatic multiple communities. Here, we used DNA (eDNA) data sets from a human-dominated in China over 3 years analyzed communities under persistent anthropogenic stressors, including land use pollutants. First, found that significantly reduced multifaceted (e.g., richness, Shannon's diversity, Simpson's diversity) but increased synchrony Second, structures interaction networks inferred an empirical meta-food web were changed for example, resulting decreased network modularity negative/positive cohesion. Third, piecewise structural equation modeling proved stress-induced decline mainly depended upon diversity-mediated pathways rather than direct effects stress per se; specifically, increase main biotic drivers variation. Overall, our study highlights destabilizing on as well mechanistic dependencies, through reducing increasing synchrony, changing networks.

Язык: Английский

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eDITH: An R‐package to spatially project eDNA‐based biodiversity across river networks with minimal prior information

Methods in Ecology and Evolution, Год журнала: 2024, Номер 15(5), С. 806 - 815

Опубликована: Март 27, 2024

Abstract Ecological and ecosystem monitoring is rapidly shifting towards using environmental DNA (eDNA) data, particularly in aquatic systems. This approach enables a combined coverage of biodiversity across all major organismal groups the assessment ecological indices. Yet, most current approaches are not exploiting full potential eDNA largely interpreting results localized perspective. In riverine networks, by explicitly modelling hydrological transport associated decay, hydrology‐based models enable upscaling eDNA‐based diversity information, providing spatially integrated inference. To capitalize on these unprecedented data translate it into space‐filling projections, streamlined implementation needed. Here, we introduce eDITH R‐package, implementing model to project networks with minimal prior information. couples species distribution relating local taxon's shedding rate streamwater covariates, mass balance expressing concentration at river's cross‐section as weighted sum upstream contributions, an observational accounting for uncertainties measurements. By leveraging replicated measurements hydro‐morphological disentangling various sources, produces maps spatial any chosen resolution. applicable both metabarcoding taxon whose can be retrieved streamwater. The package provides user‐friendly functions single‐run execution fitting Bayesian methods (via BayesianTools package) non‐linear optimization. An interface DHARMa allows validation via posterior predictive checks. Necessary preliminary steps such watershed delineation characterization implemented rivnet package. We illustrate 's workflow functionalities two case studies from published fish data. eDITH, specifically intended ecologists conservation biologists. It used without previous knowledge but also customization experienced users. Ultimately, river globally, transforming how state change systems tracked high resolution highly versatile manner.

Язык: Английский

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Cross‐boundary connections of biodiversity and ecosystem functioning in boreal ecosystems

Ecological Monographs, Год журнала: 2025, Номер 95(1)

Опубликована: Фев. 1, 2025

Abstract Relationships between biodiversity and ecosystem functioning (BEF) are typically investigated separately in different types, often neglecting connections across boundaries. Here, we examined the cross‐boundary relationships terrestrial aquatic function (here productivity terms of biomass). We collected a dataset from 100 Finnish boreal lakes for phytoplankton zooplankton, trees understory plants surrounding forest ecosystems. explored among climatic, catchment, local environmental factors, using structural equation modeling (SEM). The results indicated two realms. Terrestrial was associated with connected to lake water chemistry directly indirectly through productivity. Water turn linked Within both realms, positively effects per se were weaker realm, which nutrient availability strongest determinant Our findings underscore importance exploring cross‐ecosystem coupling, as impacts several global change drivers, such climate land‐use or eutrophication, extend beyond individual realms transcend In particular, combined warming, increasing likely increase import allochthonous nutrients ecosystems, resulting enhanced primary therein. As freshwater ecosystems integrate direct indirect changes their catchments, they serve ideal settings investigating coupling act valuable sentinels other changes.

Язык: Английский

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Regional mangrove vegetation carbon stocks predicted integrating UAV-LiDAR and satellite data

Journal of Environmental Management, Год журнала: 2024, Номер 368, С. 122101 - 122101

Опубликована: Авг. 22, 2024

Язык: Английский

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Long-term wetland biomonitoring highlights the differential impact of land use on macroinvertebrate diversity in Dongting Lake in China

Communications Earth & Environment, Год журнала: 2024, Номер 5(1)

Опубликована: Янв. 10, 2024

Abstract Freshwater wetlands have experienced disproportionate biodiversity loss due to environmental change. The lack of long-term biological data limits our understanding wetland dynamics and principal drivers. Here, we combine aquatic biomonitoring with satellite-derived imagery spatial-explicit analysis assess the changes in macroinvertebrate diversity driving factors from 1988 2017 Dongting Lake, China. results revealed declining alpha (species richness functional redundancy) but increased beta (taxonomic dissimilarity). An increase nutrients land-use intensity surrounding terrestrial ecosystem was primary mechanism for losses species groups. Alpha were most influenced by adjacent land areas 1.5 kilometers sampling sites, while affected within 50 meters. Our highlight a need attenuating effects establishing protected buffer protect future.

Язык: Английский

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Biogeographical Distribution of River Microbial Communities in Atlantic Catchments

Environmental Microbiology Reports, Год журнала: 2025, Номер 17(1)

Опубликована: Янв. 8, 2025

ABSTRACT Microbes inhabit virtually all river ecosystems, influencing energy flow and playing a key role in global sustainability climate change. Yet, there is uncertainty about how various taxonomic groups respond to large‐scale factors networks. We analysed microbial community richness composition across six European Atlantic catchments using environmental DNA sequencing. Our findings reveal different drivers for diversity composition: land use pivotal eukaryotes, while geology are crucial prokaryotes. A strong regional influence shapes these communities, with warmer, drier regions (Portugal France) differing from cooler, wetter ones (Northern Spain, Ireland the United Kingdom). These patterns suggest potential indicators change, such as taxa resistant temperature increases water scarcity, or those sensitive changes.

Язык: Английский

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Utilizing aquatic environmental DNA to address global biodiversity targets

Опубликована: Апрель 27, 2025

Язык: Английский

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Combining environmental DNA with remote sensing variables to map fish species distributions along a large river

Remote Sensing in Ecology and Conservation, Год журнала: 2023, Номер 10(2), С. 220 - 235

Опубликована: Авг. 17, 2023

Abstract Biodiversity loss in river ecosystems is much faster and more severe than terrestrial systems, spatial conservation restoration plans are needed to halt this erosion. Reliable highly resolved data on the state of change biodiversity species distributions critical for effective measures. However, high‐resolution maps fish distribution remain limited large riverine systems. Coupling from global satellite sensors with broad‐scale environmental DNA (eDNA) machine learning could enable rapid precise mapping organisms. Here, we investigated potential combining these methods using a eDNA dataset 110 sites sampled along full length Rhone River Switzerland France. Using Sentinel 2 Landsat 8 images, generated set ecological variables describing both aquatic habitats surrounding corridor. We combined eDNA‐based presence absence 29 used three machine‐learning models assess suitability species. Most showed good performance, indicating that derived remote sensing can approximate determinants distributions, but water‐derived had stronger associations river. The range indicated significant transition occupancy Rhone, its source Swiss Alps outlet into Mediterranean Sea southern Our study demonstrates feasibility map This method be expanded any support schemes.

Язык: Английский

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Integrating direct observation and environmental DNA data to enhance species distribution models in riverine environments

Ecological Informatics, Год журнала: 2025, Номер unknown, С. 103056 - 103056

Опубликована: Фев. 1, 2025

Язык: Английский

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