Quantitative monitoring of diverse fish communities on a large scale combining <scp>eDNA</scp> metabarcoding and <scp>qPCR</scp>

Pont, Didier; Meulenbroek, Paul; Bammer, V.; Déjean, Tony; Erős, Tibor; Jean, Pauline; Lenhardt, Mirjana; Nagel, Christoffer; Pekárik, Ladislav; Michael, Schabuss; Stoeckle, Bernhard C.; Stoica, Elena; Horst, Zornig; Weigand, Alexander; Valentini, Alice

doi:10.1111/1755-0998.13715

Cited by 33 publications

(29 citation statements)

References 95 publications

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“…Since the proportion of preferred habitat scales disproportionately with the square of bay area, and given that the eDNA is thoroughly mixed within the bay, this results in a dilution effect. Similar patterns of DNA dilution have been observed in rivers with elevated water discharges (Pont et al, 2023).…”

Section: Discussionsupporting

confidence: 78%

Temperature moderates eDNA–biomass relationships in northern pike

et al. 2023

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Support for eDNA as a quantitative monitoring tool is growing worldwide. Despite advances, there are still uncertainties regarding the representability of the eDNA signal over varying spatiotemporal scales, the influence of abiotic forcing, and phenological changes affecting the behavior of the study organism, particularly in open environments. To assess the spatiotemporal variability and predictive power of quantitative eDNA analysis, we applied species-specific real-time quantitative PCR on water filtrates during two visits to 22 coastal bays in the Baltic Sea. Within bays, we collected water along four transects across each bay and compared the pooled eDNA concentration to temporally matched catches from standardized angling targeting the northern pike (Esox lucius), a species for which reliable monitoring data is lacking.We found the variability in eDNA concentrations between transects to be moderate (21%) but still considerably lower than across bays and visits (52%), suggesting small-scale spatial differences are of less importance during spring when pike spawn.Standardized angling catches, bay area, and water temperature together explained 48% of the variance in eDNA concentrations. DNA concentrations decreased with the increasing bay area, likely indicating a dilution effect. Notably, the relationship between eDNA and standardized catches was positive but varied with temperature and the eDNA-abundance relationship was only significant at higher temperatures, which also coincided with a higher proportion of spawning/spent fish. We conclude that temperature is a key moderating factor driving changes in pike behavior and spring DNA-dynamics. We recommend that future surveys focus on larger spatiotemporal scales during times when the influence of changing temperatures is minimized.

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Section: Discussionsupporting

confidence: 78%

Temperature moderates eDNA–biomass relationships in northern pike

et al. 2023

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“…Even though the information obtained through metabarcoding is not as accurate as that obtained using species‐specific PCR assays, metabarcoding allows to have an overview of the trend of the community composition. Then, if some results need to be refined, species‐specific PCR (qPCR or dPCR) can be combined to metabarcoding in order to better infer the absolute abundance of fish species as performed by Pont et al (2022) who combined eDNA metabarcoding with qPCR to infer the absolute abundance of fish species. Another option is the use of internal standard DNAs which correspond to known amounts of short DNA fragments from fish species that have never been observed in a sampling area (Sato et al, 2021; Ushio et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

eDNA metabarcoding from aquatic biofilms allows studying spatial and temporal fluctuations of fish communities from Lake Geneva

et al. 2023

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Fish communities are now studied non‐invasively using environmental DNA (eDNA) recovered from water samples. The objective of this study is to evaluate the possibility of surveying these communities using fish eDNA passively “captured” by aquatic biofilms. To this end, biofilm samples developing on natural and artificial substrates were collected every 2 weeks for a year and a half in a large lake (Lake Geneva). DNA was extracted from biofilms and fish communities were targeted using a standard 12S barcode with a metabarcoding approach. The fish eDNA signal recovered from biofilms revealed temporal and spatial changes in fish communities. These changes were linked to fish habitat preferences and spawning season. Peaks in the eDNA signal of some taxa fitted with their spawning period reported in the literature. We evidenced that the nature of the biofilm's substrate (natural or artificial) does not affect the image obtained of the fish community composition. Furthermore, by using biofilms grown on artificial substrates, the studied temporal window of the eDNA signal can be controlled. With biofilms acting as environmental passive samplers, our results open up the possibility to accurately monitor fish communities and their temporal and spatial changes with eDNA in a faster and less expensive way than with the classical water filtration approach.

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“…Exploring priority effects requires abundance data to assess positive frequency dependence patterns, but eDNA metabarcoding is still limited in providing relevant abundance data [65]. Further studies might, therefore, investigate the potential of eDNA to provide fish abundance [66,67], which will provide a finer assessment of community assembly, functional structure and the impact of human activities [68,69].…”

Section: Discussionmentioning

confidence: 99%

Deforestation strengthens environmental filtering and competitive exclusion in Neotropical streams and rivers

Cantera,

Jézéquel,

Dejean

et al. 2023

Proc. R. Soc. B.

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Understanding how anthropization impacts the assembly of species onto communities is pivotal to go beyond the observation of biodiversity changes and reveal how disturbances affect the environmental and biotic processes shaping biodiversity. Here, we propose a simple framework to measure the assembly processes underpinning functional convergence/divergence patterns. We applied this framework to northern Amazonian fish communities inventoried using environmental DNA in 35 stream sites and 64 river sites. We found that the harsh and unstable environmental conditions characterizing streams conveyed communities towards functional convergence, by filtering traits related to food acquisition and, to a lower extent, dispersal. Such environmental filtering also strengthened competition by excluding species having less competitive food acquisition traits. Instead, random species assembly was more marked in river communities, which may be explained by the downstream position of rivers facilitating the dispersion of species. Although fish assembly rules differed between streams and river fish communities, anthropogenic disturbances reduced functional divergence in both ecosystems, with a reinforcement of both environmental filtering and weaker competitor exclusion. This may explain the substantial biodiversity alterations observed under slight deforestation levels in Neotropical freshwater ecosystems and underlines their vulnerability to anthropic disturbances that not only affect species persistence but also modify community assembly rules.

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Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR

Cited by 33 publications

References 95 publications

Temperature moderates eDNA–biomass relationships in northern pike

Temperature moderates eDNA–biomass relationships in northern pike

eDNA metabarcoding from aquatic biofilms allows studying spatial and temporal fluctuations of fish communities from Lake Geneva

Deforestation strengthens environmental filtering and competitive exclusion in Neotropical streams and rivers

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