Determining an effective sampling method for eDNA metabarcoding: a case study for fish biodiversity monitoring in a small, natural river

Sakata, Masato; Watanabe, Takeshi; Maki, Nobutaka; Ikeda, Kazuko; Kosuge, Toshihiro; Okada, Hiroaki; Yamanaka, Hiroki; Sadõ, Tetsuya; Miya, Masaki; Minamoto, Toshifumi

doi:10.1007/s10201-020-00645-9

Cited by 46 publications

(54 citation statements)

References 47 publications

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“…Previous studies have suggested that differences in physical environments may affect the distribution of species and that visualization of fish communities within each lake would help to determine representative study sites (Sakata et al, 2020). Here, novel applications of spatial interpolation of eDNA signal (species richness and relative abundance of N. melanostomus) are demonstrated, which could be used in the future to prioritize AIS response efforts by identifying potential locations that would maximize the effectiveness of removal efforts.…”

Section: Discussionmentioning

confidence: 96%

Section: Discussionmentioning

confidence: 99%

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eDNA metabarcoding in lakes to quantify influences of landscape features and human activity on aquatic invasive species prevalence and fish community diversity

Pukk

Kanefsky

Heathman

et al. 2021

Diversity and Distributions

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Aim Our goal was to use eDNA metabarcoding to characterize fish community diversity, detect aquatic invasive species (AIS) and assess how measures of community (or AIS) diversity are influenced by lake physical and environmental covariates, measures of hydrological connectivity and human accessibility. Location Michigan, USA. Methods eDNA samples collected from 22 lakes were sequenced using two mitochondrial gene regions (12S and 16S rRNA). Metabarcoding data were compared to traditional fisheries survey data for a subset of lakes, and data from all 22 lakes were combined with environmental information to identify significant associations with community diversity and AIS relative abundance. Results Occupancy modelling indicated that detection probabilities were generally higher with eDNA than traditional fisheries gear. Measures of connectivity with upstream aquatic habitats were positively associated with both AIS relative abundance and fish species diversity. We also demonstrate the use of spatial interpolation methods to map distributions of species diversity and AIS relative abundance within lakes. Main conclusions eDNA metabarcoding methods provided information on the composition and diversity of fish assemblages and the presence of AIS in freshwater lakes that varied greatly in drainage connectivity and anthropogenic development. Our case study identified associations between environmental covariates and fish diversity or AIS relative abundance across lakes. This information is of particular importance given increasing anthropogenic disturbance, invasive species spread and associated declines in aquatic biodiversity. Incorporating eDNA metabarcoding as a supplement to traditional fisheries surveys will permit managers to identify greater numbers of taxa, including early detection of AIS, with less field effort and fish mortality. Further, eDNA methods may more accurately identify physical and biological features that correlate with diversity and abundance and allow agencies to more effectively direct AIS management activities.

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Section: Discussionmentioning

confidence: 96%

Section: Discussionmentioning

confidence: 99%

eDNA metabarcoding in lakes to quantify influences of landscape features and human activity on aquatic invasive species prevalence and fish community diversity

Pukk

Kanefsky

Heathman

et al. 2021

Diversity and Distributions

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“…Considering the PCR conditions, we faced a major limitation: some extracted DNA solutions were brown-colored ( S2 Table ), which means that the samples might have been contaminated with PCR inhibitors such as humic acids in the soil. Here, we applied a DNA extraction method developed for sedimentary soils of river bottoms [ 20 ]; however, the soil moisture contents were different for each land use, which might have influenced the PCR amplification. For subsequent MiSeq analysis targeting ribosomal ITS2, the colored DNA samples were diluted in the 1st PCR to produce accurate results.…”

Section: Discussionmentioning

confidence: 99%

“…The DNA extraction protocol was broadly followed as previously reported to increase the amount of DNA extracted from the soil samples [ 19 , 20 ]. We used the integrated method of alkaline DNA extraction with ethanol precipitation and a commercial DNA extraction kit for soil samples (PowerSoil DNA Isolation Kit, Qiagen, Germany).…”

Section: Methodsmentioning

confidence: 99%

Detection of multiple mycetoma pathogens using fungal metabarcoding analysis of soil DNA in an endemic area of Sudan

et al. 2022

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Mycetoma is a tropical disease caused by several fungi and bacteria present in the soil. Fungal mycetoma and eumycetoma are especially challenging to treat; therefore, prevention, early diagnosis, and early treatment are important, but it is also necessary to understand the geographic distribution of these pathogenic fungi. In this study, we used DNA metabarcoding methodology to identify fungal species from soil samples. Soil sampling was implemented at seven villages in an endemic area of Sennar State in Sudan in 2019, and ten sampling sites were selected in each village according to land-use conditions. In total, 70 soil samples were collected from ground surfaces, and DNA in the soil was extracted with a combined method of alkaline DNA extraction and a commercial soil DNA extraction kit. The region for universal primers was selected to be the ribosomal internal transcribed spacer one region for metabarcoding. After the second PCR for DNA library preparation, the amplicon-based DNA analysis was performed using next-generation sequencing with two sets of universal primers. A total of twelve mycetoma-causative fungal species were identified, including the prime agent, Madurella mycetomatis, and additional pathogens, Falciformispora senegalensis and Falciformispora tompkinsii, in 53 soil samples. This study demonstrated that soil DNA metabarcoding can elucidate the presence of multiple mycetoma-causative fungi, which may contribute to accurate diagnosis for patient treatment and geographical mapping.

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“…For instance, direct filtration, ethanol precipitation, and centrifugation are three major first-step filtration methods used for concentrating eDNA from aquatic environments ( Tsuji et al, 2019 ). DNA collection and extraction are crucial for capturing eDNA from water, and their success is dependent on the selected filtration and extraction methods, as well as filtration water volumes ( Sakata et al, 2021 ). Notably, different extraction techniques can result in differences in DNA quantity and quality, which can subsequently impact biodiversity assessment ( Coutant et al, 2021 ; Deiner et al, 2015 ; Jeunen et al, 2019 ; Piggott, 2016 ; Wittwer et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Effects of sampling strategies and DNA extraction methods on eDNA metabarcoding: A case study of estuarine fish diversity monitoring

Ruan¹,

Wang²,

Li³

et al. 2022

Zoological Research

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Environmental DNA (eDNA) integrated with metabarcoding is a promising and powerful tool for species composition and biodiversity assessment in aquatic ecosystems and is increasingly applied to evaluate fish diversity. To date, however, no standardized eDNA-based protocol has been established to monitor fish diversity. In this study, we investigated and compared two filtration methods and three DNA extraction methods using three filtration water volumes to determine a suitable approach for eDNA-based fish diversity monitoring in the Pearl River Estuary (PRE), a highly anthropogenically disturbed estuarine ecosystem. Compared to filtration-based precipitation, direct filtration was a more suitable method for eDNA metabarcoding in the PRE. The combined use of DNeasy Blood and Tissue Kit (BT) and traditional phenol/chloroform (PC) extraction produced higher DNA yields, amplicon sequence variants (ASVs), and Shannon diversity indices, and generated more homogeneous and consistent community composition among replicates. Compared to the other combined protocols, the PC and BT methods obtained better species detection, higher fish diversity, and greater consistency for the filtration water volumes of 1 000 and 2 000 mL, respectively. All eDNA metabarcoding protocols were more sensitive than bottom trawling in the PRE fish surveys and combining two techniques yielded greater taxonomic diversity. Furthermore, combining traditional methods with eDNA analysis enhanced accuracy. These results indicate that methodological decisions related to eDNA metabarcoding should be made with caution for fish community monitoring in estuarine ecosystems.

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Determining an effective sampling method for eDNA metabarcoding: a case study for fish biodiversity monitoring in a small, natural river

Cited by 46 publications

References 47 publications

eDNA metabarcoding in lakes to quantify influences of landscape features and human activity on aquatic invasive species prevalence and fish community diversity

eDNA metabarcoding in lakes to quantify influences of landscape features and human activity on aquatic invasive species prevalence and fish community diversity

Detection of multiple mycetoma pathogens using fungal metabarcoding analysis of soil DNA in an endemic area of Sudan

Effects of sampling strategies and DNA extraction methods on eDNA metabarcoding: A case study of estuarine fish diversity monitoring

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