Standardized high-throughput biomonitoring using DNA metabarcoding: Strategies for the adoption of automated liquid handlers

Buchner, Dominik; Macher, Till‐Hendrik; Beermann, Arne J.; Werner, Marie-Thérése; Leese, Florian

doi:10.1016/j.ese.2021.100122

Cited by 24 publications

(23 citation statements)

References 52 publications

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“…A detailed description of the benchmark can be found in Supplementary material S1 . The datasets were produced according to the workflow presented in Buchner et al (2021) . In short, APSCALE showed significantly lower runtimes while recovering similar communities ( Supplementary Figs S1 and S2 ).…”

Section: Benchmarkmentioning

confidence: 99%

APSCALE: advanced pipeline for simple yet comprehensive analyses of DNA metabarcoding data

2022

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Summary DNA metabarcoding is an emerging approach to assess and monitor biodiversity worldwide and consequently the number and size of data sets increases exponentially. To date no published DNA metabarcoding data processing pipeline exists that is i) platform independent, ii) easy to use (incl. GUI), iii) fast (does scale well with dataset size), and iv) complies with data protection regulations of e.g., environmental agencies. The presented pipeline APSCALE meets these requirements and handles the most common tasks of sequence data processing, such as paired-end merging, primer trimming, quality filtering, clustering and denoising of any popular metabarcoding marker, such as ITS (internal transcribed spacer), 16S, or COI (cytochrome c oxidase subunit I). APSCALE comes in a command-line and a GUI version. The latter provides the user with additional summary statistics options and links to GUI-based downstream applications. Availability APSCALE is written in Python, a platform-independent language, and integrates functions of the open-source tools, VSEARCH (Rognes et al. 2016), cutadapt (Martin et al, 2011) and LULU (Frøslev et al. 2017). All modules support multithreading to allow fast processing of larger DNA metabarcoding datasets. Further information, and troubleshooting are provided on the respective GitHub pages for the command line version (https://github.com/DominikBuchner/apscale) and the GUI-based version (https://github.com/TillMacher/apscale_gui), including a detailed tutorial. Supplementary information Supplementary data are available at Bioinformatics online.

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Section: Benchmarkmentioning

confidence: 99%

APSCALE: advanced pipeline for simple yet comprehensive analyses of DNA metabarcoding data

2022

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“…Nonetheless, the advantages of the eDNA method are the low cost, time, and labor needed for field sampling as well as the potential scalability of the library preparation process (Buchner et al 2021;Ushio et al 2022). Therefore, frequent (Ushio 2022) and large spatial-scale ecological monitoring is possible, which will provide a more detailed understanding of the temperature-interaction strength relationships of organisms on a larger spatial scale.…”

Section: Potential Limitations Of the Present Studymentioning

confidence: 99%

Temperature sensitivity of the interspecific interaction strength of coastal marine fish communities

Ushio

Sadõ

Fukuchi

et al. 2022

Preprint

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Interspecific interactions influence the dynamics and stability of a marine ecological community, and thus, are key to understanding marine ecosystem dynamics. The effects of temperature on interaction strengths are important for understanding and forecasting how global climate change impacts marine ecosystems; however, it currently remains unclear how temperature influences interaction strengths in marine communities. We herein performed quantitative fish environmental DNA (eDNA) metabarcoding on 550 seawater samples that were collected twice a month from 11 coastal sites in the Boso Peninsula, Japan, and analyzed eDNA monitoring data (a proxy of fish community dynamics) using nonlinear time-series analytical tools. We detected and quantified fish-fish interactions as information flow between eDNA time series, and reconstructed interaction networks for the top 50 frequently detected species from the 11 sites. Water temperature positively influenced fish-fish interaction strengths in general, supporting the view that warming temperature intensifies interspecific interactions. Furthermore, the impact of water temperature on interspecific interaction strengths varied among fish species, suggesting that fish species identity influences the effects of temperature on interactions. Therefore, an increase in water temperature induced by global climate change may intensify fish interactions, consequently influencing marine community dynamics and stability.

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“…S3), the tissue was lysed with 195 µl of lysis buffer (T1) and 5 µl of Proteinase K (250 ng/µl working concentration), followed by an incubation at 55 o C for 3h. Afterwards, 5µl of RNAse A (10mg/ml, Thermo Scienti c) was added and the samples were incubated for 30min at 37 o C. Then, DNA was extracted in a 96-well plate format using the Biomek FX P , following the protocol as described in [57]. For the full body extracts for libraries 2-4, the specimens were rst homogenised using 1 and 2mm Zirconia bead-beating beads in a solution of 477µl TNES buffer, 20µl…”

Section: Ddrad-seq Librariesmentioning

confidence: 99%

COI is not enough: integrative taxonomy reveals striking overestimation of species diversity in a Mediterranean freshwater amphipod

Hupało

Copilaş‐Ciocianu²,

Leese

et al. 2022

Preprint

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BackgroundThe emergence of DNA taxonomy sparked a paradigm shift in biodiversity assessments and revealed the existence of many morphologically cryptic species in all ecosystems worldwide. For animals, DNA-based assessments of species diversity usually rely on the mitochondrial cytochrome c oxidase subunit I (COI) gene. However, an increasing number of studies report patterns of mito-nuclear discordance originating for example from shared ancestral polymorphisms or introgression, leading to an over- or underestimation of true species diversity. Therefore, reports of mitochondrial lineages should be verified by other methods. Freshwater amphipods are ideal model organisms since putative cryptic species have been reported in many of the nominal taxa. In this study, we investigated the species status of the numerous mitochondrial molecular operational taxonomic units (MOTUs) found within the Mediterranean freshwater amphipod Echinogammarus sicilianus on Sicily. For validation, we used an integrative taxonomic approach combining DNA barcoding with behavioural data, detailed morphometrics and genome-wide double digest restriction site-associated DNA sequencing (ddRAD-seq). Results Within a relatively small sampling area (approx. 200 km2), we detected 12 divergent COI MOTUs, with genetic distances ranging from 1.8% to 20.3% and a mean distance of 11%. At 17 of the 25 sampling sites up to six MOTUs occurred in syntopy. The four most common MOTUs were analysed with high resolution morphometric data (49 measurements per specimen), but we found no clear evidence of morphological differentiation among them. We also observed a high level of MOTU intermixing (38%) in precopulatory pairs. Similarly, ten of the mitochondrial MOTUs were not supported by the genome-wide ddRAD-seq data. However, for the two remaining mitochondrial MOTUs found at sites outside of the main river stretch, ddRAD-seq and COI data were congruent, indicating that those MOTUs might indeed represent cryptic species. Conclusions Our study on the amphipod E. sicilianus reveals another prominent example of mito-nuclear discordance indicating that species delimitation based solely on mitochondrial markers can significantly overestimate species diversity. The study highlights that integrative taxonomy approaches are important for validating species status, especially in hyperdiverse species complexes, where many mitochondrial MOTUs occur in close proximity or even syntopy.

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Standardized high-throughput biomonitoring using DNA metabarcoding: Strategies for the adoption of automated liquid handlers

Cited by 24 publications

References 52 publications

APSCALE: advanced pipeline for simple yet comprehensive analyses of DNA metabarcoding data

APSCALE: advanced pipeline for simple yet comprehensive analyses of DNA metabarcoding data

Temperature sensitivity of the interspecific interaction strength of coastal marine fish communities

COI is not enough: integrative taxonomy reveals striking overestimation of species diversity in a Mediterranean freshwater amphipod

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