Diatom DNA metabarcoding for ecological assessment: Comparison among bioinformatics pipelines used in six European countries reveals the need for standardization

Bailet, Bonnie; Apothéloz-Perret-Gentil, Laure; Baričević, Ana; Chonova, Teofana; Franc, Alain; Frigério, Jean‐Marc; Kelly, Martyn; Mora, Demetrio; Pfannkuchen, Martin; Proft, Sebastian; Ramon, Mathieu; Vasselon, Valentin; Zimmermann, Jonas; Kahlert, Maria

doi:10.1016/j.scitotenv.2020.140948

Cited by 64 publications

(36 citation statements)

References 52 publications

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“…Moreover, the amplification of larger (577 bp) rbcL fragments could be achieved from more recent sedimentary deposits [142,247], while the amplification of the hypervariable V4 region of the 18S results in the detection of additional taxa next to diatoms [248], which include other Stramenopiles, Alveolata and Rhizaria. A more specific diatom amplification with 18S V4 is enabled when applying the marker to filtered water DNA [249] or modern biofilm samples [250]. In addition, primers targeting a 230-bp region of the viral major capsid protein (mcp) gene have been used to study the diversity of dsDNA algal viruses (Phycodnaviridae) in Holocene sediments [88] Complete zooplankton assemblages have not yet been extensively studied from sedimentary archives.…”

Section: Dna Markers and Reference Databases Used In Current Sedadna mentioning

confidence: 99%

Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

et al. 2021

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The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.

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Section: Dna Markers and Reference Databases Used In Current Sedadna mentioning

confidence: 99%

Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

et al. 2021

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“…In the case of some genera, they are over-represented in terms of species diversity, due to the database that was used for the taxonomic assignment. For instance, genus Eunotia was represented by a greater number of species using HTS, which [54] associated with the pipeline used. Several lightly silicified taxa could not be found by light microscopy because of the oxidant reactives that were used during the permanent slide preparation process [55].…”

Section: Discussionmentioning

confidence: 99%

“…As emphasised by many similar studies (e.g., [54]), one of the key steps for the correct application of DNA barcoding for biomonitoring purposes is the bioinformatic protocol. Standardised protocols are needed to reach an agreement about bioinformatic analysis.…”

Section: Discussionmentioning

confidence: 99%

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Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches

Borrego-Ramos

Bécares

Garcı́a

et al. 2021

Water

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Benthic diatoms have traditionally been used as bioindicators of aquatic ecosystems. Because diatom-based monitoring of water quality is required by European legislation, molecular-based methods had emerged as useful alternatives to classical methods based on morphological identification using light microscopy. The aim of this study was to test the reliability of DNA metabarcoding combined with High-Throughput Sequencing (HTS) techniques in the bioassessment of the trophic status of 22 Mediterranean shallow ponds in NW Spain. For each pond, the Trophic Diatom Index (TDI) was calculated from inventories obtained by identification using light microscopy (LM) followed by high-throughput sequencing (HTS) at the molecular level. Ponds were subsequently classified into five water quality classes. The results showed a good correspondence between both methods, especially after applying a correction factor that depended on the biovolume of the cells. This correspondence led to the assignment to the same quality class in 59% of the ponds. The determination and quantification of valves or DNA sequences was one of the main pitfalls, which mainly included those related to the variability in the relative abundances of some species. Accordingly, ponds with similar relative abundances for the dominant species were assigned to the same quality class. Moreover, other difficulties leading the discrepancies were the misidentification of some species due to the presence of semi-cryptic taxa, the incompleteness of the reference database and the bioinformatic protocol. Thus, the validation of DNA-based methods for the identification of freshwater diatoms represents an important goal, as an alternative to using traditional methods in Mediterranean shallow ponds.

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“…Additionally, the V4 region has been found to have a bigger taxonomic resolution compared to the V9 region [97,98]. The use of different pipelines results in not-reproducible outputs and differences in assigned taxa as it has been shown for diatoms [99], which makes it important to include all potential parameters in the methodology. While tuning on parameters might increase coverage of community composition, we focused on using a strict parameter set and a high confidence cut-off of annotation aiming for a high reliability.…”

Section: Plos Onementioning

confidence: 99%

Host-parasitoid associations in marine planktonic time series: Can metabarcoding help reveal them?

et al. 2021

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In this study, we created a dataset of a continuous three-year 18S metabarcoding survey to identify eukaryotic parasitoids, and potential connections to hosts at the Long-Term Ecological Research station Helgoland Roads. The importance of parasites and parasitoids for food web dynamics has previously been recognized mostly in terrestrial and freshwater systems, while marine planktonic parasitoids have been understudied in comparison to those. Therefore, the occurrence and role of parasites and parasitoids remains mostly unconsidered in the marine environment. We observed high abundances and diversity of parasitoid operational taxonomic units in our dataset all year round. While some parasitoid groups were present throughout the year and merely fluctuated in abundances, we also detected a succession of parasitoid groups with peaks of individual species only during certain seasons. Using co-occurrence and patterns of seasonal occurrence, we were able to identify known host-parasitoid dynamics, however identification of new potential host-parasitoid interactions was not possible due to their high dynamics and variability in the dataset.

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Diatom DNA metabarcoding for ecological assessment: Comparison among bioinformatics pipelines used in six European countries reveals the need for standardization

Cited by 64 publications

References 52 publications

Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches

Host-parasitoid associations in marine planktonic time series: Can metabarcoding help reveal them?

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