ArticleISME communications2021
Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics.
Article in ISME communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Article
- A Roadmap for Using Hybridisation Capture-Based Target Enrichment of Ancient Environmental DNA in Palaeoecology.Molecular ecology resources · 2026Review
- A Comparative Analysis of DNA Metabarcoding and Morphological Identification in Diatoms Reveals Similar Patterns of Environmental Response.Ecology and evolution · 2026Article
- Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA.Molecular ecology resources · 2025Article
- Metagenomics reveals contrasted responses of microbial communities to wheat straw amendment in cropland and grassland soils.Scientific reports · 2025Article
- Plankton community changes during the last 124 000 years in the subarctic Bering Sea derived from sedimentary ancient DNA.The ISME journal · 2024Article
- Diverse patterns of correspondence between protist metabarcodes and protist metagenome-assembled genomes.PloS one · 2024Article
- Article
- Marine ecosystem shifts with deglacial sea-ice loss inferred from ancient DNA shotgun sequencing.Nature communications · 2023Article
- Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential.Environmental microbiology · 2022Review
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Authors and funding
11 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Sedimentary ancient DNA (sedaDNA) analyses are increasingly used to reconstruct marine ecosystems. The majority of marine sedaDNA studies use a metabarcoding approach (extraction and analysis of specific DNA fragments of a defined length), targeting short taxonomic marker genes. Promising examples are 18S-V9 rRNA (~121-130 base pairs, bp) and diat-rbcL (76 bp), targeting eukaryotes and diatoms, respectively. However, it remains unknown how 18S-V9 and diat-rbcL derived compositional profiles compare to metagenomic shotgun data, the preferred method for ancient DNA analyses as amplification biases are minimised. We extracted DNA from five Santa Barbara Basin sediment samples (up to ~11 000 years old) and applied both a metabarcoding (18S-V9 rRNA, diat-rbcL) and a metagenomic shotgun approach to (i) compare eukaryote, especially diatom, composition, and (ii) assess sequence length and database related biases. Eukaryote composition differed considerably between shotgun and metabarcoding data, which was related to differences in read lengths (~112 and ~161 bp, respectively), and overamplification of short reads in metabarcoding data. Diatom composition was influenced by reference bias that was exacerbated in metabarcoding data and characterised by increased representation of Chaetoceros, Thalassiosira and Pseudo-nitzschia. Our results are relevant to sedaDNA studies aiming to accurately characterise paleo-ecosystems from either metabarcoding or metagenomic data.
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