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Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics

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Armbrecht, L ORCID: 0000-0002-1213-1257, Eisenhofer, R, Utge, J, Sibert, EC, Rocha, F, Ward, R, Karlusich, JJP, Tirichine, L, Norris, R, Summers, M and Bowler, C 2021 , 'Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics' , ISME Communications, vol. 1 , pp. 1-10 , doi: 10.1038/s43705-021-00070-8.

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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.

Item Type: Article
Authors/Creators:Armbrecht, L and Eisenhofer, R and Utge, J and Sibert, EC and Rocha, F and Ward, R and Karlusich, JJP and Tirichine, L and Norris, R and Summers, M and Bowler, C
Keywords: marine sedimentary ancient DNA, metagenomics, metabarcoding, Santa Barbara Basin, phytoplankton, diatoms
Journal or Publication Title: ISME Communications
Publisher: Nature Publishing Group
ISSN: 2730-6151
DOI / ID Number: 10.1038/s43705-021-00070-8
Copyright Information:

Copyright 2021 the authors. Licensed under Creative Commons Attribution 4.0 International (CC BY 4.0) https://creativecommons.org/licenses/by/4.0/

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