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

Richard Norris,Fabio Rocha,Elizabeth C Sibert,Raphael Eisenhofer,Ryan Ward,Leila Tirichine,Chris Bowler,Linda Armbrecht,Juan José Pierella Karlusich,Mindi Summers,José Utge

doi:10.1038/s43705-021-00070-8

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.

Highlights

Sedimentary ancient DNA analyses have become increasingly applied to the sub-seafloor for the reconstruction of marine ecosystems
Studying marine eukaryotes by means of Sedimentary ancient DNA (sedaDNA) has remained complicated as only minuscule amounts of their DNA are preserved in the subseafloor (~1.5% of total DNA is of eukaryote origin when using the small subunit ribosomal RNA (SSU) taxonomic marker gene as a ref. [10])
Our comparison of paleo-eukaryote, especially diatom, composition via metabarcoding and shotgun metagenomics showed considerable differences in taxonomic profiles, which were related to differences in sequence length distributions, and influenced by the choice of reference database

Summary

Introduction

Sedimentary ancient DNA (sedaDNA) analyses have become increasingly applied to the sub-seafloor for the reconstruction of marine ecosystems. Using sedaDNA, taxa across all three domains of life (archaea, bacteria, eukaryota) have been detected, including non-fossilising species (e.g., [1, 2]). The latter shows the enormous potential of sedaDNA techniques to go beyond standard environmental proxies and facilitate the reconstruction of paleo-ecosystems across the entire marine food web, rather than the small proportion of marine biodiversity detectable from fossils alone. Diatom microfossils have been characterised extensively in sediment cores to predict past ecosystems (e.g., [8, 9]). Studying marine eukaryotes by means of sedaDNA has remained complicated as only minuscule amounts of their DNA are preserved in the subseafloor (~1.5% of total DNA is of eukaryote origin when using the small subunit ribosomal RNA (SSU) taxonomic marker gene as a ref. [10])

Results

Discussion

Conclusion