Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes

L Armbrecht,C J S Bolch,C Woodward,A Cooper,G Hallegraeff

doi:10.1038/s41598-021-82578-6

Abstract

Marine sedimentary ancient DNA (sedaDNA) is increasingly used to study past ocean ecosystems, however, studies have been severely limited by the very low amounts of DNA preserved in the subseafloor, and the lack of bioinformatic tools to authenticate sedaDNA in metagenomic data. We applied a hybridisation capture ‘baits’ technique to target marine eukaryote sedaDNA (specifically, phyto- and zooplankton, ‘Planktonbaits1’; and harmful algal bloom taxa, ‘HABbaits1’), which resulted in up to 4- and 9-fold increases, respectively, in the relative abundance of eukaryotes compared to shotgun sequencing. We further used the bioinformatic tool ‘HOPS’ to authenticate the sedaDNA component, establishing a new proxy to assess sedaDNA authenticity, “% eukaryote sedaDNA damage”, that is positively correlated with subseafloor depth. We used this proxy to report the first-ever DNA damage profiles from a marine phytoplankton species, the ubiquitous coccolithophore Emiliania huxleyi. Our approach opens new avenues for the detailed investigation of long-term change and evolution of marine eukaryotes over geological timescales.

Highlights

Over the past decade marine sedimentary ancient DNA has become increasingly used to study past ocean ecosystems and oceanographic conditions
The 3 samples were MCS3 0–1.5 cm with Shotgun, GC2B 115–116.5 cm with Planktonbaits[1] and HABbaits[1], and GC2A 85–86.5 cm with HABbaits1—likely due to low template DNA concentrations
Our results show that hybridisation capture improves the yield of target eukaryote sedimentary ancient DNA (sedaDNA), and preserves DNA damage patterns, allowing us to assess sedaDNA authenticity, and generate the first ancient DNA damage profiles of a keystone marine phytoplankton organism, the ubiquitous coccolithophore Emiliania huxleyi

Summary

Introduction

Over the past decade marine sedimentary ancient DNA (sedaDNA) has become increasingly used to study past ocean ecosystems and oceanographic conditions. Phytoplankton are free-floating, unicellular microalgae fulfilling two important functions: (1) they form the base of the marine food web supporting virtually all higher trophic organisms (e.g., 5), and (2) are highly useful environmental indicators due to their sensitivity to changing physical and chemical oceanographic conditions[6] After phytoplankton die, they sink to the seafloor where small proportions of their DNA are able to become entombed and preserved in sediments under favorable conditions, over time forming long-term records of past ocean and climate conditions. Careful bait design (i.e., selection of target sequences) and optimisation of the application protocol (e.g., hybridisation-temperature settings) allow differing levels of specificity in the capture process While such ‘baits’ approaches have previously been used to investigate human, animal and even environmental DNA14–16, their application to marine sediments to capture sedaDNA from key primary producers and environmental indicator organisms (e.g., eukaryotic phytoplankton) remains untested

Methods

Results

Discussion

Conclusion