﻿Shifts in DNA yield and biological community composition in stored sediment: implications for paleogenomic studies

Katie A. Brasell,Jamie Howarth,John K. Pearman,Xavier Pochon,Lucy Thompson,Susanna A. Wood,Kevin S. Simon,Anastasija Zaiko,Marcus J. Vandergoes

doi:10.3897/mbmg.6.78128

Abstract

Lake sediments hold a wealth of information from past environments that is highly valuable for paleolimnological reconstructions. These studies increasingly apply modern molecular tools targeting sedimentary DNA (sedDNA). However, sediment core sampling can be logistically difficult, making immediate subsampling for sedDNA challenging. Sediment cores are often refrigerated (4 °C) for weeks or months before subsampling. We investigated the impact of storage time on changes in DNA (purified or as cell lysate) concentrations and shifts in biological communities following storage of lake surface sediment at 4 °C for up to 24 weeks. Sediment samples (~ 0.22 g, in triplicate per time point) were spiked with purified DNA (100 or 200 ng) or lysate from a brackish water cyanobacterium that produces the cyanotoxin nodularin or non-spiked. Samples were analysed every 1–4 weeks over a 24-week period. Droplet digital PCR showed no significant decrease in the target gene (nodularin synthetase – subunit F; ndaF) over the 24-week period for samples spiked with purified DNA, while copy number decreased by more than half in cell lysate-spiked samples. There was significant change over time in bacteria and eukaryotic community composition assessed using metabarcoding. Amongst bacteria, the cyanobacterial signal became negligible after 5 weeks while Proteobacteria increased. In the eukaryotic community, Cercozoa became dominant after 6 weeks. These data demonstrate that DNA yields and community composition data shift significantly when sediments are stored chilled for more than 5 weeks. This highlights the need for rapid subsampling and appropriate storage of sediment core samples for paleogenomic studies.

Highlights

Molecular techniques, in particular metabarcoding, are increasingly being used to monitor biological communities and assess ecological conditions in aquatic environments (Pawlowski et al 2014; Rawlence et al 2014; Domaizon et al 2017; Pochon et al 2017; Baho et al 2019; Ellegaard et al 2020; Tsukamoto et al 2021)
Our aim was to determine the effects of chilled storage on DNA yield and compositional shifts of bacterial and eukaryotic communities in lake sediment samples
A total of 17,548 Amplicon Sequence Variants (ASVs) were reduced to 13,096 ASVs after quality control, taxonomic filtering and rarefaction

Summary

Introduction

In particular metabarcoding, are increasingly being used to monitor biological communities and assess ecological conditions in aquatic environments (Pawlowski et al 2014; Rawlence et al 2014; Domaizon et al 2017; Pochon et al 2017; Baho et al 2019; Ellegaard et al 2020; Tsukamoto et al 2021). Molecular analysis of sedimentary DNA (sedDNA; intraand extra-cellular DNA from bulk sediment samples) is being used in paleogenomics to supplement traditional proxies through the provision of high-resolution community composition data (Capo et al 2017a; Ficetola et al 2018). Capo et al (2019) detected changes in lake microbial communities that corresponded with seasonal shifts in landscape and climate at an inter-annual scale over a 40-year period using a combination of molecular techniques targeting sedDNA, sediment. Molecular techniques have been used to reconstruct historic phytoplankton communities, allowing the extension of lake water quality records beyond limited historical monitoring periods (Ibrahim et al 2021)

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