Minimal Influence of Extracellular DNA on Molecular Surveys of Marine Sedimentary Communities.

Gustavo A Ramírez,Steffen L Jørgensen,Rui Zhao,Steven D’Hondt

doi:10.3389/fmicb.2018.02969

Gustavo A Ramírez, Steffen L Jørgensen + Show 2 more

Open Access

https://doi.org/10.3389/fmicb.2018.02969

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Abstract

Extracellular DNA has been reported to comprise a large fraction of total DNA in near-seafloor sediment. However, the potential effect of extracellular DNA, arising from dead or moribund cells, on sequencing surveys is a critical concern that has largely not been addressed for marine sedimentary habitats. To address this concern, we interrogated freshly collected Arctic and Pacific sediment for extracellular 16S rRNA genes using the photoactive DNA-binding dye Propidium Monoazide. Significant differences between relative abundances of total (intracellular + extracellular) Bacterial 16S rRNA genes and relative abundances of intracellular Bacterial 16S rRNA genes are only detected in three of twelve shallow [10 cm below seafloor (cmbsf)] samples. Relative abundances of total Bacterial 16S rRNA genes are statistically indistinguishable from relative abundances of intracellular Bacterial 16S rRNA genes in all interrogated samples from depths greater than 10 cmbsf. 16S rRNA gene sequencing shows that even where significantly higher abundances of extracellular genes are detected, they have little or no influence on prokaryote community composition. Taxon-level analyses suggest that extracellular DNA, arising from in situ death, may be sourced from different organisms in sediment of different ages. However, the overall effect of extracellular genes on sequencing surveys of marine sedimentary prokaryotes is minimal.

Highlights

Despite extreme energy limitation (D’Hondt et al, 2002; Jørgensen and Marshall, 2016), marine sediment contains a vast microbial community (Kallmeyer et al, 2012) that remains active over geologically long time-scales (D’Hondt, 2004; Parkes et al, 2005; Schippers et al, 2005)
We address the effect of eDNA on important ecological metrics of subseafloor sedimentary communities, : (i) 16S rRNA gene abundance, a common proxy for cell abundance, and (ii) prokaryotic community structure and composition based on highthroughput sequencing (HTS)
In the Pacific cores, interstitial oxygen was below the detection limit at every depth, nitrate was depleted near the water-sediment interface, ammonium concentrations increased with depth, and total percent organic carbon (TOC) was high, ranging between 2–5% (Figures 1A–C)

Summary

Introduction

Despite extreme energy limitation (D’Hondt et al, 2002; Jørgensen and Marshall, 2016), marine sediment contains a vast microbial community (Kallmeyer et al, 2012) that remains active over geologically long time-scales (D’Hondt, 2004; Parkes et al, 2005; Schippers et al, 2005). Exponential declines in prokaryotic cell counts and community richness occur with sediment depth and sediment age (Kallmeyer et al, 2012; Walsh et al, 2016), indicating that most taxa from surface sediment communities are poorly equipped for long-term subseafloor lifestyles and die within the first few hundred thousand years following sediment deposition. Prokaryotic moribundity and death compromise cellular membranes, exposing cytoplasmic contents to the extracellular environment (Nyström, 2001; Cangelosi and Meschke, 2014).

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