Abstract
Marine sediments harbor a vast amount of Earth’s microbial biomass, yet little is understood regarding how cells subsist in this low-energy, presumably slow-growth environment. Cells in marine sediments may require additional methods for genetic regulation, such as epigenetic modification via DNA methylation. We investigated this potential phenomenon within a shallow estuary sediment core spanning 100 years of age. Here, we provide evidence of dynamic community m5-cytosine methylation within estuarine sediment metagenomes. The methylation states of individual CpG sites were reconstructed and quantified across three depths within the sediment core. A total of 6,254 CpG sites were aligned for direct comparison of methylation states between samples, and 4,235 of these sites mapped to taxa and genes. Our results demonstrate the presence of differential methylation within environmental CpG sites across an age gradient of sediment. We show that epigenetic modification can be detected via Illumina sequencing within complex environmental communities. The change in methylation state of environmentally relevant genes across depths may indicate a dynamic role of DNA methylation in regulation of biogeochemical processes.
Highlights
Marine sediments are some of the largest reservoirs of microbial biomass on Earth (Whitman et al, 1998; Kallmeyer et al, 2012), and describing the relationships between community structure, activity, and ecosystem function in these habitats remains a challenge (Biddle et al, 2008; Fuhrman, 2009; Orsi et al, 2013; Zinke et al, 2017)
Operational taxonomic unit (OTU) were clearly shared between the three depths, and the diversity of 16S rRNA genes was generally higher at 3–6 cm than the 12–15 and 24–27 cm samples (Supplementary Figure S4)
Shifts in community composition observed through both 16S rRNA gene and metagenomic Genomic DNA (gDNA) sequencing appear to be related to the drastic change in sediment age suggested by radionuclide constraints (Supplementary Figures S3–S6)
Summary
Marine sediments are some of the largest reservoirs of microbial biomass on Earth (Whitman et al, 1998; Kallmeyer et al, 2012), and describing the relationships between community structure, activity, and ecosystem function in these habitats remains a challenge (Biddle et al, 2008; Fuhrman, 2009; Orsi et al, 2013; Zinke et al, 2017). Isolates obtained from the deep biosphere are genetically similar to members of surface communities (Inagaki et al, 2015; Russell et al, 2016), suggesting that microbial cells able to adapt to the subsurface possibly suspend certain life processes to subsist at low levels of activity without global genetic changes. Epigenetic mechanisms may offer potential microbial survival strategies within low-energy sediment, allowing for cell maintenance and acclimation to environmental stressors (Bird, 2002; Casadesús and Low, 2006; Low and Casadesús, 2008)
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