Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics

Seong, Hoon Je; Roux, Simon; Hwang, Chung Yeon; Sul, Woo Jun

doi:10.1186/s40168-022-01340-w

Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics

Journal Article · Wed Sep 28 00:00:00 EDT 2022 · Microbiome

DOI:https://doi.org/10.1186/s40168-022-01340-w· OSTI ID:1902679

Seong, Hoon Je ^[1]; Roux, Simon ^[2]; Hwang, Chung Yeon ^[3]; Sul, Woo Jun ^[1]

Chung-Ang Univ. (Korea, Republic of)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Seoul National Univ. (Korea, Republic of)

Background: DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life. Results: We reconstructed 15,056 viral, 252 prokaryotic, 56 giant viral, and 6 eukaryotic metagenome-assembled genomes from northwest Pacific Ocean seawater samples using short- and long-read sequencing approaches. These metagenome-derived genomes mostly represented novel taxa, and recruited a majority of reads. Thanks to single-molecule real-time (SMRT) sequencing technology, base modification could also be detected for these genomes. This showed that DNA methylation can readily be detected across dominant oceanic bacterial, archaeal, and viral populations, and microbial epigenetic changes correlate with population differentiation. Furthermore, our genome-wide epigenetic analysis of Pelagibacter suggests that GANTC, a DNA methyltransferase target motif, is related to the cell cycle and is affected by environmental conditions. Yet, the presence of this motif also partitions the phylogeny of the Pelagibacter phages, possibly hinting at a competitive co-evolutionary history and multiple effects of a single methylation mark. Conclusions: Overall, this study elucidates that DNA methylation patterns are associated with ecological changes and virus-host dynamics in the ocean microbiome.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: National Research Foundation of Korea (NRF); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1902679

Journal Information:: Microbiome, Journal Name: Microbiome Journal Issue: 1 Vol. 10; ISSN 2049-2618

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
DNA methylation
host-phage
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Additional file 1 of Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics Seong, Hoon Je; Roux, Simon; Hwang, Chung Yeon https://doi.org/10.6084/m9.figshare.21220384 The current record is supplemented by this text	text	January 2022
Additional file 1 of Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics Seong, Hoon Je; Roux, Simon; Hwang, Chung Yeon https://doi.org/10.6084/m9.figshare.21220384.v1 The current record is supplemented by this text	text	January 2022
Additional file 2 of Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics Seong, Hoon Je; Roux, Simon; Hwang, Chung Yeon https://doi.org/10.6084/m9.figshare.21220387 The current record is supplemented by this dataset	dataset	January 2022
Additional file 2 of Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics Seong, Hoon Je; Roux, Simon; Hwang, Chung Yeon https://doi.org/10.6084/m9.figshare.21220387.v1 The current record is supplemented by this dataset	dataset	January 2022
Additional file 3 of Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics Seong, Hoon Je; Roux, Simon; Hwang, Chung Yeon https://doi.org/10.6084/m9.figshare.21220393 The current record is supplemented by this dataset	dataset	January 2022
Additional file 3 of Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics Seong, Hoon Je; Roux, Simon; Hwang, Chung Yeon https://doi.org/10.6084/m9.figshare.21220393.v1 The current record is supplemented by this dataset	dataset	January 2022
Additional file 4 of Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics Seong, Hoon Je; Roux, Simon; Hwang, Chung Yeon https://doi.org/10.6084/m9.figshare.21220396 The current record is supplemented by this dataset	dataset	January 2022
Additional file 4 of Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics Seong, Hoon Je; Roux, Simon; Hwang, Chung Yeon https://doi.org/10.6084/m9.figshare.21220396.v1 The current record is supplemented by this dataset	dataset	January 2022
Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics Seong, Hoon Je; Roux, Simon; Hwang, Chung Yeon https://doi.org/10.6084/m9.figshare.c.6220603 The current record is supplemented by this collection	collection	January 2022

Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics

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