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Community-wide epigenetics provides novel perspectives on the ecology and evolution of marine microbiome

View ORCID ProfileHoon Je Seong, View ORCID ProfileSimon Roux, Chung Yeon Hwang, View ORCID ProfileWoo Jun Sul
doi: https://doi.org/10.1101/2021.11.30.470565
Hoon Je Seong
1Department of Systems Biotechnology, Chung-Ang University; Anseong, Republic of Korea
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Simon Roux
2DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Chung Yeon Hwang
3School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University; Seoul, Republic of Korea
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Woo Jun Sul
1Department of Systems Biotechnology, Chung-Ang University; Anseong, Republic of Korea
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  • For correspondence: sulwj@cau.ac.kr
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Abstract

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. We show that overall, 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.

One-Sentence Summary DNA methylation patterns are associated with ecological changes and virus-host dynamics in the marine microbiome.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 01, 2021.
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Community-wide epigenetics provides novel perspectives on the ecology and evolution of marine microbiome
Hoon Je Seong, Simon Roux, Chung Yeon Hwang, Woo Jun Sul
bioRxiv 2021.11.30.470565; doi: https://doi.org/10.1101/2021.11.30.470565
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Community-wide epigenetics provides novel perspectives on the ecology and evolution of marine microbiome
Hoon Je Seong, Simon Roux, Chung Yeon Hwang, Woo Jun Sul
bioRxiv 2021.11.30.470565; doi: https://doi.org/10.1101/2021.11.30.470565

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