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Labonté JM, Pachiadaki M, Fergusson E, et al. Single Cell Genomics-Based Analysis of Gene Content and Expression of Prophages in a Diffuse-Flow Deep-Sea Hydrothermal System. Front Microbiol. 2019;10:1262doi: 10.3389/fmicb.2019.01262.
Labonté, J. M., Pachiadaki, M., Fergusson, E., McNichol, J., Grosche, A., Gulmann, L. K., Vetriani, C., Sievert, S. M., & Stepanauskas, R. (2019). Single Cell Genomics-Based Analysis of Gene Content and Expression of Prophages in a Diffuse-Flow Deep-Sea Hydrothermal System. Frontiers in microbiology, 101262. https://doi.org/10.3389/fmicb.2019.01262
Labonté, Jessica M, et al. "Single Cell Genomics-Based Analysis of Gene Content and Expression of Prophages in a Diffuse-Flow Deep-Sea Hydrothermal System." Frontiers in microbiology vol. 10 (2019): 1262. doi: https://doi.org/10.3389/fmicb.2019.01262
Labonté JM, Pachiadaki M, Fergusson E, McNichol J, Grosche A, Gulmann LK, Vetriani C, Sievert SM, Stepanauskas R. Single Cell Genomics-Based Analysis of Gene Content and Expression of Prophages in a Diffuse-Flow Deep-Sea Hydrothermal System. Front Microbiol. 2019 Jun 12;10:1262. doi: 10.3389/fmicb.2019.01262. eCollection 2019. PMID: 31244796; PMCID: PMC6581674.
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Front Microbiol. 2019 Jun 12;10:1262. doi: 10.3389/fmicb.2019.01262. eCollection 2019.

Single Cell Genomics-Based Analysis of Gene Content and Expression of Prophages in a Diffuse-Flow Deep-Sea Hydrothermal System.

Frontiers in microbiology

Jessica M Labonté, Maria Pachiadaki, Elizabeth Fergusson, Jesse McNichol, Ashley Grosche, Lara K Gulmann, Costantino Vetriani, Stefan M Sievert, Ramunas Stepanauskas

Affiliations

  1. Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States.
  2. Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, United States.
  3. Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States.
  4. Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States.
  5. Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States.

PMID: 31244796 PMCID: PMC6581674 DOI: 10.3389/fmicb.2019.01262

Abstract

Phage-host interactions likely play a major role in the composition and functioning of many microbiomes, yet remain poorly understood. Here, we employed single cell genomics to investigate phage-host interactions in a diffuse-flow, low-temperature hydrothermal vent that may be reflective of a broadly distributed biosphere in the subseafloor. We identified putative prophages in 13 of 126 sequenced single amplified genomes (SAGs), with no evidence for lytic infections, which is in stark contrast to findings in the surface ocean. Most were distantly related to known prophages, while their hosts included bacterial phyla Campylobacterota, Bacteroidetes, Chlorobi, Proteobacteria, Lentisphaerae, Spirochaetes, and Thermotogae. Our results suggest the predominance of lysogeny over lytic interaction in diffuse-flow, deep-sea hydrothermal vents, despite the high activity of the dominant Campylobacteria that would favor lytic infections. We show that some of the identified lysogens have co-evolved with their host over geological time scales and that their genes are transcribed in the environment. Functional annotations of lysogeny-related genes suggest involvement in horizontal gene transfer enabling host's protection against toxic metals and antibacterial compounds.

Keywords: hydrothermal vent; lysogeny; phage life cycle; prophages; single cell genomics

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