Life-Style and Genome Structure of Marine Pseudoalteromonas Siphovirus B8b Isolated from the Northwestern Mediterranean Sea

Lara, Elena; Holmfeldt, Karin; Solonenko, Natalie; Sà, Elisabet Laia; Ignacio-Espinoza, J. Cesar; Cornejo-Castillo, Francisco M.; Verberkmoes, Nathan C.; Vaqué, Dolors; Sullivan, Matthew B.; Acinas, Silvia G.; Kellogg, Christina A.

doi:10.1371/journal.pone.0114829

Title: Life-Style and Genome Structure of Marine Pseudoalteromonas Siphovirus B8b Isolated from the Northwestern Mediterranean Sea

Abstract

Marine viruses (phages) alter bacterial diversity and evolution with impacts on marine biogeochemical cycles, and yet few well-developed model systems limit opportunities for hypothesis testing. We isolate phage B8b from the Mediterranean Sea using Pseudoalteromonas sp. QC-44 as a host and characterize it using myriad techniques. Morphologically, phage B8b was classified as a member of the Siphoviridae family. One-step growth analyses showed that this siphovirus had a latent period of 70 min and released 172 new viral particles per cell. In the host range analysis against 89 bacterial host strains revealed that phage B8b infected 3 Pseudoalteromonas strains (52 tested, >99.9% 16S rRNA gene nucleotide identity) and 1 non-Pseudoaltermonas strain belonging to Alteromonas sp. (37 strains from 6 genera tested), which helps bound the phylogenetic distance possible in a phage-mediated horizontal gene transfer event. The Pseudoalteromonas phage B8b genome size was 42.7 kb, with clear structural and replication modules where the former were delineated leveraging identification of 16 structural genes by virion structural proteomics, only 4 of which had any similarity to known structural proteins. In nature, this phage was common in coastal marine environments in both photic and aphotic layers (found in 26.5% of available viral metagenomes), but notmore »« less

Authors:

Lara, Elena ^[1]; Holmfeldt, Karin ^[2]; Solonenko, Natalie ^[2]; Sà, Elisabet Laia ^[1]; Ignacio-Espinoza, J. Cesar ^[2]; Cornejo-Castillo, Francisco M. ^[1]; Verberkmoes, Nathan C. ^[3]; Vaqué, Dolors ^[1]; Sullivan, Matthew B. ^[2]; Acinas, Silvia G. ^[1]; Kellogg, Christina A. ^[4]

Inst. of Ocean Sciences (CSIC), Barcelona (Spain)
Univ. of Arizona, Tucson, AZ (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
United States Geological Survey, Reston, VA (United States)

Publication Date:: Wed Jan 14 00:00:00 EST 2015

Research Org.:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Org.:: USDOE; Work for Others (WFO)

OSTI Identifier:: 1286995

Grant/Contract Number:: AC05-00OR22725

Resource Type:: Accepted Manuscript

Journal Name:: PLoS ONE

Additional Journal Information:: Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 1932-6203

Publisher:: Public Library of Science

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Lara, Elena, Holmfeldt, Karin, Solonenko, Natalie, Sà, Elisabet Laia, Ignacio-Espinoza, J. Cesar, Cornejo-Castillo, Francisco M., Verberkmoes, Nathan C., Vaqué, Dolors, Sullivan, Matthew B., Acinas, Silvia G., and Kellogg, Christina A. Life-Style and Genome Structure of Marine Pseudoalteromonas Siphovirus B8b Isolated from the Northwestern Mediterranean Sea.  United States: N. p., 2015. 
Web.  doi:10.1371/journal.pone.0114829.

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                    Lara, Elena, Holmfeldt, Karin, Solonenko, Natalie, Sà, Elisabet Laia, Ignacio-Espinoza, J. Cesar, Cornejo-Castillo, Francisco M., Verberkmoes, Nathan C., Vaqué, Dolors, Sullivan, Matthew B., Acinas, Silvia G., & Kellogg, Christina A. Life-Style and Genome Structure of Marine Pseudoalteromonas Siphovirus B8b Isolated from the Northwestern Mediterranean Sea.  United States.  https://doi.org/10.1371/journal.pone.0114829

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                    Lara, Elena, Holmfeldt, Karin, Solonenko, Natalie, Sà, Elisabet Laia, Ignacio-Espinoza, J. Cesar, Cornejo-Castillo, Francisco M., Verberkmoes, Nathan C., Vaqué, Dolors, Sullivan, Matthew B., Acinas, Silvia G., and Kellogg, Christina A. Wed .  
"Life-Style and Genome Structure of Marine Pseudoalteromonas Siphovirus B8b Isolated from the Northwestern Mediterranean Sea".  United States.  https://doi.org/10.1371/journal.pone.0114829.  https://www.osti.gov/servlets/purl/1286995.

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@article{osti_1286995,

  title        = {Life-Style and Genome Structure of Marine Pseudoalteromonas Siphovirus B8b Isolated from the Northwestern Mediterranean Sea},

  author       = {Lara, Elena and Holmfeldt, Karin and Solonenko, Natalie and Sà, Elisabet Laia and Ignacio-Espinoza, J. Cesar and Cornejo-Castillo, Francisco M. and Verberkmoes, Nathan C. and Vaqué, Dolors and Sullivan, Matthew B. and Acinas, Silvia G. and Kellogg, Christina A.},

  abstractNote = {Marine viruses (phages) alter bacterial diversity and evolution with impacts on marine biogeochemical cycles, and yet few well-developed model systems limit opportunities for hypothesis testing. We isolate phage B8b from the Mediterranean Sea using Pseudoalteromonas sp. QC-44 as a host and characterize it using myriad techniques. Morphologically, phage B8b was classified as a member of the Siphoviridae family. One-step growth analyses showed that this siphovirus had a latent period of 70 min and released 172 new viral particles per cell. In the host range analysis against 89 bacterial host strains revealed that phage B8b infected 3 Pseudoalteromonas strains (52 tested, >99.9% 16S rRNA gene nucleotide identity) and 1 non-Pseudoaltermonas strain belonging to Alteromonas sp. (37 strains from 6 genera tested), which helps bound the phylogenetic distance possible in a phage-mediated horizontal gene transfer event. The Pseudoalteromonas phage B8b genome size was 42.7 kb, with clear structural and replication modules where the former were delineated leveraging identification of 16 structural genes by virion structural proteomics, only 4 of which had any similarity to known structural proteins. In nature, this phage was common in coastal marine environments in both photic and aphotic layers (found in 26.5% of available viral metagenomes), but not abundant in any sample (average per sample abundance was 0.65% of the reads). Together these data improve our understanding of siphoviruses in nature, and provide foundational information for a new 'rare virosphere' phage-host model system.},

  doi          = {10.1371/journal.pone.0114829},

  journal      = {PLoS ONE},

  number       = 1,

  volume       = 10,

  place        = {United States},

  year         = {Wed Jan 14 00:00:00 EST 2015},

  month        = {Wed Jan 14 00:00:00 EST 2015}

}

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