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References

  1. Collins CA, Pennington JT, Castro CG, Rago TA, Chavez FP. 2003. The California Current system off Monterey, California: physical and biological coupling. Deep Sea Res. Part II Top. Stud. Oceanogr. 50: 2389-2404.
    CrossRef
  2. Danovaro R, Corinaldesi C, Dell’Anno A, Fuhrman JA, Middelburg JJ, Noble RT, et al. 2011. Marine viruses and global climate change. FEMS Microbiol. Rev. 35: 993-1034.
    CrossRef
  3. Gifford SM, Sharma S, Booth M, Moran MA. 2013. Expression patterns reveal niche diversification in a marine microbial assemblage. ISME J. 7: 281-298.
    CrossRef
  4. Giovannoni SJ, Vergin KL. 2012. Seasonality in ocean microbial communities. Science 335: 671-676.
    CrossRef
  5. Grote J, Bayindirli C, Bergauer K, Moraes PC, Chen H, D’Ambrosio L, et al. 2011. Complete genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria. Stand. Genomic Sci. 5:269-278.
    CrossRef
  6. Hurwitz BL, Sullivan MB. 2013. The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One 8:e57355.
    CrossRef
  7. Kang I, Oh H-M, Kang D, Cho J-C. 2013. Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans. Proc. Natl. Acad. Sci. USA 110: 1234312348.
    CrossRef
  8. Karl DM. 1999. A sea of change: biogeochemical variability in the North Pacific Subtropical Gyre. Ecosystems 2: 181-214.
    CrossRef
  9. Lin Y-C, Campbell T, Chung C-C, Gong G-C, Chiang K-P, Worden AZ. 2012. Distribution patterns and phylogeny of marine stramenopiles in the North Pacific Ocean. Appl. Environ. Microbiol. 78: 3387-3399.
    CrossRef
  10. Morris RM, Rappe MS, Connon SA, Vergin KL, Siebold WA, Carlson CA, et al. 2002. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420: 806-810.
    CrossRef
  11. Oh H-M, Kwon KK, Kang I, Kang SG, Lee J-H, Kim S-J, et al. 2010. Complete genome sequence of “Candidatus Puniceispirillum marinum” IMCC1322, a representative of the SAR116 clade in the Alphaproteobacteria. J. Bacteriol. 192: 3240-3241.
    CrossRef
  12. Paerl RW, Johnson KS, Welsh RM, Worden AZ, Chavez FP, Zehr JP. 2011. Differential distributions of Synechococcus subgroups across the California Current system. Front. Microbiol. 2: 59.
    CrossRef
  13. Pham VD, Konstantinidis KT, Palden T, DeLong EF. 2008. Phylogenetic analyses of ribosomal DNA-containing bacterioplankton genome fragments from a 4000 m vertical profile in the North Pacific Subtropical Gyre. Environ. Microbiol. 10: 2313-2330.
    CrossRef
  14. Rappé MS, Kemp PF, Giovannoni SJ. 1997. Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina. Limnol. Oceanogr. 42: 811-826.
    CrossRef
  15. Rappé MS, Vergin K, Giovannoni SJ. 2000. Phylogenetic comparisons of a coastal bacterioplankton community with its counterparts in open ocean and freshwater systems. FEMS Microbiol. Ecol. 33: 219-232.
    CrossRef
  16. Sun S, Chen J, Li W, Altintas I, Lin A, Peltier S, et al. 2011. Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res. 39: D546-D551.
    CrossRef
  17. Suzuki MT, Preston CM, Béjà O, de la Torre JR, Steward GF, DeLong EF. 2004. Phylogenetic screening of ribosomal RNA gene-containing clones in bacterial artificial chromosome (BAC) libraries from different depths in Monterey Bay. Microb. Ecol. 48: 473-488.
    CrossRef
  18. Treusch AH, Vergin KL, Finlay LA, Donatz MG, Burton RM, Carlson CA, et al. 2009. Seasonality and vertical structure of microbial communities in an ocean gyre. ISME J. 3: 1148-1163.
    CrossRef
  19. Zhao Y, Temperton B, Thrash JC, Schwalbach MS, Vergin KL, Landry ZC, et al. 2013. Abundant SAR11 viruses in the ocean. Nature 494: 357-360.
    CrossRef

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Note

J. Microbiol. Biotechnol. 2014; 24(5): 592-596

Published online May 28, 2014 https://doi.org/10.4014/jmb.1312.12062

Copyright © The Korean Society for Microbiology and Biotechnology.

Depth-Specific Distribution of the SAR116 Phages Revealed by Virome Binning

Ilnam Kang 1 and Jang-Cheon Cho 1*

Department of Biological Sciences, Inha University, Incheon 402-751, Republic of Korea

Received: December 24, 2013; Accepted: February 10, 2014

Abstract

HMO-2011, a recently isolated lytic phage that infects the SAR116 bacterial clade, represents
one of the most abundant phage types in the oceans. In this study, the HMO-2011 genome
sequence was compared with virome sequences obtained from various depths of the Pacific
Ocean regions using metagenome binning. HMO-2011 was confirmed to be one of the most
highly assigned viruses, with a maximum of 7.6% of total reads assigned. The HMO-2011-type
phages demonstrated a depth-specific distribution, showing more abundance in the euphotic
zone of coastal, transition, and open ocean regions as compared with the dark ocean.

Keywords: SAR116, “Candidatus Puniceispirillum marinum” IMCC1322, Marine Virus, HMO-2011, Viral Metagenome, Metagenome Binning

References

  1. Collins CA, Pennington JT, Castro CG, Rago TA, Chavez FP. 2003. The California Current system off Monterey, California: physical and biological coupling. Deep Sea Res. Part II Top. Stud. Oceanogr. 50: 2389-2404.
    CrossRef
  2. Danovaro R, Corinaldesi C, Dell’Anno A, Fuhrman JA, Middelburg JJ, Noble RT, et al. 2011. Marine viruses and global climate change. FEMS Microbiol. Rev. 35: 993-1034.
    CrossRef
  3. Gifford SM, Sharma S, Booth M, Moran MA. 2013. Expression patterns reveal niche diversification in a marine microbial assemblage. ISME J. 7: 281-298.
    CrossRef
  4. Giovannoni SJ, Vergin KL. 2012. Seasonality in ocean microbial communities. Science 335: 671-676.
    CrossRef
  5. Grote J, Bayindirli C, Bergauer K, Moraes PC, Chen H, D’Ambrosio L, et al. 2011. Complete genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria. Stand. Genomic Sci. 5:269-278.
    CrossRef
  6. Hurwitz BL, Sullivan MB. 2013. The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One 8:e57355.
    CrossRef
  7. Kang I, Oh H-M, Kang D, Cho J-C. 2013. Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans. Proc. Natl. Acad. Sci. USA 110: 1234312348.
    CrossRef
  8. Karl DM. 1999. A sea of change: biogeochemical variability in the North Pacific Subtropical Gyre. Ecosystems 2: 181-214.
    CrossRef
  9. Lin Y-C, Campbell T, Chung C-C, Gong G-C, Chiang K-P, Worden AZ. 2012. Distribution patterns and phylogeny of marine stramenopiles in the North Pacific Ocean. Appl. Environ. Microbiol. 78: 3387-3399.
    CrossRef
  10. Morris RM, Rappe MS, Connon SA, Vergin KL, Siebold WA, Carlson CA, et al. 2002. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420: 806-810.
    CrossRef
  11. Oh H-M, Kwon KK, Kang I, Kang SG, Lee J-H, Kim S-J, et al. 2010. Complete genome sequence of “Candidatus Puniceispirillum marinum” IMCC1322, a representative of the SAR116 clade in the Alphaproteobacteria. J. Bacteriol. 192: 3240-3241.
    CrossRef
  12. Paerl RW, Johnson KS, Welsh RM, Worden AZ, Chavez FP, Zehr JP. 2011. Differential distributions of Synechococcus subgroups across the California Current system. Front. Microbiol. 2: 59.
    CrossRef
  13. Pham VD, Konstantinidis KT, Palden T, DeLong EF. 2008. Phylogenetic analyses of ribosomal DNA-containing bacterioplankton genome fragments from a 4000 m vertical profile in the North Pacific Subtropical Gyre. Environ. Microbiol. 10: 2313-2330.
    CrossRef
  14. Rappé MS, Kemp PF, Giovannoni SJ. 1997. Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina. Limnol. Oceanogr. 42: 811-826.
    CrossRef
  15. Rappé MS, Vergin K, Giovannoni SJ. 2000. Phylogenetic comparisons of a coastal bacterioplankton community with its counterparts in open ocean and freshwater systems. FEMS Microbiol. Ecol. 33: 219-232.
    CrossRef
  16. Sun S, Chen J, Li W, Altintas I, Lin A, Peltier S, et al. 2011. Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res. 39: D546-D551.
    CrossRef
  17. Suzuki MT, Preston CM, Béjà O, de la Torre JR, Steward GF, DeLong EF. 2004. Phylogenetic screening of ribosomal RNA gene-containing clones in bacterial artificial chromosome (BAC) libraries from different depths in Monterey Bay. Microb. Ecol. 48: 473-488.
    CrossRef
  18. Treusch AH, Vergin KL, Finlay LA, Donatz MG, Burton RM, Carlson CA, et al. 2009. Seasonality and vertical structure of microbial communities in an ocean gyre. ISME J. 3: 1148-1163.
    CrossRef
  19. Zhao Y, Temperton B, Thrash JC, Schwalbach MS, Vergin KL, Landry ZC, et al. 2013. Abundant SAR11 viruses in the ocean. Nature 494: 357-360.
    CrossRef