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Depth-Specific Distribution of the SAR116 Phages Revealed by Virome Binning
Depth-Specific Distribution of the SAR116 Phages Revealed by Virome Binning
Journal of Microbiology and Biotechnology. 2014. May, 24(5): 592-596
Copyright © 2014, The Korean Society For Microbiology And Biotechnology
  • Received : December 24, 2013
  • Accepted : February 11, 2014
  • Published : May 28, 2014
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About the Authors
Ilnam Kang
Jang-Cheon Cho
chojc@inha.ac.kr

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.
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Acknowledgements
This work was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF-2013R1A1A2063660: to I.K.) and also by the Mid-Career Research Program through NRF funded by the Ministry of Science, ICT and Future Planning (NRF-2013R1A2A2A01068004).
References
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    DOI : 10.1016/S0967-0645(03)00134-6
Danovaro R , Corinaldesi C , Dell’Anno A , Fuhrman JA , Middelburg JJ , Noble RT 2011 Marine viruses and global climate change. FEMS Microbiol. Rev. 35 993 - 1034    DOI : 10.1111/j.1574-6976.2010.00258.x
Gifford SM , Sharma S , Booth M , Moran MA 2013 Expression patterns reveal niche diversification in a marine microbial assemblage. ISME J. 7 281 - 298    DOI : 10.1038/ismej.2012.96
Giovannoni SJ , Vergin KL 2012 Seasonality in ocean microbial communities. Science 335 671 - 676    DOI : 10.1126/science.1198078
Grote J , Bayindirli C , Bergauer K , Moraes PC , Chen H , D’Ambrosio L 2011 Complete genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria. Stand. Genomic Sci. 5 269 - 278    DOI : 10.4056/sigs.1854551
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 -    DOI : 10.1371/journal.pone.0057355
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 12343 - 12348    DOI : 10.1073/pnas.1219930110
Karl DM 1999 A sea of change: biogeochemical variability in the North Pacific Subtropical Gyre. Ecosystems 2 181 - 214    DOI : 10.1007/s100219900068
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    DOI : 10.1128/AEM.06952-11
Morris RM , Rappe MS , Connon SA , Vergin KL , Siebold WA , Carlson CA 2002 SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420 806 - 810    DOI : 10.1038/nature01240
Oh H-M , Kwon KK , Kang I , Kang SG , Lee J-H , Kim S-J 2010 Complete genome sequence of “Candidatus Puniceispirillum marinum” IMCC1322, a representative of the SAR116 clade in the Alphaproteobacteria. J. Bacteriol. 192 3240 - 3241    DOI : 10.1128/JB.00347-10
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 -    DOI : 10.3389/fmicb.2011.00059
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    DOI : 10.1111/j.1462-2920.2008.01657.x
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    DOI : 10.4319/lo.1997.42.5.0811
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    DOI : 10.1016/S0168-6496(00)00064-7
Sun S , Chen J , Li W , Altintas I , Lin A , Peltier S 2011 Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res. 39 D546 - D551    DOI : 10.1093/nar/gkq1102
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    DOI : 10.1007/s00248-004-0213-5
Treusch AH , Vergin KL , Finlay LA , Donatz MG , Burton RM , Carlson CA 2009 Seasonality and vertical structure of microbial communities in an ocean gyre. ISME J. 3 1148 - 1163    DOI : 10.1038/ismej.2009.60
Zhao Y , Temperton B , Thrash JC , Schwalbach MS , Vergin KL , Landry ZC 2013 Abundant SAR11 viruses in the ocean. Nature 494 357 - 360    DOI : 10.1038/nature11921