Identification of a Marine Cyanophage in a Protist Single-cell Metagenome Assembly

Debashish Bhattacharya, Dana C. Price, Cedric Bicep, Eric Bapteste, Mihir Sarwade, Veeran D. Rajah, Hwan Su Yoon

Research output: Contribution to journalArticlepeer-review

12 Scopus citations

Abstract

Analysis of microbial biodiversity is hampered by a lack of reference genomes from most bacteria, viruses, and algae. This necessitates either the cultivation of a restricted number of species for standard sequencing projects or the analysis of highly complex environmental DNA metagenome data. Single-cell genomics (SCG) offers a solution to this problem by constraining the studied DNA sample to an individual cell and its associated symbionts, prey, and pathogens. We used SCG to study marine heterotrophic amoebae related to Paulinella ovalis (A. Wulff) P.W. Johnson, P.E. Hargraves & J.M. Sieburth (Rhizaria). The genus Paulinella is best known for its photosynthetic members such as P. chromatophora Lauterborn that is the only case of plastid primary endosymbiosis known outside of algae and plants. Here, we studied the phagotrophic sister taxa of P. chromatophora that are related to P. ovalis and found one SCG assembly to contain α-cyanobacterial DNA. These cyanobacterial contigs are presumably derived from prey. We also uncovered an associated cyanophage lineage (provisionally named phage PoL_MC2). Phylogenomic analysis of the fragmented genome assembly suggested a minimum genome size of 200 Kbp for phage PoL_MC2 that encodes 179 proteins and is most closely related to Synechococcus phage S-SM2. For this phage, gene network analysis demonstrates a highly modular genome structure typical of other cyanophages. Our work demonstrates that SCG is a powerful approach for discovering algal and protist biodiversity and for elucidating biotic interactions in natural samples.

Original languageEnglish (US)
Pages (from-to)207-212
Number of pages6
JournalJournal of Phycology
Volume49
Issue number1
DOIs
StatePublished - Feb 2013

All Science Journal Classification (ASJC) codes

  • Aquatic Science
  • Plant Science

Keywords

  • Cyanophage
  • Gene network
  • Horizontal gene transfer
  • Paulinella
  • Phylogenomics
  • Single cell genomics

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