Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

• Published in: eLife Vol. 3; p. e03125
• Main Authors: Roux, Simon, Hawley, Alyse K, Torres Beltran, Monica, Scofield, Melanie, Schwientek, Patrick, Stepanauskas, Ramunas, Woyke, Tanja, Hallam, Steven J, Sullivan, Matthew B
• Format: Journal Article
• Language: English
• Published: England eLife Sciences Publications Ltd 29-08-2014; eLife Sciences Publications, Ltd
• Subjects: Assimilation; Bacteria; bacteriophages; BASIC BIOLOGICAL SCIENCES; Bioinformatics; British Columbia; Carbon; Caudovirales - genetics; Caudovirales - metabolism; Caudovirales - physiology; Concurrent infection; DNA, Single-Stranded - genetics; Ecology; Ecosystem; Ecosystems; Energy metabolism; Evolution, Molecular; Gammaproteobacteria - classification; Gammaproteobacteria - genetics; Gammaproteobacteria - virology; Genes; Genome, Bacterial - genetics; Genome, Viral - genetics; Genomes; Genomics; Host-Pathogen Interactions; Life Sciences & Biomedicine - Other Topics; Metabolism; Metagenome - genetics; Microbiology and Infectious Disease; Microviridae - genetics; Microviridae - metabolism; Microviridae - physiology; New genera; Nitrogen; Oxygen; Oxygen - metabolism; oxygen minimum zone; Phylogeny; Seawater - chemistry; Seawater - microbiology; Seawater - virology; single cell genomic; Software; Sulfite; Sulfite reductase; Sulfur; Sulfur - metabolism; SUP05; viral dark matter; virus; Viruses; British Columbia; ecology; viruses; infectious disease; viral dark matter; bacteriophages; microbiology; SUP05; single cell genomics; oxygen minimum zone
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/elife.03125

Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks, specific virus-host interaction dynamics remain cryptic. In this study, we examined 127 single-cell amplified genomes (SAGs) from uncultivated SUP05 bacteria isolated from a model marine oxygen minimum zone (OMZ) to identify 69 viral contigs representing five new genera within dsDNA Caudovirales and ssDNA Microviridae. Infection frequencies suggest that ∼1/3 of SUP05 bacteria is viral-infected, with higher infection frequency where oxygen-deficiency was most severe. Observed Microviridae clonality suggests recovery of bloom-terminating viruses, while systematic co-infection between dsDNA and ssDNA viruses posits previously unrecognized cooperation modes. Analyses of 186 microbial and viral metagenomes revealed that SUP05 viruses persisted for years, but remained endemic to the OMZ. Finally, identification of virus-encoded dissimilatory sulfite reductase suggests SUP05 viruses reprogram their host's energy metabolism. Together, these results demonstrate closely coupled SUP05 virus-host co-evolutionary dynamics with the potential to modulate biogeochemical cycling in climate-critical and expanding OMZs.