Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics
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 ox...
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2014-08-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/03125 |
| _version_ | 1811253218582200320 |
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| author | Simon Roux Alyse K Hawley Monica Torres Beltran Melanie Scofield Patrick Schwientek Ramunas Stepanauskas Tanja Woyke Steven J Hallam Matthew B Sullivan |
| author_facet | Simon Roux Alyse K Hawley Monica Torres Beltran Melanie Scofield Patrick Schwientek Ramunas Stepanauskas Tanja Woyke Steven J Hallam Matthew B Sullivan |
| author_sort | Simon Roux |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T16:47:33Z |
| format | Article |
| id | doaj.art-ece888727a0f4a7c8ecbbc814106f7ad |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T16:47:33Z |
| publishDate | 2014-08-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-ece888727a0f4a7c8ecbbc814106f7ad2022-12-22T03:24:32ZengeLife Sciences Publications LtdeLife2050-084X2014-08-01310.7554/eLife.03125Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomicsSimon Roux0Alyse K Hawley1Monica Torres Beltran2Melanie Scofield3Patrick Schwientek4Ramunas Stepanauskas5Tanja Woyke6Steven J Hallam7Matthew B Sullivan8Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United StatesDepartment of Microbiology and Immunology, University of British Columbia, Vancouver, CanadaDepartment of Microbiology and Immunology, University of British Columbia, Vancouver, CanadaDepartment of Microbiology and Immunology, University of British Columbia, Vancouver, CanadaU.S Department of Energy Joint Genome Institute, Walnut Creek, United StatesBigelow Laboratory for Ocean Sciences, East Boothbay, United StatesU.S Department of Energy Joint Genome Institute, Walnut Creek, United StatesDepartment of Microbiology and Immunology, University of British Columbia, Vancouver, Canada; Graduate Program in Bioinformatics, University of British Columbia, Vancouver, CanadaDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, United StatesViruses 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.https://elifesciences.org/articles/03125SUP05bacteriophagesvirussingle cell genomicoxygen minimum zoneviral dark matter |
| spellingShingle | Simon Roux Alyse K Hawley Monica Torres Beltran Melanie Scofield Patrick Schwientek Ramunas Stepanauskas Tanja Woyke Steven J Hallam Matthew B Sullivan Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics eLife SUP05 bacteriophages virus single cell genomic oxygen minimum zone viral dark matter |
| title | Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics |
| title_full | Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics |
| title_fullStr | Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics |
| title_full_unstemmed | Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics |
| title_short | Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics |
| title_sort | ecology and evolution of viruses infecting uncultivated sup05 bacteria as revealed by single cell and meta genomics |
| topic | SUP05 bacteriophages virus single cell genomic oxygen minimum zone viral dark matter |
| url | https://elifesciences.org/articles/03125 |
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