Single Cell Genomics Reveals Viruses Consumed by Marine Protists
The predominant model of the role of viruses in the marine trophic web is that of the “viral shunt,” where viral infection funnels a substantial fraction of the microbial primary and secondary production back to the pool of dissolved organic matter. Here, we analyzed the composition of non-eukaryoti...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2020-09-01
|
| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2020.524828/full |
| _version_ | 1818309514787553280 |
|---|---|
| author | Julia M. Brown Jessica M. Labonté Joseph Brown Nicholas R. Record Nicole J. Poulton Michael E. Sieracki Ramiro Logares Ramunas Stepanauskas |
| author_facet | Julia M. Brown Jessica M. Labonté Joseph Brown Nicholas R. Record Nicole J. Poulton Michael E. Sieracki Ramiro Logares Ramunas Stepanauskas |
| author_sort | Julia M. Brown |
| collection | DOAJ |
| description | The predominant model of the role of viruses in the marine trophic web is that of the “viral shunt,” where viral infection funnels a substantial fraction of the microbial primary and secondary production back to the pool of dissolved organic matter. Here, we analyzed the composition of non-eukaryotic DNA associated with individual cells of small, planktonic protists in the Gulf of Maine (GoM) and the Mediterranean Sea. We found viral DNA associated with a substantial fraction cells from the GoM (51%) and the Mediterranean Sea (35%). While Mediterranean SAGs contained a larger proportion of cells containing bacterial sequences (49%), a smaller fraction of cells contained bacterial sequences in the GoM (19%). In GoM cells, nearly identical bacteriophage and ssDNA virus sequences where found across diverse lineages of protists, suggesting many of these viruses are non-infective. The fraction of cells containing viral DNA varied among protistan lineages and reached 100% in Picozoa and Choanozoa. These two groups also contained significantly higher numbers of viral sequences than other identified taxa. We consider mechanisms that may explain the presence of viral DNA in protistan cells and conclude that protistan predation on free viral particles contributed to the observed patterns. These findings confirm prior experiments with protistan isolates and indicate that the viral shunt is complemented by a viral link in the marine microbial food web. This link may constitute a sink of viral particles in the ocean and has implications for the flow of carbon through the microbial food web. |
| first_indexed | 2024-12-13T07:31:23Z |
| format | Article |
| id | doaj.art-2dfa6aa616b148c6b063a46ca583f78c |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-13T07:31:23Z |
| publishDate | 2020-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-2dfa6aa616b148c6b063a46ca583f78c2022-12-21T23:55:12ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2020-09-011110.3389/fmicb.2020.524828524828Single Cell Genomics Reveals Viruses Consumed by Marine ProtistsJulia M. Brown0Jessica M. Labonté1Joseph Brown2Nicholas R. Record3Nicole J. Poulton4Michael E. Sieracki5Ramiro Logares6Ramunas Stepanauskas7Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United StatesDepartment of Marine Biology, Texas A&M University at Galveston, Galveston, TX, United StatesDepartment of Human Genetics, University of Utah, Salt Lake City, UT, United StatesBigelow Laboratory for Ocean Sciences, East Boothbay, ME, United StatesBigelow Laboratory for Ocean Sciences, East Boothbay, ME, United StatesDivision of Ocean Sciences, National Science Foundation, Alexandria, VA, United StatesInstitute of Marine Sciences (ICM), CSIC, Barcelona, SpainBigelow Laboratory for Ocean Sciences, East Boothbay, ME, United StatesThe predominant model of the role of viruses in the marine trophic web is that of the “viral shunt,” where viral infection funnels a substantial fraction of the microbial primary and secondary production back to the pool of dissolved organic matter. Here, we analyzed the composition of non-eukaryotic DNA associated with individual cells of small, planktonic protists in the Gulf of Maine (GoM) and the Mediterranean Sea. We found viral DNA associated with a substantial fraction cells from the GoM (51%) and the Mediterranean Sea (35%). While Mediterranean SAGs contained a larger proportion of cells containing bacterial sequences (49%), a smaller fraction of cells contained bacterial sequences in the GoM (19%). In GoM cells, nearly identical bacteriophage and ssDNA virus sequences where found across diverse lineages of protists, suggesting many of these viruses are non-infective. The fraction of cells containing viral DNA varied among protistan lineages and reached 100% in Picozoa and Choanozoa. These two groups also contained significantly higher numbers of viral sequences than other identified taxa. We consider mechanisms that may explain the presence of viral DNA in protistan cells and conclude that protistan predation on free viral particles contributed to the observed patterns. These findings confirm prior experiments with protistan isolates and indicate that the viral shunt is complemented by a viral link in the marine microbial food web. This link may constitute a sink of viral particles in the ocean and has implications for the flow of carbon through the microbial food web.https://www.frontiersin.org/article/10.3389/fmicb.2020.524828/fullnanoeukaryotemarine eukaryotevirusphagemicrobial ecologymarine food web |
| spellingShingle | Julia M. Brown Jessica M. Labonté Joseph Brown Nicholas R. Record Nicole J. Poulton Michael E. Sieracki Ramiro Logares Ramunas Stepanauskas Single Cell Genomics Reveals Viruses Consumed by Marine Protists Frontiers in Microbiology nanoeukaryote marine eukaryote virus phage microbial ecology marine food web |
| title | Single Cell Genomics Reveals Viruses Consumed by Marine Protists |
| title_full | Single Cell Genomics Reveals Viruses Consumed by Marine Protists |
| title_fullStr | Single Cell Genomics Reveals Viruses Consumed by Marine Protists |
| title_full_unstemmed | Single Cell Genomics Reveals Viruses Consumed by Marine Protists |
| title_short | Single Cell Genomics Reveals Viruses Consumed by Marine Protists |
| title_sort | single cell genomics reveals viruses consumed by marine protists |
| topic | nanoeukaryote marine eukaryote virus phage microbial ecology marine food web |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2020.524828/full |
| work_keys_str_mv | AT juliambrown singlecellgenomicsrevealsvirusesconsumedbymarineprotists AT jessicamlabonte singlecellgenomicsrevealsvirusesconsumedbymarineprotists AT josephbrown singlecellgenomicsrevealsvirusesconsumedbymarineprotists AT nicholasrrecord singlecellgenomicsrevealsvirusesconsumedbymarineprotists AT nicolejpoulton singlecellgenomicsrevealsvirusesconsumedbymarineprotists AT michaelesieracki singlecellgenomicsrevealsvirusesconsumedbymarineprotists AT ramirologares singlecellgenomicsrevealsvirusesconsumedbymarineprotists AT ramunasstepanauskas singlecellgenomicsrevealsvirusesconsumedbymarineprotists |