Novel Protocol for Estimating Viruses Specifically Infecting the Marine Planktonic Diatoms
Since their discovery, at least 15 diatom viruses have been isolated and characterised using a culture method with two cycles of extinction dilution. However, the method is time consuming and laborious, and it isolates only the most dominant virus in a water sample. Recent studies have suggested int...
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MDPI AG
2020-06-01
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| Online Access: | https://www.mdpi.com/1424-2818/12/6/225 |
| _version_ | 1797566119126499328 |
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| author | Yuji Tomaru Kei Kimura |
| author_facet | Yuji Tomaru Kei Kimura |
| author_sort | Yuji Tomaru |
| collection | DOAJ |
| description | Since their discovery, at least 15 diatom viruses have been isolated and characterised using a culture method with two cycles of extinction dilution. However, the method is time consuming and laborious, and it isolates only the most dominant virus in a water sample. Recent studies have suggested inter-species host specificity of diatom viruses. Here, we describe a new protocol to estimate previously unrecognised host-virus relationships. Host cell cultures after inoculation of natural sediment pore water samples were obtained before complete lysis. The proliferated viral genomes in the host cells were amplified using degenerate primer pairs targeting protein replication regions of single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA) viruses, and then sequenced. Diverse ssRNA virus types within known diatom virus group were detected from inoculated <i>Chaetoceros tenuissimus</i> and <i>C. setoensis</i> cells. A previously unknown ssDNA virus type was detected in inoculated <i>C. tenuissimus</i> cells, but not in <i>C. setoensis</i> cells. Despite the possible protocol biases, for example non-specific adsorptions of virions onto the host cells, the present method helps to estimate the viruses infectious to a single host species. Further improvements to this protocol targeting the proliferated viral genomes might reveal unexpected diatom–virus ecological relationships. |
| first_indexed | 2024-03-10T19:22:13Z |
| format | Article |
| id | doaj.art-d8a4e348b60c49d497f3dea1cb8e1f0b |
| institution | Directory Open Access Journal |
| issn | 1424-2818 |
| language | English |
| last_indexed | 2024-03-10T19:22:13Z |
| publishDate | 2020-06-01 |
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| spelling | doaj.art-d8a4e348b60c49d497f3dea1cb8e1f0b2023-11-20T02:52:37ZengMDPI AGDiversity1424-28182020-06-0112622510.3390/d12060225Novel Protocol for Estimating Viruses Specifically Infecting the Marine Planktonic DiatomsYuji Tomaru0Kei Kimura1National Research Institute of Fisheries and Environment of the Inland Sea, Japan Fisheries Research and Education Agency, Hiroshima 739-0452, JapanFaculty of Agriculture, Saga University, Saga 840-8502, JapanSince their discovery, at least 15 diatom viruses have been isolated and characterised using a culture method with two cycles of extinction dilution. However, the method is time consuming and laborious, and it isolates only the most dominant virus in a water sample. Recent studies have suggested inter-species host specificity of diatom viruses. Here, we describe a new protocol to estimate previously unrecognised host-virus relationships. Host cell cultures after inoculation of natural sediment pore water samples were obtained before complete lysis. The proliferated viral genomes in the host cells were amplified using degenerate primer pairs targeting protein replication regions of single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA) viruses, and then sequenced. Diverse ssRNA virus types within known diatom virus group were detected from inoculated <i>Chaetoceros tenuissimus</i> and <i>C. setoensis</i> cells. A previously unknown ssDNA virus type was detected in inoculated <i>C. tenuissimus</i> cells, but not in <i>C. setoensis</i> cells. Despite the possible protocol biases, for example non-specific adsorptions of virions onto the host cells, the present method helps to estimate the viruses infectious to a single host species. Further improvements to this protocol targeting the proliferated viral genomes might reveal unexpected diatom–virus ecological relationships.https://www.mdpi.com/1424-2818/12/6/225marine diatom<i>Chaetoceros tenuissimus</i><i>Chaetoceros setoensis</i>host-virus specificityRdRpssRNA virus |
| spellingShingle | Yuji Tomaru Kei Kimura Novel Protocol for Estimating Viruses Specifically Infecting the Marine Planktonic Diatoms Diversity marine diatom <i>Chaetoceros tenuissimus</i> <i>Chaetoceros setoensis</i> host-virus specificity RdRp ssRNA virus |
| title | Novel Protocol for Estimating Viruses Specifically Infecting the Marine Planktonic Diatoms |
| title_full | Novel Protocol for Estimating Viruses Specifically Infecting the Marine Planktonic Diatoms |
| title_fullStr | Novel Protocol for Estimating Viruses Specifically Infecting the Marine Planktonic Diatoms |
| title_full_unstemmed | Novel Protocol for Estimating Viruses Specifically Infecting the Marine Planktonic Diatoms |
| title_short | Novel Protocol for Estimating Viruses Specifically Infecting the Marine Planktonic Diatoms |
| title_sort | novel protocol for estimating viruses specifically infecting the marine planktonic diatoms |
| topic | marine diatom <i>Chaetoceros tenuissimus</i> <i>Chaetoceros setoensis</i> host-virus specificity RdRp ssRNA virus |
| url | https://www.mdpi.com/1424-2818/12/6/225 |
| work_keys_str_mv | AT yujitomaru novelprotocolforestimatingvirusesspecificallyinfectingthemarineplanktonicdiatoms AT keikimura novelprotocolforestimatingvirusesspecificallyinfectingthemarineplanktonicdiatoms |