Elusive Recurrent Bacterial Contamination in a Diatom Culture: A Case Study
In preparation for whole-genome sequencing, the axenic culture for two strains of a freshwater diatom <i>Fragilaria radians</i> were produced. Although their axenicity was controlled for the cultures’ entire lifetime, the published genomic assembly was later found to contain a large amou...
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| Format: | Article |
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MDPI AG
2021-10-01
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| Series: | Applied Sciences |
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| Online Access: | https://www.mdpi.com/2076-3417/11/21/10131 |
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| author | Alexey A. Morozov Yuri P. Galachyants Artyom M. Marchenkov Darya P. Petrova Yulia R. Zakharova |
| author_facet | Alexey A. Morozov Yuri P. Galachyants Artyom M. Marchenkov Darya P. Petrova Yulia R. Zakharova |
| author_sort | Alexey A. Morozov |
| collection | DOAJ |
| description | In preparation for whole-genome sequencing, the axenic culture for two strains of a freshwater diatom <i>Fragilaria radians</i> were produced. Although their axenicity was controlled for the cultures’ entire lifetime, the published genomic assembly was later found to contain a large amount of bacterial sequences. Using various in silico analyses of whole genome read libraries and 16S rRNA sequencing of culture samples, we reconstruct the history of the contamination and document the failures of various axenicity control methods. This knowledge is used to discuss how these failures could have been avoided, and to provide guidelines for future works on axenic diatom cultures. |
| first_indexed | 2024-03-10T06:06:23Z |
| format | Article |
| id | doaj.art-45cde7f6384244b8a6a3a29c0cb3599a |
| institution | Directory Open Access Journal |
| issn | 2076-3417 |
| language | English |
| last_indexed | 2024-03-10T06:06:23Z |
| publishDate | 2021-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Applied Sciences |
| spelling | doaj.art-45cde7f6384244b8a6a3a29c0cb3599a2023-11-22T20:28:16ZengMDPI AGApplied Sciences2076-34172021-10-0111211013110.3390/app112110131Elusive Recurrent Bacterial Contamination in a Diatom Culture: A Case StudyAlexey A. Morozov0Yuri P. Galachyants1Artyom M. Marchenkov2Darya P. Petrova3Yulia R. Zakharova4Department of Cell Ultrastructure, Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, RussiaDepartment of Cell Ultrastructure, Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, RussiaDepartment of Cell Ultrastructure, Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, RussiaDepartment of Cell Ultrastructure, Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, RussiaDepartment of Cell Ultrastructure, Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, RussiaIn preparation for whole-genome sequencing, the axenic culture for two strains of a freshwater diatom <i>Fragilaria radians</i> were produced. Although their axenicity was controlled for the cultures’ entire lifetime, the published genomic assembly was later found to contain a large amount of bacterial sequences. Using various in silico analyses of whole genome read libraries and 16S rRNA sequencing of culture samples, we reconstruct the history of the contamination and document the failures of various axenicity control methods. This knowledge is used to discuss how these failures could have been avoided, and to provide guidelines for future works on axenic diatom cultures.https://www.mdpi.com/2076-3417/11/21/10131diatomsaxenic culturescontamination16S rRNA amplicon sequencing<i>Sphingomonas</i><i>Fragilaria</i> |
| spellingShingle | Alexey A. Morozov Yuri P. Galachyants Artyom M. Marchenkov Darya P. Petrova Yulia R. Zakharova Elusive Recurrent Bacterial Contamination in a Diatom Culture: A Case Study Applied Sciences diatoms axenic cultures contamination 16S rRNA amplicon sequencing <i>Sphingomonas</i> <i>Fragilaria</i> |
| title | Elusive Recurrent Bacterial Contamination in a Diatom Culture: A Case Study |
| title_full | Elusive Recurrent Bacterial Contamination in a Diatom Culture: A Case Study |
| title_fullStr | Elusive Recurrent Bacterial Contamination in a Diatom Culture: A Case Study |
| title_full_unstemmed | Elusive Recurrent Bacterial Contamination in a Diatom Culture: A Case Study |
| title_short | Elusive Recurrent Bacterial Contamination in a Diatom Culture: A Case Study |
| title_sort | elusive recurrent bacterial contamination in a diatom culture a case study |
| topic | diatoms axenic cultures contamination 16S rRNA amplicon sequencing <i>Sphingomonas</i> <i>Fragilaria</i> |
| url | https://www.mdpi.com/2076-3417/11/21/10131 |
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