Discovery of Prevalent Ciliophora, Discoba, and Copepoda Protists in Deep Sea Water by In Situ Nucleotide Extraction
Deep-sea eukaryotic microorganisms play a vital role in degrading organic matter and geochemically cycling elements in the deep ocean. However, the impact of sampling methods on detection of these microorganisms under high hydrostatic pressure remains uncertain. In this study, we compared a traditio...
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MDPI AG
2023-12-01
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| Series: | Journal of Marine Science and Engineering |
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| Online Access: | https://www.mdpi.com/2077-1312/12/1/61 |
| _version_ | 1797343370367991808 |
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| author | Peikuan Xu Ming Yang Lisheng He Hongxi Zhang Zhaoming Gao Yuelu Jiang Yong Wang |
| author_facet | Peikuan Xu Ming Yang Lisheng He Hongxi Zhang Zhaoming Gao Yuelu Jiang Yong Wang |
| author_sort | Peikuan Xu |
| collection | DOAJ |
| description | Deep-sea eukaryotic microorganisms play a vital role in degrading organic matter and geochemically cycling elements in the deep ocean. However, the impact of sampling methods on detection of these microorganisms under high hydrostatic pressure remains uncertain. In this study, we compared a traditional water sampling method using a Niskin bottle, an in situ microbial filtration and fixation method (ISMIFF), and a multiple in situ nucleic acid collection (MISNAC) method to exhibit differences in the community structures that were collected at ~590–3100 m in the South China Sea (SCS). The classification and biodiversity indices of 18S rDNA Illumina sequencing reads from the V9 variation region revealed higher diversity for MISNAC DNA absorption column samples compared to others. Importantly, the relative abundance of Ciliophora (19.49%), Copepoda (23.31%), and Diplonemea (10.67%) was higher in MISNAC adsorption column samples, while Retaria (48.86%) were dominant in the MISNAC membrane samples. This indicates that MISNAC columns might collect more DNA in situ for the naked protists, while Retaria with a carbonate shell were more likely retained on the membrane. In conclusion, MISNAC is an effective method for DNA collection of deep-sea eukaryotic microorganisms and provides valuable materials for studying deep-sea microbial ecosystems. |
| first_indexed | 2024-03-08T10:46:39Z |
| format | Article |
| id | doaj.art-d82df05073234f1c9c92e5f4eb93ea90 |
| institution | Directory Open Access Journal |
| issn | 2077-1312 |
| language | English |
| last_indexed | 2024-03-08T10:46:39Z |
| publishDate | 2023-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Journal of Marine Science and Engineering |
| spelling | doaj.art-d82df05073234f1c9c92e5f4eb93ea902024-01-26T17:14:50ZengMDPI AGJournal of Marine Science and Engineering2077-13122023-12-011216110.3390/jmse12010061Discovery of Prevalent Ciliophora, Discoba, and Copepoda Protists in Deep Sea Water by In Situ Nucleotide ExtractionPeikuan Xu0Ming Yang1Lisheng He2Hongxi Zhang3Zhaoming Gao4Yuelu Jiang5Yong Wang6Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, ChinaInstitute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, ChinaInstitute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, ChinaInstitute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, ChinaInstitute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, ChinaInstitute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, ChinaInstitute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, ChinaDeep-sea eukaryotic microorganisms play a vital role in degrading organic matter and geochemically cycling elements in the deep ocean. However, the impact of sampling methods on detection of these microorganisms under high hydrostatic pressure remains uncertain. In this study, we compared a traditional water sampling method using a Niskin bottle, an in situ microbial filtration and fixation method (ISMIFF), and a multiple in situ nucleic acid collection (MISNAC) method to exhibit differences in the community structures that were collected at ~590–3100 m in the South China Sea (SCS). The classification and biodiversity indices of 18S rDNA Illumina sequencing reads from the V9 variation region revealed higher diversity for MISNAC DNA absorption column samples compared to others. Importantly, the relative abundance of Ciliophora (19.49%), Copepoda (23.31%), and Diplonemea (10.67%) was higher in MISNAC adsorption column samples, while Retaria (48.86%) were dominant in the MISNAC membrane samples. This indicates that MISNAC columns might collect more DNA in situ for the naked protists, while Retaria with a carbonate shell were more likely retained on the membrane. In conclusion, MISNAC is an effective method for DNA collection of deep-sea eukaryotic microorganisms and provides valuable materials for studying deep-sea microbial ecosystems.https://www.mdpi.com/2077-1312/12/1/61eukaryotic microbeMISNACRetariaSouth China SeaNiskin |
| spellingShingle | Peikuan Xu Ming Yang Lisheng He Hongxi Zhang Zhaoming Gao Yuelu Jiang Yong Wang Discovery of Prevalent Ciliophora, Discoba, and Copepoda Protists in Deep Sea Water by In Situ Nucleotide Extraction Journal of Marine Science and Engineering eukaryotic microbe MISNAC Retaria South China Sea Niskin |
| title | Discovery of Prevalent Ciliophora, Discoba, and Copepoda Protists in Deep Sea Water by In Situ Nucleotide Extraction |
| title_full | Discovery of Prevalent Ciliophora, Discoba, and Copepoda Protists in Deep Sea Water by In Situ Nucleotide Extraction |
| title_fullStr | Discovery of Prevalent Ciliophora, Discoba, and Copepoda Protists in Deep Sea Water by In Situ Nucleotide Extraction |
| title_full_unstemmed | Discovery of Prevalent Ciliophora, Discoba, and Copepoda Protists in Deep Sea Water by In Situ Nucleotide Extraction |
| title_short | Discovery of Prevalent Ciliophora, Discoba, and Copepoda Protists in Deep Sea Water by In Situ Nucleotide Extraction |
| title_sort | discovery of prevalent ciliophora discoba and copepoda protists in deep sea water by in situ nucleotide extraction |
| topic | eukaryotic microbe MISNAC Retaria South China Sea Niskin |
| url | https://www.mdpi.com/2077-1312/12/1/61 |
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