| Complementary DNA sequencing (cDNA): an effective approach for assessing the diversity and distribution of marine benthic ciliates along hydrographic gradients | |
Huang Pingping1,3 ; Zhao Feng1,2,4; Xu Kuidong1,2,3,4
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| 2020-03-25 | |
| 发表期刊 | JOURNAL OF OCEANOLOGY AND LIMNOLOGY
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| ISSN | 2096-5508 |
| 页码 | 15 |
| 通讯作者 | Xu Kuidong(kxu@qdio.ac.cn) |
| 摘要 | The Yellow Sea Cold Water Mass (YSCWM) is a distinct hydrographic phenomenon of the Yellow Sea, and the distribution pattern of meio- and macrobenthos differs inside and outside of the YSCWM. However, such a pattern has never been observed in the microbenthic ciliate communities. Therefore, we hypothesized that benthic ciliates followed a similar distribution pattern as meio- and macrobenthos, but this pattern has not been uncovered by morphological methods. We evaluated the diversity and distribution of benthic ciliates at five stations along hydrographic gradients across the YSCWM and adjacent shallow water by using morphology and DNA and complementary DNA (cDNA) high-throughput sequencing of the V4 region of 18S rRNA gene. Results showed that the diversity of benthic ciliates detected by DNA (303 OTUs), and the cDNA (611 OTUs) sequencing was much higher than that detected by the morphological method (79 species). Morphological method detected roughly different ciliate communities inside and outside of the YSCWM, but without statistical significance. No clear pattern was obtained by DNA sequencing. In contrast, cDNA sequencing revealed a distinct distribution pattern of benthic ciliate communities like meio-and macrobenthos, which coincided well with the results of the environmental parameter analysis. More than half of the total sequences detected by DNA sequencing belonged to planktonic ciliates, most (if not all) of which were recovered from historic DNA originating through the sedimentation of pelagic forms because none of them were observed morphologically. The irrelevant historic DNA greatly influenced the recovery of rare species and thus limited the understanding of the benthic ciliate diversity and distribution. Our research indicates that the methods used have significant effects on the investigation of benthic ciliate communities and highlights that cDNA sequencing has great advantages in estimating the diversity and distribution of benthic ciliates, as well as the potential for benthic environmental assessments. |
| 关键词 | benthic ciliates cDNA high-throughput sequencing c ommunity comparison DNA high-throughput sequencing morphology |
| DOI | 10.1007/s00343-020-9234-2 |
| 收录类别 | SCI |
| 语种 | 英语 |
| 资助项目 | National Natural Science Foundation of China[41876171] ; National Natural Science Foundation of China[41506167] ; National Natural Science Foundation of China[41476144] |
| WOS研究方向 | Marine & Freshwater Biology ; Oceanography |
| WOS类目 | Limnology ; Oceanography |
| WOS记录号 | WOS:000521782200004 |
| 出版者 | SCIENCE PRESS |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://ir.qdio.ac.cn/handle/337002/167021 |
| 专题 | 海洋生物分类与系统演化实验室 |
| 通讯作者 | Xu Kuidong |
| 作者单位 | 1.Chinese Acad Sci, Inst Oceanol, Lab Marine Organism Taxon & Phylogeny, Qingdao 266071, Peoples R China 2.Pilot Natl Lab Marine Sci & Technol Qingdao, Lab Marine Biol & Biotechnol, Qingdao 266237, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 4.Chinese Acad Sci, Ctr Ocean Megasci, Qingdao 266071, Peoples R China |
| 第一作者单位 | 中国科学院海洋研究所 |
| 通讯作者单位 | 中国科学院海洋研究所; 中国科学院海洋大科学研究中心 |
| 推荐引用方式 GB/T 7714 | Huang Pingping,Zhao Feng,Xu Kuidong. Complementary DNA sequencing (cDNA): an effective approach for assessing the diversity and distribution of marine benthic ciliates along hydrographic gradients[J]. JOURNAL OF OCEANOLOGY AND LIMNOLOGY,2020:15. |
| APA | Huang Pingping,Zhao Feng,&Xu Kuidong.(2020).Complementary DNA sequencing (cDNA): an effective approach for assessing the diversity and distribution of marine benthic ciliates along hydrographic gradients.JOURNAL OF OCEANOLOGY AND LIMNOLOGY,15. |
| MLA | Huang Pingping,et al."Complementary DNA sequencing (cDNA): an effective approach for assessing the diversity and distribution of marine benthic ciliates along hydrographic gradients".JOURNAL OF OCEANOLOGY AND LIMNOLOGY (2020):15. |
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| 文件名称/大小 | 文献类型 | 版本类型 | 开放类型 | 使用许可 | ||
| Complementary DNA se（1385KB） | 期刊论文 | 出版稿 | 限制开放 | CC BY-NC-SA | 浏览 | |
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