Complementary DNA sequencing (cDNA): an effective approach for assessing the diversity and distribution of marine benthic ciliates along hydrographic gradients | |
Huang Pingping1,4; Zhao Feng2,3,4; Xu Kuidong1,2,3,4 | |
刊名 | JOURNAL OF OCEANOLOGY AND LIMNOLOGY |
2020-03-25 | |
页码 | 15 |
关键词 | benthic ciliates cDNA high-throughput sequencing c ommunity comparison DNA high-throughput sequencing morphology |
ISSN号 | 2096-5508 |
DOI | 10.1007/s00343-020-9234-2 |
通讯作者 | Xu Kuidong(kxu@qdio.ac.cn) |
英文摘要 | 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. |
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 |
语种 | 英语 |
出版者 | SCIENCE PRESS |
WOS记录号 | WOS:000521782200004 |
内容类型 | 期刊论文 |
源URL | [http://ir.qdio.ac.cn/handle/337002/167020] |
专题 | 海洋研究所_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.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 2.Chinese Acad Sci, Ctr Ocean Megasci, Qingdao 266071, Peoples R China 3.Pilot Natl Lab Marine Sci & Technol Qingdao, Lab Marine Biol & Biotechnol, Qingdao 266237, Peoples R China 4.Chinese Acad Sci, Inst Oceanol, Lab Marine Organism Taxon & Phylogeny, Qingdao 266071, Peoples R China |
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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