Complementary DNA sequencing (cDNA): an effective approach for assessing the diversity and distribution of marine benthic ciliates along hydrographic gradients
Complementary DNA sequencing (cDNA): an effective approach for assessing the diversity and distribution of marine benthic ciliates along hydrographic gradients
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互补 DNA 测序 (cDNA)：评估海洋底栖纤毛虫沿水文梯度多样性和分布的有效方法
DOI：
10.1007/s00343-020-9234-2
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发表时间：
2020-03
影响因子：
1.6
通讯作者：
Kuidong Xu
中科院分区：
文献类型：
--
作者：
Pingping Huang;Feng Zhao;Kuidong Xu
黄海冷水团(YSCWM)是黄海一种独特的水文现象，小型底栖动物和大型底栖动物在YSCWM内外的分布格局不同。然而，这种模式从未在小型底栖纤毛虫群落中观察到。因此，我们假设底栖纤毛虫遵循与小型底栖动物和大型底栖动物相似的分布模式，但这种模式尚未被形态学方法发现。我们利用18S rRNA基因V4区的形态、DNA和互补DNA(CDNA)高通量测序的方法，评估了沿YSCWM及其邻近浅水的水文梯度上5个站位的底栖纤毛虫的多样性和分布。结果表明，DNA(303个OTUS)和DNA测序(611个OTUS)检测到的底栖纤毛虫多样性明显高于形态学方法(79个种)。形态学方法检测到的纤毛虫群落在YSCWM内外大致不同，但无统计学意义。DNA测序没有得到清晰的条带。与之相反，测序揭示了小型和大型底栖动物等底栖纤毛虫群落的明显分布格局，这与环境参数分析的结果很好地吻合。DNA测序检测到的全部序列中有一半以上属于浮游纤毛虫，其中大部分(如果不是全部)是从起源于远洋形式的历史DNA中恢复的，因为在形态上没有观察到它们。无关的历史DNA极大地影响了稀有物种的恢复，从而限制了对底栖纤毛虫多样性和分布的了解。我们的研究表明，所使用的方法对底栖纤毛虫群落的调查具有重要的影响，并强调了cDNA测序在估计底栖纤毛虫的多样性和分布以及进行底栖环境评估方面具有很大的优势。
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.
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影响因子：
3.7
作者：
Seimon TA;Olson SH;Lee KJ;Rosen G;Ondzie A;Cameron K;Reed P;Anthony SJ;Joly DO;Karesh WB;McAloose D;Lipkin WI
通讯作者：
Lipkin WI
影响因子：
2.9
作者：
Zhao Meng;Kuidong Xu;Renhai Dai;Y. Lei
通讯作者：
Zhao Meng;Kuidong Xu;Renhai Dai;Y. Lei
影响因子：
4.6
作者：
Nascimento FJA;Lallias D;Bik HM;Creer S
通讯作者：
Creer S
DOI：
--
发表时间：
2010-06
期刊：
--
影响因子：
--
作者：
D. Lynn
通讯作者：
D. Lynn
基于DNA和RNA高通量测序的南海水体微生物真核生物多样性和活性
影响因子：
5.2
作者：
Xu D;Li R;Hu C;Sun P;Jiao N;Warren A
通讯作者：
Warren A