海洋生物分类与系统演化实验室知识库

有孔虫古DNA研究是近年来古海洋学新兴的研究领域，传统柱状样中的有孔虫研究是以化石标本为基础，通过利用古DNA对有孔虫群落进行重建可以与以化石标本为基础的传统形态学研究结果进行比较与补充，给海洋全球变化提供新的视角，进而更好地对古海洋进行重建。目前有孔虫古DNA领域的有关工作主要集中在南大西洋、斯瓦尔巴群岛或北冰洋等有利于古DNA保存的深海或极地环境，但国内外有关陆架浅海环境中的有孔虫古DNA的研究尚未开展。

本实验通过采集黄海海域的沉积物柱状样，以探索适合陆架浅海环境沉积物柱状样中的有孔虫古DNA提取和扩增的有效方法。实验过程中使用商用试剂盒DNeasy PowerSoil Kit（Qiagen, 德国）进行环境基因组提取，通过延长提取过程中涡旋振荡的时间以及减少洗脱过程中洗脱液的体积、比较不同PCR扩增参数和有孔虫特异性引物，探索出适合陆架浅海地区沉积物柱状样中有孔虫古DNA提取和PCR扩增的有效方法。实验结果借助ImageJ软件对PCR产物凝胶电泳图像中的目的条带进行了定量分析，为验证实验设计方法的可行性，重新对8个沉积物样品进行DNA提取与PCR扩增，并对得到的有孔虫古DNA数据进行了多样性分析。研究结果显示，增加DNA提取过程中涡旋振荡的时间和减少洗脱液体积可以有效提高古DNA的提取效果，使用引物对s14F0和s15以及调节适合的PCR程序能成功黄海沉积物柱状样中的有孔虫古DNA。对8个沉积物样品的多样性进行分析后发现，有孔虫类群及种类在8个样品中没有太大差异，但其相对丰度随沉积物深度变化而变化，并且在全部样品中软壳类、单房室有孔虫都占较大比例，平均相对丰度为57.4%，结果证明有孔虫古DNA是重建古海洋环境的潜在指标。本文首次给出了一套适用于陆架浅海环境沉积物柱状样的有孔虫古DNA的防污染方法、DNA提取方法和PCR扩增方法，为古海洋和古环境的重建提供了新的研究思路和技术。

Foraminifera ancient DNA research is an emerging research field in paleooceanography in recent years. By comparing and supplementing the results of traditional morphological research based on fossil specimens, it can provide a new perspective on global changes in the ocean, and then better understand the ancient oceans are reconstructed. At present, the related work in the field of foraminifera ancient DNA mainly focuses on the deep-sea or polar environments that are conducive to the preservation of ancient DNA, such as the South Atlantic, Svalbard or the Arctic Ocean. Not yet launched.

In this experiment, we collected sediment column samples from the Yellow Sea to explore an effective method for extraction and amplification of foraminifera ancient DNA from sediment column samples in shallow sea environments on the continental shelf. During the experiment, a commercial kit DNeasy PowerSoil Kit (Qiagen, Germany) was used for environmental genome extraction. By prolonging the time of vortexing during the extraction process, reducing the volume of the eluate during the elution process, comparing different PCR amplification parameters and having different parameters. Foraminifera-specific primers were used to explore an effective method for foraminifera ancient DNA extraction and PCR amplification in sediment columnar samples in shallow sea areas on the shelf. Experimental results Using ImageJ software, the target bands in the gel electrophoresis images of PCR products were quantitatively analyzed. In order to verify the feasibility of the experimental design method, DNA extraction and PCR amplification were performed on 8 sediment samples again. Foraminifera ancient DNA data were analyzed for diversity. The results show that increasing the time of vortexing and reducing the volume of eluate during DNA extraction can effectively improve the extraction effect of ancient DNA. Using primer pairs s14F0 and s15 and adjusting the appropriate PCR program can successfully extract the yellow sea sediment columnar samples. After analyzing the diversity of foraminifera in the 8 sediment samples, it was found that there was no significant difference in the foraminifera groups and species in the 8 samples, but the relative abundance of the 8 samples changed with the depth of the sediment,  the soft-walled and the monothalamous foraminifera accounted for a large proportion in all samples, with an average relative abundance of 57.4%. The results show that foraminifera DNA is a potential indicator for reconstructing the paleomarine environment.For the first time, this paper presents a set of research techniques for foraminiferal ancient DNA of columnar sediments in shallow marine environment on the shelf, which provides new research ideas and technical methods for the reconstruction of paleo-ocean and paleo-environment.