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热带西太平洋底栖与浮游有孔虫分子多样性及进化关系的初步研究
石峻峰
Subtype博士
Thesis Advisor类彦立
2020-05-21
Degree Grantor中国科学院大学
Place of Conferral中国科学院海洋研究所
Degree Name理学博士
Keyword有孔虫 热带西太平洋 进化 分子多样性
Abstract

    有孔虫以其丰富的化石记录而闻名,古海洋学研究中常使用有孔虫的壳体指标来标定地层年代,以及反演古环境和古气候。有孔虫尤其是浮游有孔虫具有超高的遗传多样性以及异乎寻常的进化速率,但对不同类群间进化关系的研究尚不够充分。传统的有孔虫多样性研究多基于形态学调查,以分子手段研究有孔虫多样性的工作尚为空白。为研究热带西太平洋浮游有孔虫的进化关系与有孔虫的遗传多样性,本论文的实验开展基于五个航次调查,分别是2014-2016年的雅浦海山航次和马里亚纳海山航次、2016年热带西太平洋基金委共享航次、2017年卡罗琳海山航次和2018年麦哲伦海山航次。本研究采用浮游生物垂直拖网及ROV的方式,采集了浮游样本107个,沉积物样本28个,其中用于高通量分析的环境样本125个,分离并鉴定浮游有孔虫单体样本700余枚。本文具体研究工作如下:

1. 雅浦海山和马里亚纳海山及其邻近深海平原沉积物中的有孔虫多样性

    本研究以雅浦海山Y3和马里亚纳海山M2两个海山以及邻近深海平原采集到的16个沉积物为研究对象,使用高通量测序方法,总共发现了1399个OTU,其中浮游 有孔虫OTU 27个,底栖有孔虫OTU 1372个。两个海山的有孔虫多样性明显高 于临近的深海平原,这说明了海山生态的独特性。Y3海山与邻近深海平原的物 种组成相似,表明海山是物种迁徙的节点。有孔虫的分布受温度和水深的影响。 这些结果为热带西太平洋深海有孔虫的调查提供了第一手资料。

2. 西太平洋浮游有孔虫Globigerinita glutinata种内SSU rDNA多样性研究

    以搭乘“2016年热带西太平洋共享航次”采自热带西太平洋的浮游有孔虫Globigerinita glutinata活体标本作为研究对象,利用单细胞PCR和克隆技术,获得5个虫体的20条SSU rDNA目的片段,同时对其序列结构进行了研究。序列成对分析显示,该种遗传距离差异最长可达0.249,远高于其它物种。序列的差异主要集中在三个不同的高变异区,高可变区的长度范围为21 bp到63 bp。本工作在国内首次揭示了热带西太平洋浮游有孔虫G. glutinata种内的SSU rDNA核酸型,研究结果表明G. glutinata的种内SSU rDNA变异性极大,复杂的生活史以及假基因的存在或许是造成该现象的原因。在本实验中活体G. glutinata出现了4种不同SSU rDNA核酸型,暗示将来的分子鉴定工作若将97%基因差异相似度阈值作为物种鉴定标准在G. glutinata中可能不太适用。

3. 热带西太平洋浮游有孔虫的进化研究

    以“麦哲伦”海山区浮游有孔虫单体样本为研究对象,利用单细胞PCR和克隆技术,借助Sanger测序,获得了20种浮游有孔虫的SSU rDNA序列。将序列比对后,使用最大似然法与贝叶斯法分别建树。将这些数据与化石数据结合分析,构建出浮游有孔虫分子钟。结果显示:多数浮游种类的分化时间在距今150 Ma-160 Ma,化石出现的时间比进化时间要晚,这说明早在形态学分化之前,浮游有孔虫的序列已将发生了变化,形态学变化是分子进化累计的结果;浮游有孔虫的起源为多起源进化,即由不同类群的底栖有孔虫分别进化而来,这佐证了前人关于浮游有孔虫进化起源的研究。

4. 卡罗琳海山表层海水中浮游有孔虫多样性研究

    以“卡罗琳”海山航次的48个环境样本为研究对象,通过高通量测序,总共得到386个OTU,这些OTU被注释到43个属,66个种。在浮游类群中发现了底栖有孔虫的存在。除高通量的数据外,形态学的数据也证实了底栖类群的存在。这些被分离出来的底栖种类,包含着幼体和成体。这一方面说明浅水海山区存在着泰勒柱环流,这种环流机制对有孔虫的传播起到了一定的作用,尤其是水浅的海山山顶附近,生物受这种环流影响会更大;另一方面说明了有孔虫传播途径的多样,以前的研究结果认为有孔虫多会以繁殖体等幼体形态跟随海水中的其他物质一同转移,浮游类群中底栖类群成体的发现为有孔虫传播的研究作出了补充。

5. 麦哲伦海山表层海水中浮游有孔虫多样性研究

    本研究以2018年“麦哲伦”海山航次的50个环境样本为研究对象,通过对有孔虫特异性片段的扩增,构建序列文库。文库经Illumina Hiseq 2500平台测序,总共得到96个OTU。OTU被分别注释到8个属,10个种。研究结果表明,在同一个站位取到的三个样本的样本内差异巨大,这说明在海水中获得的浮游生物样本的空间异质性,而海水的流动性与相对均一的特性又使得有孔虫物种组成在宏观层面趋于一致;在这个数据集中,每个样本中序列与数据库序列的低相似度表明麦哲伦海山有孔虫群落可能具有较高的遗传新颖性。

6. 麦哲伦海山沉积物中的浮游有孔虫

    为了了解麦哲伦海山沉积物中的有孔虫多样性,我们提取了沉积物中的环境DNA,并扩增了有孔虫的部分SSU rDNA。每个站位采集了3个重复样品,利用Illumina Hiseq 2500平台进行SSU rDNA片段测序。质量过滤后,保留了912,979个有孔虫序列,这些序列被聚成266个OTU。有孔虫类群的相对丰度在不同重复之间差异很大,这可能是由于在扩增过程中存在偏差或者深海沉积物斑块效应引起的。我们证实,大部分序列来自底栖有孔虫,代表了原位群落,但相当数量的浮游有孔虫序列存在于这个数据集。这些序列有可能重建水体中浮游有孔虫的群落。这为了解浮游有孔虫在水体中的动态沉积过程提供了新的视角。

    本研究是对热带西太平洋浮游有孔虫进化与分子多样性的首次研究,也是国内第一次对海山系统有孔虫分类与多样性的系统调查。但是由于研究过程中,浮游采样仅仅对200 m以浅的海水进行采样,无法得知浮游有孔虫多样性的垂直分布,这些有待于后期进一步探索。本文为有孔虫多样性的地理分布提供了依据,同时也为浮游有孔虫分子生物学的物种判定的标准修改提供了建议,进化学的研究可以为有孔虫地质定年以及古环境重建提供参考。

Other Abstract

    Foraminifera were well known for their rich fossil records. In geological research, foraminiferal shells were often used to infer the stratigraphic age and to invert the paleoenvironment. However, due to the extremely high genetic diversity of foraminifera especially planktonic foraminifera and their extraordinary evolution rate, the research on their evolutionary relationship was insufficient. At the same time, the traditional research on the diversity of foraminifera was mostly based on morphological investigation, but the research on the diversity of foraminifera by molecular technology was still blank. In order to study the evolutionary relationship and genetic diversity of foraminifera in the tropical Western Pacific Ocean, we participated in five voyages. 107 planktonic samples and 28 sediments were collected by using plankton trawl and ROV, 125 environmental samples were used for high-throughput analysis, and more than 700 planktonic foraminifera individuals were isolated and identified. The specific researches in this paper are as follows:

1. Foraminifera diversity in Yap Seamount, Mariana Seamount and their adjacent abyssal plains

    In this study, 16 sediments collected from Y3 (Yap Seamount) and M2 (Mariana Seamount) seamounts and their adjacent abyssal plains in Yap Seamounts area were taken as the research objects. A total of 1399 OTUs were observed by high-throughput sequencing, including 27 planktonic and 1372 benthic foraminifera OTUs. The diversities of foraminifera in the two seamounts are significantly higher than that in the adjacent abyssal plain, which indicates the specific of seamount ecology. The species composition of Y3 seamount is similar to that of the adjacent abyssal plain, indicating that seamounts are the nodes of species migration. The diversity of foraminifera is affected by water temperature and water depth. These results provide first-hand data for the investigation of deep-sea foraminifera in the tropical western Pacific Ocean.

2. Intraspecific SSU rDNA Diversity of Planktonic Foraminifera Globigerinita glutinata in the Western Pacific Ocean

    In this study, 20 SSU rDNA target fragments were obtained by single-cell PCR and cloning techniques from five planktonic foraminifera Globigerinita glutinata individuals. Sequence paired analysis showed that the longest genetic distance was 0.249, which was much higher than that of other species. Sequence differences were mainly concentrated in three different high-variant regions, the length of which ranges from 21 bp to 63 bp. The SSU rDNA nucleic acid patterns of G. glutinata in the tropical western Pacific were first revealed in China. The results showed that the SSU rDNA variability of G. glutinata was very high. The complex life history and the presence of pseudogenes may be the reasons for this phenomenon. In this experiment, four different SSU rDNA nucleic acid types were found in G. glutinata, suggesting that 97% similarity threshold might not be suitable for species identification in G. glutinata.

3. Evolution of planktonic foraminifera in the tropical Western Pacific Ocean

    Using single-cell PCR, cloning technique and Sanger sequencing technique, 20 planktonic foraminifera SSU rDNA sequences from Magellan seamount were obtained. After sequences aligning, the maximum likelihood method and Bayesian method were used to construct trees respectively. The molecular clocks of planktonic foraminifera were constructed by combining these data with fossil data. The results showed that the divergence time of most planktonic species since 150 Ma to 160 Ma. The fossils appeared later than the evolution time, this indicated that the sequence of planktonic foraminifera changed before the morphological differentiation, and the morphological change was the result of the accumulation of molecular evolution. The origin of planktonic foraminifera was multi-origin evolution and this support previous studies on the evolutionary origin of planktonic foraminifera. 

4. Diversity of planktonic foraminifera in Caroline seamount surface seawater

    A total of 386 OTUs were obtained by high-throughput sequencing from 48 environmental samples. These OTUs were annotated to 43 genera and 66 species. At the same time, a huge number of benthic foraminifera had been found in planktonic groups. In addition, morphological data also confirmed the existence of benthic groups. These isolated benthic species include larvae and adults. Taylor column circulation existed in shallow sea mountainous areas, and this circulation mechanism played a certain role in foraminifera transmission, it also illustrated the diversity of foraminifera transmission routes. Previous studies had shown that foraminifera mostly spread in the form of larvae such as propagules, the discovery of benthic groups in planktonic groups complements the study of foraminifera transmission.

5. Diversity of planktonic foraminifera in Magellan seamount surface seawater

    In this study, 50 environmental samples from the Magellan Seamount voyage in 2018 were used to construct a sequence library by amplifying specific fragments of foraminifera. The library was sequenced on Illumina Hiseq 2500 platform and 96 OTUs were obtained. OTUs were assigned to 8 genera and 10 species respectively. The results showed that there were great differences among the three sub-samples, which shows that the spatial heterogeneity of plankton samples obtained in seawater, and the mobility and relative homogeneity of seawater make the species composition of foraminifera tend to be uniform at the macro level; in this dataset, the low similarity between the sequences in each sample and the database sequence indicates that the foraminifera in Magellan seamount may have high genetic novelty.

6. Planktonic foraminifera in sedements from Magellan seamount

    Environmental DNA in sediments was extracted and partial SSU rDNA of foraminifera was amplified in order to understand foraminiferal diversity in Magellan Seamount. For each 3 replicate samples per site, partial SSU rDNA sequencing was performed by Illumina HiSeq 2500 platform. After quality filtering, 912,979 foraminifera reads were retained which these gathered into 266 OTUs. The relative abundance of foraminifera groups varied between replications, this may be caused by existence of bias during amplification process and the deep-sea floor patchiness. We confirmed that the largest portion of sequences came from benthic foraminifera which represented in situ community, but a considerable number of planktonic foraminifera sequences existed in this dataset. These sequences had the potential to reconstruct planktonic foraminifera communities in water column. This provided a new perspective for understanding the dynamic sedimentation process of planktonic foraminifera in water column.

    This work was the first attempt on the evolution and molecular diversity of planktonic foraminifera in the tropical Western Pacific Ocean, and this was the first systematic survey on the foraminifera diversity of the seamount system in China. However, the planktonic sampling only sampled the shallow water with a depth of 200 m, and the vertical distribution of planktonic foraminifera diversity could not be known, which needed to be further explored in the later study. This paper provided a basis for the geographical distribution and diversity of foraminifera, and also provided suggestions for species determination of molecular biology of planktonic foraminifera. Evolutionary studies of planktonic foraminifera can provide references for geological dating and paleoenvironment reconstruction.

MOST Discipline Catalogue理学::海洋科学 ; 理学::生物学
Language中文
Document Type学位论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/164644
Collection海洋生物分类与系统演化实验室
Recommended Citation
GB/T 7714
石峻峰. 热带西太平洋底栖与浮游有孔虫分子多样性及进化关系的初步研究[D]. 中国科学院海洋研究所. 中国科学院大学,2020.
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