IOCAS-IR
汇泉湾潮间带多细胞趋磁原核生物和西沙珊瑚礁趋磁硝化螺菌的特征及基因组研究
赵怡聪
Subtype博士
Thesis Advisor张武昌
2023-05-13
Degree Grantor中国科学院大学
Place of Conferral中国科学院海洋研究所
Degree Name海洋生态学
Keyword趋磁细菌 潮间带 珊瑚礁 多样性 基因组
Abstract

趋磁细菌(Magnetotactic Bacteria,MTB)是一类能够沿着磁力线做定向运动的革兰氏阴性细菌。趋磁细菌具有形态、生理代谢、系统发育及功能多样化的特点。其中,多细胞趋磁原核生物(Multicellular Magnetotactic Prokaryotes,MMPs)和硝化螺旋菌门趋磁细菌(Nitrospirota MTB)是两类特殊的趋磁细菌。MMPs具有独特的多细胞结构、生活史中没有发现单细胞阶段,目前仅在海洋环境中发现;Nitrospirota MTB是在系统发育学中处于比较古老的地位,具有极强的生物矿化能力和丰富多样的代谢能力。目前对于MTB的多样性、季节变化规律、基因组的研究主要集中于单细胞MTB,但对潮间带MMPs的物种多样性、基因组比较解析与环境适应性的相关研究较少。目前与Nitrospirota MTB相关的研究主要集中于淡水陆域环境,缺乏海洋环境中的相关研究。本论文通过结合生态调查、光学显微镜和电子透射显微镜、分子生物学和高通量测序等技术方法,分别对青岛汇泉湾潮间沉积物中MMPs和南海西沙群岛珊瑚礁沉积物中Nitrospirota MTB的基因组和生态功能进行分析和探讨。

针对汇泉湾潮间带MMPs丰度的季节变化和物种多样性进行周年调查研究和MMPs的基因组信息进行分析。汇泉湾潮间带的MMPs由常见种类sMMPs(spherical MMPs,sMMPs)和eMMPs(elliptical MMPs,eMMPs),偶见种类cMMPs(pinecone-shaped MMPs,cMMPs)组成。在周年季节变化中,sMMPs和eMMPs表现出不同的季节变化现象。在物种组成上,sMMPs的种类多样性呈现出夏秋季节较高,冬季低的季节变化,sMMPs的优势种具有季节变化现象;eMMPs的种类多样性和优势种均没有明显的季节变化现象。在该区域共获得15个MMPs的OTUs,其中6个OTUs在分类学上属于潜在新种,代表了MMPs潜在新种。本论文获得了sMMPs和eMMPs的高质量基因组草图各一个。sMMPs(QD.A1)和eMMPs(QD.G1)的基因组分析结果揭示了MMPs可能具有自养生活的方式,包括具有通过WL途径、rTCA途径进行CO2固碳的代谢潜能;通过异化硫酸盐途径产生能量的代谢能力;通过多种转运体和T2SS实现细胞内外物质运输的能力。sMMPs(QD.A1)比eMMPs(QD.G1)具有更完整的碳代谢和昼夜节律调控机制,更多参与趋化和感光相关基因,这可能是sMMPs对复杂多变环境的适应性特征。sMMPs和eMMPs基因组均注释到完整的磁小体基因簇,在eMMPs的磁小体基因簇上有mamN-mad22基因序列的三个重复。

在南海西沙群岛珊瑚礁沉积物样品中Nitrospirota MTB的新物种Candidatus Magnetocorallium paracelense XS-1(XS-1)的研究分析。XS-1菌体为弧状,细胞大小为2.50 × 1.29 μm,在沉积物中丰度为103-104 inds./cm3。XS-1在外加磁场中表现为极向的趋磁运动,聚集在液滴边缘时展现出“Ping-Pong”的运动行为。XS-1除了能够生物矿化合成子弹头型Fe3O4磁小体外,细胞内还含有硫颗粒和类似液泡的细胞结构。基因组的注释和代谢潜能预测分析的结果显示XS-1具有丰富多样的代谢潜力,包括通过WL途径进行固碳、通过异化硫酸盐还原途径产能和昼夜节律调控的能力。比较基因组的结果显示,cbb3型细胞色素c氧化酶可能是海洋Nitrospirota MTB所依赖的电子末端氧化酶,该酶具有高亲氧性,使得海洋Nitrospirota MTB在含氧量有限的环境中具有生存优势。XS-1的基因组上也有保守的Nitrospirota MTB的磁小体基因簇。XS-1可能代表了一类在珊瑚礁生态系统中具有重要生态功能的MTB,它们在珊瑚礁生态系统中能够有效地推动C、N、S和Fe多种元素的生物地球化学循环。

对MMPs和Nitrospirota MTB两类特殊的MTB的生物学特征、物种多样性和基因组特征的研究结果分别丰富了汇泉湾潮间带MMPs的生物多样性和种质资源和填补了海洋环境中Nitrospirota MTB的相关研究的缺乏。本研究获得了sMMPs、eMMPs和海洋Nitrospirota MTB的高质量基因组,基因组信息的分析结果不仅为进一步研究趋磁细菌在潮间带及珊瑚礁环境的生态分布提供新的依据,而且为研究这两类特殊的趋磁细菌的生态功能奠定了重要前期工作基础。

Other Abstract

Magnetotactic Bacteria (MTB) are a group of gram-negative bacteria that produce magnetosomes and can orient and migrate along the geomagnetic lines. They are ubiquitous in sediments and stratified water columns, distributed predominantly in the oxic-anoxic transition zone (OATZ). MTB are cauterized by high diversity of morphology, physiology, metabolism, phylogeny and ecological functions. Multicellular magnetotactic prokaryotes (MMPs) and Nitrospirota MTB are two special groups of MTB. MMPs are a unique group with respect to their multicellular forms and widely distributed in marine environments. Nitrospirota MTB are a member of deep-branching MTB group and have excellent biomineralization ability and diverse metabolic potential. At present, there is a lack of researches on the diversity, seasonal variation, genomic information and environmental adaptability of MMPs, especially in intertidal zones, which mainly focus on unicellular MTB. Currently, there is a lack of relevant studies on Nitrospirota MTB in marine ecosystems, while research focusing on this group of MTB from freshwater and terrestrial ecosystems exists. In this study, the diversity, seasonal variation and genome of MMPs in the sediments of Huiquan Bay were studied by combining ecological investigation, optical and electron transmission microscopy technology, molecular biology and high-throughput sequencing technology. Additionally, the morphologic and ultrastructural characteristics, phylogenetic status and genomic information of Candidatus Magnetocorallium paracelense XS-1 from coral reef sediments in the Xisha Islands were also studied.

In Huiquan Bay intertidal zone, sMMPs (spherical MMPs, sMMPs) and eMMPs (elliptical MMPs, eMMPs) are the common groups, while cMMPs (pinecone-shaped MMPs) is the occasional group. The seasonal variation in the abundance of sMMPs and eMMPs are different. The species diversity of sMMPs was higher in autumn than in summer and winter, and the dominant species of sMMPs exhibited seasonal variation. Both the species diversity and dominant species of eMMPs showed no obvious seasonal variation. A total of 15 MMPs OTUs were identified in this study, among which 6 potentially represent novel species of MMPs. Two high-quality genomes, sMMPs (QD.A1) and eMMPs (QD.G1), were obtained and genomic analysis revealed that both possess an autotrophic lifestyle with the metabolic potential for CO2 fixation via the WL pathway and rTCA pathway. They were capable of producing energy through the dissimilatory sulfate pathway and possess multiple transporters and secretion systems. sMMPs (QD.A1) had more complete carbon metabolism pathways and circadian rhythm regulation mechanisms. Moreover, sMMPs (QD.A1) also exhibited a higher abundance of chemotaxis- and phototaxis-related genes. These genetic characteristics suggested that sMMPs possessed a high degree of adaptability and robustness in various environments. Both MMP genomes contained complete magnetosome gene clusters, while the magnetosome gene cluster of eMMPs (QD.G1) contained three repeats of the mamN-mad22 gene sequence.

In this study, a new genus of Nitrospirota MTB was discovered and identified from coral reef sediments, named as Candidatus Magnetocorallium paracelense XS-1 (XS-1). The morphology of XS-1 was vibrio and the average cell size was 2.50 × 1.29 μm with an abundance of 103-104 cells/cm3. XS-1 showed “North-Seeking” magnetotactic behavior in the applied magnetic field and exhibited “Ping-Pong” motion when cells gathered at the edge of the droplet. XS-1 not only can biomineralize the bullet-shaped magnetosomes, but also contained sulfur globules and vacuole-like structures. Genome annotation and metabolic potential prediction analysis revealed that XS-1 had a wide variety of metabolic potential. XS-1 had the ability to carry out carbon fixation via the WL pathway and anaerobic respiration with nitrate and sulfate to produce energy. Both XS-1 and marine Proteobacteria MTB had cbb3-type cytochrome c oxidases encoding genes, while these genes were not detected in the genomes of the known freshwater Nitrospirota MTB. The cbb3-type cytochrome c oxidases might provide marine MTB an advantage to survival in the marine environment. Furthermore, the XS-1 genome contained genes encoding the Pta-AckA pathway and the kaiBC-based circadian rhythm gene clusters. These genetic pathways had the capacity to regulate the XS-1 metabolic pathway or improve the metabolic efficiency of XS-1 cells. The results of genomic analysis suggested that XS-1 may represent a group of MTB with important ecological functions in coral reef ecosystems, where they can effectively promote biogeochemical cycles of C, N, S and Fe elements.

In summary, the diversity, biological and genomic characteristics of MMPs and marine Nitrospirota MTB had been studied and analyzed. The results provided new insights into the seasonal variation, diversity and genetic information of MMPs in the sediments of Huiquan Bay intertidal zone, and explored potential ecological roles of Nitrospirota MTB in the coral reef ecosystems. A total of three high-quality uncultured MTB draft genomes had been identified in this study, including two of MMPs genomes and the first marine Nitrospirota MTB genomes, which will provide new the groundwork for future research on the ecological distribution of MTB in the intertidal zone and coral reef ecosystems, and lay an important foundation for the study of the ecological functions of MMPs and marine Nitrospirota MTB.

Subject Area地球科学 ; 海洋科学
MOST Discipline Catalogue理学 ; 理学::海洋科学
Language中文
Document Type学位论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/181124
Collection中国科学院海洋研究所
海洋生态与环境科学重点实验室
Recommended Citation
GB/T 7714
赵怡聪. 汇泉湾潮间带多细胞趋磁原核生物和西沙珊瑚礁趋磁硝化螺菌的特征及基因组研究[D]. 中国科学院海洋研究所. 中国科学院大学,2023.
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