中国南海微型蓝细菌与蓝细菌噬菌体的遗传多样性与生态位适应性研究

Marine picocyanobacteria Prochlorococcus and Synechococcus are the most abundant primary producers in the world's oceans. Cyanophages (viruses that infect cyanobacteria) regulate picocyanobacterial community composition and impact global biogeochemical cycle through lysing their hosts, and influence host evolution through horizontal gene transfer. Previous studies on the genetic diversity, phyletic distribution and niche adaptation of picocyanobacteria and cyanophages mainly focused on several hotspot sea areas, while novel lineages were continuously found in other newly studied marine environments. Thus, it is worthy to conduct a comprehensive study on this topic in the South China Sea where little information was known in this field. Despite the fact that the genomics studies of cyanomyoviruses and cyanopodoviruses have delineated a comprehensive scenario of their genome contents and phage-host interactions, due to the much more divergent genomes of cyanosiphoviruses, sequencing more genomes of this cyanophage group is essential to gain a better understanding of ecology and evolution of the picocyanobacteria-cyanophage system. On the basis of previous works by the leading applicant, we propose here a study that focuses on the genetic diversity and niche adaptation of picocyanobacteria and their phages in the South China Sea. This work will provide new informations shedding light on the scientific questions as, i) what is the genetic diversity and community structures of picocyanobacteria and cyanophages in the estuary, continental shelf and oceanic basin in the South China Sea, are there novel lineages inhabiting those environments and possible niche partitioning? ii) is there co-occurrence and co-variation of picocyanobacteria and cyanophage phyletic groups, and if yes, how does it happen? iii) what is the unexplored diversity extent of cyanosiphoviruses at a genome-wide level and is there new information on the genetic exchange between cyanophages and hosts

海洋微型蓝细菌包括原绿球藻与聚球藻，是海洋中丰度最高的初级生产者。蓝细菌噬菌体对调控宿主的群落结构、驱动海洋生物地球化学循环以及影响宿主遗传进化上具有重要作用。目前对海洋微型蓝细菌及其噬菌体的遗传多样性、基因型类群组成与适应性的研究主要集中于少数热点海区，而不断在其它海域发现新的基因型说明有必要对中国南海这一缺乏相关研究的海区开展系统、全面的研究。同时，虽然蓝细菌肌尾与短尾噬菌体的基因组学研究成果丰硕，但是对长尾噬菌体基因组及其与宿主的关系缺乏深入的了解。本项目申请人将在博士论文工作的基础上探讨南海微型蓝细菌及其噬菌体的基因型类群组成与环境适应机制。本项目拟解决的关键科学问题是：1）南海河口、陆架与开阔海盆区域微型蓝细菌及其噬菌体的群落结构以及生态适应性；2）蓝细菌噬菌体与宿主的基因型类群共存、共变以及相互作用规律；3）蓝细菌长尾噬菌体在基因组水平上的多样性及其与宿主之间基因交换特征。

海洋微型蓝细菌是海洋中丰度最高的初级生产者，它包含的两个属，原绿球藻和聚球藻具有丰富的遗传多样性、典型的分布特征与特征鲜明的生理生态适应性。蓝细菌噬菌体是指感染蓝细菌的病毒，是目前海洋病毒生态学研究最成功的典型。本项目开展了南海微型蓝细菌及其噬菌体的多样性研究，并深入分析了蓝细菌噬菌体的基因组以及生物地理分布，取得了一些新的认识。1）研究了珠江口微型蓝细菌的多样性与群落时空变异，发现珠江口微型蓝细菌类群均为聚球藻，多样性较高，且具有显著的盐度适应性的类群分化，形成了明显的淡水类群，咸水类群与海水类群。同时，聚球藻类群对盐度的响应具有明显的季节变化，与夏冬两季冲淡水的强弱具有可验证的相关性。2）分析了南海开阔海区的原绿球藻与聚球藻的遗传类群组成，再次验证了原绿球藻的高光HLVI型的存在。3）通过比较基因组学方法研究了蓝细菌短尾噬菌体的遗传特征，深入分析了共20株蓝细菌短尾噬菌体的基因组，确定了蓝细菌短尾噬菌体的核心基因组由15个保守基因组成，泛基因组由349个基因组成；进化分析证实海洋蓝细菌短尾噬菌体主要由两个类群组成，分别是MPP-A与MPP-B类群，这两个类群具有一项明显的基因组组成差别，即前者不含有光合作用基因，后者都含有。原绿球藻短尾噬菌体都含有与碳代谢相关的基因talC，而聚球藻短尾噬菌体在同样的基因组位点却编码另一个与DNA代谢相关的基因thyX，这一差别可能是这两种宿主不同的病毒适应宿主的DNA代谢而产生的自然选择。4）深入解析了短尾、肌尾噬菌体的子类群以及原绿球藻、聚球藻在全球海洋的相对丰度。分析发现海洋蓝细菌噬菌体在不同营养条件的海域具有高度分化、结构化的群落组成，且与原绿球藻和聚球藻的群落结构显著相关，虽然肌尾噬菌体可交叉感染原绿球藻与聚球藻、而短尾噬菌体基本不能，但肌尾与短尾噬菌体的全球地理格局均受到宿主的强烈约束，因此，我们认为宿主是介导病毒适应环境与响应环境变化的主要因素，病毒与宿主具有显著的协同分布格局。