海洋浮游态玫瑰杆菌基因组的多样性及其生态与进化机制的研究

Members of the Roseobacter clade are among the most abundant bacteria in some ocean regions, and are significant drivers in global carbon and sulfur cycles. Genomic sequences of over 60 cultured isolates and partial genomes of 4 uncultivated members have become available, which have already displayed a tremendous diversity in genome size, G+C content, and gene repertoire. What remain unknown are the ecological and evolutionary mechanisms that gave rise to this diversity. Ecotype, for instance, is a straightforward concept describing how the evolutionary path of a bacterial lineage was shaped by an environmental factor. It has been repeatedly documented in other major marine bacterial lineages, including, among others, Prochlorococcus, Synechococcus, and SAR11, but has not been found in any Roseobacter lineage. The generally accepted role of natural selection has also recently been questioned, and other evolutionary mechanisms such as genetic drift have been hypothesized to drive the genetic diversification of some Roseobacter lineages. ..This proposed project builds on a number of relevant studies and preliminary results, and aims to understand the genetic diversity of planktonic Roseobacters from global oceans and elucidate the ecological and evolutionary mechanisms underlying this diversity. The single cell genome sequencing technique will be employed to obtain partial genome sequences of 48 single cells from various uncultivated Roseobacter lineages. This will add valuable information regarding the metabolic diversity of planktonic Roseobacters, most of which remain uncultivated. In addition, new bioinformatic software will be developed to study the macroevolutionary pattern explaining the difference in major genomic traits such as genome size and G+C content between cultured and uncultivated Roseobacter lineages. Finally, genomes of 100 cultured Roseobacter strains varying at the strain level will be sequenced, and a variety of population genomic approaches will be used to investigate the microevolutionary mechanisms and environmental factors shaping the genetic diversity of incipient populations.

玫瑰杆菌是海洋中丰度最广的细菌之一，也是全球碳和硫循环的重要驱动者。目前对60多个可培养的菌株和4株未培养成员的基因组序列分析表明，玫瑰杆菌在基因组的大小，GC含量，以及功能基因等方面显示了及其高的多样性。目前尚不清楚产生高多样性的生态和进化机制。此申请项目旨在进一步了解海洋浮游态玫瑰杆菌的遗传多样性，并且阐明产生高多样性背后的机制。申请者将利用单细胞基因组学技术获得48个玫瑰杆菌单细胞的基因组序列。这将提供浮游态玫瑰杆菌代谢多样性的信息。此外，申请者团队将开发新的生物信息学软件，研究玫瑰杆菌的宏观进化模式，以此来解释玫瑰杆菌不同谱系，特别是可培养与未培养的菌之间存在的基因组特征上的巨大差异。最后，申请者将测定100株可培养的浮游态玫瑰杆菌的基因组，这些菌株在进化关系上及其相近，将通过群体基因组学的方法来研究微观进化机制和探讨环境因素导致的在种群处于初期分化阶段产生的遗传多样性。

开发了基于自发突变速率的分子定年方法并应用于玫瑰杆菌类群。传统的DNA分子定年的方法必须依赖于化石。通俗的讲，要估算一个系统发育树中物种的分化时间，至少有一个祖先节点发生的时间范围是已知的。这对于蓝细菌和很多真核生物较易做到，但是异养细菌（如海洋玫瑰杆菌）并没有谱系特有的化石。要对它们的系统发育树进行定年，往往需要依赖于蓝细菌的化石。当系统发育树包含了蓝细菌，分子定年的成熟软件就可以把该树中玫瑰杆菌的出现和分化时间计算出来。这类方法的缺点是玫瑰杆菌与蓝细菌的亲缘关系太远，难以预计预测年代的准确性。申请人团队开发了一种基于自发突变速率（μ）的且完全独立于化石校正的方法来定年。目前用基于这个新方法和基于蓝细菌化石分别推断出来的时间区间有很大的交集，表明这个新方法是合理的且有潜力推广到其它类型的细菌中。..发现了长期的碳限制是部分玫瑰杆菌基因组向高GC含量演化的驱动因子。表层海水普遍缺氮，同时表层海水中由携带低GC含量基因组的细菌占主导。这个重要的关联经常被生态学家解释为一种环境适应性，因为GC比AT碱基对多用氮素。换句话说，朝着低GC含量的基因组的进化被认为是细菌在海洋中的主要适应途径，但生态学家无法解释富含GC的细菌在该环境中也普遍存在。一个典型的例子就是在全球海洋中丰度很高的玫瑰杆菌类群，其绝大部分成员的GC含量都在50-65%之间。申请人联合数学模型专家Ferdi Hellweger博士，通过设计agent-based model，量化了多种中性和自然选择因子对玫瑰杆菌类群中富含GC的模式菌株Ruegeria pomeroyi DSS-3基因组中GC含量演化的贡献。模拟显示，通过实验测得的倾向于GC的自发突变不足以演化出现代海洋中富含GC的DSS-3基因组，只有DSS-3及其祖先在主要受碳限制的海洋环境中不断演化而来。