Nitrate Assimilation and the Ecology of Prochlorococcus: Features and Implications of Intraspecific Diversity in a Model Marine Phototroph

原氯球菌于1988年首次被发现，现在被认为是海洋中最丰富的光合作用细胞，并对全球初级生产力的很大一部分负责。可以说是迄今为止研究得最好的海洋微生物之一，原氯球菌作为一个促进我们对微生物生态学的理解的模型系统发展得很好。它由一组遗传和生理上不同的种群组成，这些种群共存并沿着光、温度和无机营养的可量化梯度不同地分布。使用培养的分离物进行的早期生理研究表明，这组蓝藻无法同化硝酸盐，硝酸盐通常是开放海洋中最丰富的无机氮源。这一观察结果得到了原氯球菌前12个基因组序列的支持，这些基因组序列都缺乏硝酸盐同化所必需的基因。原氯球菌中缺乏这些基因令人费解，因为聚球藻细胞拥有这些基因，而且氮的有效性可能是海洋生态系统初级生产的一个重要限制因素。我们的理解在2009年发生了变化，在野生原氯球菌基因组中发现了硝酸盐同化基因，并分离出了一种能够在硝酸盐上生长的无菌菌株(未发表的数据)。这一发现引出了这个项目的主要问题：-野生原氯球菌属的哪个亚群含有硝酸盐同化基因，这个亚群的动态在时间和空间上是如何变化的？-具有这种功能特征的细胞选择了什么环境特征？-原氯球菌硝酸盐同化基因的系统发育与当地环境更相关还是与原氯球菌属的16S-23S的系统发育关系更好？-含有硝酸盐同化基因的细胞基因组有共同的特定特征吗？关于影响硝酸盐同化细胞适合性的其他环境变量，他们告诉了我们什么？-在特定菌株中，同化基因的丢失或获得背后的生理权衡是什么？这些问题将通过一个综合的跨尺度方法来解决，以在种群、细胞和基因组水平上表征原氯球菌对硝酸盐的同化作用。具体地说，硝酸盐同化原氯球菌的分布和丰度将在两个不同的开放海洋时间序列站(HOT和BATS)上测量，并沿着大西洋的纵向梯度(AMT)进行测量。PI将检查硝酸盐同化的调节，硝酸盐在硝酸盐上的生长动力学，以及原氯球菌在氮素限制条件下与聚球藻竞争的能力。此外，他们将使用一种独立于培养的单细胞基因组学方法，在几种核型的基因组背景下评估硝酸盐同化基因的系统发育多样性。这些研究将促进我们对微生物功能特征的生物地理学，它是如何由选择塑造的，以及种内功能多样性在原氯球菌总体种群动态中的作用的理解。广泛的影响：PI将利用麻省理工学院可用的几种途径与代表性不足的群体合作。其中包括：麻省理工学院暑期研究计划Converge(周末预览)；SEED(周六教育计划)；Keys(女孩计划)，以及MIT Edgerton中心，为当地K-12班的访问提供便利。PI致力于向广大受众传播科学。例如，奇泽姆出版了一本关于光合作用的儿童书籍(《活着的阳光》，《学术》)，目前正在写关于海洋食物网的续集。她的作品曾出现在NPR、MITWorld和MicrobeWorld上。贝鲁贝参与了SEA-IT-LIVE项目，拍摄了一系列纪录片，旨在教育普通公众了解船上的海洋研究。贝鲁贝将参加2011年秋季的指南针科学交流研讨会。这个项目的提案主要是由参与其中的博士后设计和撰写的，这项工作将在他的职业发展中发挥核心作用。该项目产生的数据将在一个公共网站上公布：原氯球菌门户网站(http://proportal.mit.edu/).

First discovered in 1988, Prochlorococcus is now recognized as the most abundant photosynthetic cell in the oceans and is responsible for a significant fraction of global primary productivity. Arguably one of the best studied marine microorganisms to date, Prochlorococcus is well-developed as a model system for advancing our understanding of microbial ecology. It is comprised of a collection of genetically and physiologically distinct populations that co-exist and are differentially distributed along quantifiable gradients of light, temperature, and inorganic nutrients. Early physiological studies using cultured isolates indicated that this group of cyanobacteria was unable to assimilate nitrate, typically the most abundant inorganic nitrogen source in the open ocean. This observation was supported by the first 12 genome sequences of Prochlorococcus which all lacked the genes necessary for nitrate assimilation. The lack of these genes in Prochlorococcus was puzzling given that closely related, and co-occurring, Synechococcus cells have them, and that nitrogen availability can be a significant limiting factor for primary production in marine ecosystems. Our understanding changed in 2009 with the discovery of nitrate assimilation genes in wild Prochlorococcus genomes and the isolation of an axenic strain capable of growth on nitrate (unpublished data). This discovery has lead to the overarching questions that are the subject of this project:- What subset of the Prochlorococcus meta-population in the wild contains nitrate assimilation genes and how do the dynamics of this sub-population vary in time and space?- What features of the environment select for cells with this functional trait? - Is the phylogeny of Prochlorococcus nitrate assimilation genes better correlated with the local environment or the overall 16S-23S ITS phylogeny of Prochlorococcus?- Do the genomes of cells that contain nitrate assimilation genes share specific features? What do they tell usabout what other environmental variables influence the fitness of nitrate-assimilating cells? - What are the physiological tradeoffs underlying the loss or gain of assimilation genes in particular strains?These questions will be addressed using an integrative cross-scale approach to characterize nitrate assimilation by Prochlorococcus at the population, cellular, and genomic levels. Specifically, the distribution and abundance of nitrate assimilating Prochlorococcus will be measured at two contrasting open ocean time-series stations (HOT and BATS), and along a longitudinal gradient in the Atlantic (AMT). The PI will examine the regulation of nitrate assimilation, the kinetics of growth on nitrate, and the ability of Prochlorococcus to compete with Synechococcus under nitrogen limiting conditions. Further, they will use a culture independent single cell genomics approach to assess the phylogenetic diversity of nitrate assimilation genes within the genomic context of several ribotypes. These studies will advance our understanding the biogeography of functional traits in microbes, how it is shaped by selection, and the role of intra-species functional diversity in the overall population dynamics of Prochlorococcus.Broader Impacts:The PIs will take advantage of several avenues available at MIT to work with under-represented groups. These include: the MIT Summer Research Program, CONVERGE (a preview weekend); SEED (a Saturday education program); KEYs (a program for girls), and the MIT Edgerton Center which facilitates visits from local K-12 classes. The PI is committed to communicating science to broad audiences. Chisholm, for example, has published a children's book on photosynthesis (Living Sunlight, Scholastic), and is currently working on the sequel about ocean food webs. Her work has been featured on NPR, MITWorld, and MicrobeWorld. Berube has participated with the SEA-IT-LIVE Project in the filming of a documentary series aimed at educating the general public about shipboard oceanographic research. Berube will participate in a COMPASS science communication workshop in Fall 2011. The proposal for this project was designed and written primarily by the post-doc involved, and the work will play a central role in his professional development. Data resulting from the project will be posted on a public web site: Prochlorococcus Portal (http://proportal.mit.edu/).