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

原绿球藻于1988年首次被发现，现在被认为是海洋中最丰富的光合细胞，并负责全球初级生产力的很大一部分。原绿球藻可以说是迄今为止研究得最好的海洋微生物之一，它是一个很好的模型系统，可以促进我们对微生物生态学的理解。它由一系列基因和生理上不同的种群组成，这些种群共存，并沿着可量化的光、温度和无机营养梯度差异分布。早期的生理研究表明，这群蓝藻不能吸收硝酸盐，而硝酸盐通常是开阔海洋中最丰富的无机氮源。原绿球藻的前12个基因组序列都缺乏硝酸盐同化所需的基因，支持了这一观察结果。原绿球藻中缺乏这些基因令人困惑，因为密切相关且共同发生的聚球藻细胞具有这些基因，并且氮有效性可能是海洋生态系统初级生产的重要限制因素。我们的认识在2009年发生了变化，在野生原绿球藻基因组中发现了硝酸盐同化基因，并分离出了一株能够在硝酸盐上生长的无菌菌株（未发表的数据）。这一发现引发了作为该项目的主题的首要问题：-野生原绿球藻元种群的哪个子集包含硝酸盐同化基因以及该亚种群的动态如何随时间和空间变化？-环境的哪些特征选择了具有这种功能特征的细胞？-硝酸原绿球藻同化基因的系统发育与当地环境的关系更好，还是与原绿球藻16S-23S ITS整体系统发育的关系更好？-含有硝酸盐同化基因的细胞基因组是否具有特定的特征？它们告诉了我们什么其他环境变量影响硝酸盐同化细胞的适应性？-在特定菌株中同化基因的丧失或获得背后的生理权衡是什么？这些问题将使用综合的跨尺度方法来描述原绿球藻在群体、细胞和基因组水平上的硝酸盐同化。具体而言，将在两个不同的开放海洋时间序列站（HOT和BATS）和大西洋（AMT）沿纵向梯度测量硝酸盐同化原绿球藻的分布和丰度。该项目将研究硝酸盐同化的调节，硝酸盐的生长动力学，以及原绿球藻在氮限制条件下与聚球藻竞争的能力。此外，他们将使用培养独立的单细胞基因组学方法来评估几种核糖型基因组背景下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性状的生物地理学的理解，它是如何通过选择形成的，以及种内功能多样性在原绿球藻整体种群动态中的作用。更广泛的影响：pi将利用麻省理工学院提供的几种途径与代表性不足的群体合作。这些包括：麻省理工学院夏季研究项目，CONVERGE（周末预览）；SEED（周六教育项目）；KEYs（一个针对女孩的项目），以及麻省理工学院埃杰顿中心（MIT Edgerton Center），该中心为当地K-12班的学生提供便利。PI致力于向广大受众传播科学。例如，Chisholm已经出版了一本关于光合作用的儿童书籍（Living Sunlight, Scholastic），目前正在编写关于海洋食物网的续集。她的作品曾被美国国家公共电台、麻省理工学院世界和微世界报道。Berube参与了SEA-IT-LIVE项目，拍摄了一系列记录片，目的是向公众宣传船上海洋学研究。Berube将参加2011年秋季举行的COMPASS科学传播研讨会。该项目的提案主要由所涉及的博士后设计和撰写，这项工作将在他的专业发展中发挥核心作用。该项目的数据将发布在一个公共网站上：原绿球藻门户网站（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/).