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，负责全球初级生产力的很大一部分。可以说是迄今为止研究得最好的海洋微生物之一，原绿球藻是一个很好的模型系统，以促进我们对微生物生态学的理解。它是由一个集合的遗传和生理上不同的种群共存，并有差异地分布沿着可量化的梯度的光，温度和无机营养。早期的生理学研究表明，这组蓝细菌不能同化硝酸盐，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绿球藻前12个基因组序列的支持，它们都缺乏硝酸盐同化所必需的基因。原绿球藻中缺乏这些基因是令人困惑的，因为密切相关的，共同发生的，聚球藻细胞有它们，氮的可用性可能是海洋生态系统初级生产的一个重要限制因素。2009年，随着野生原绿球藻基因组中硝酸盐同化基因的发现和能够在硝酸盐上生长的纯菌株的分离，我们的理解发生了变化（未发表的数据）。这一发现导致了作为该项目主题的首要问题：-野生原绿球藻集合种群的哪个子集包含硝酸盐同化基因，以及该亚群的动态如何在时间和空间上变化？环境的哪些特征选择了具有这种功能特征的细胞？- 原绿球藻硝酸盐同化基因的遗传与当地环境或原绿球藻的整体16 S-23 S ITS遗传相关性更好吗？含有硝酸盐同化基因的细胞的基因组是否具有共同的特征？他们告诉我们什么其他环境变量影响硝酸盐同化细胞的适应性？- 在特定的品系中，同化基因的丧失或获得背后的生理权衡是什么？这些问题将得到解决，使用综合跨尺度的方法来表征硝酸盐同化原绿球藻在人口，细胞和基因组水平。具体而言，硝酸盐同化原绿球藻的分布和丰度将在两个对比开阔的海洋时间序列站（HOT和BATS），并沿着在大西洋（AMT）的纵向梯度进行测量。PI将研究硝酸盐同化的调节、硝酸盐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，他们将使用独立于培养的单细胞基因组学方法来评估几种核糖体基因组背景下硝酸盐同化基因的系统发育多样性。这些研究将推进我们的理解微生物的功能性状，它是如何形成的选择，和物种内的功能多样性在原绿球藻的整体人口动态的作用的微生物学。更广泛的影响：PI将利用几个途径可在麻省理工学院与代表性不足的群体。其中包括：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（女孩项目），以及麻省理工学院埃杰顿中心，该中心方便当地K-12班级的访问。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读物（《活的阳光》，Scholastic出版），目前正在撰写关于海洋食物网的续集。她的作品曾在NPR，MITWorld和MicrobeWorld上展出。Berube参与了SEA-IT-LIVE项目，拍摄了一系列纪录片，旨在教育公众了解船上海洋学研究。Berube将参加2011年秋季的COMPASS科学交流研讨会。该项目的建议书主要由博士后设计和撰写，这项工作将在他的专业发展中发挥核心作用。该项目产生的数据将张贴在一个公共网站上：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/).