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

硝酸盐同化和原绿球藻生态学：模型海洋光养生物种内多样性的特征和意义

• 批准号: 1153588
• 负责人: Sallie Chisholm
• 金额: $ 80.32万
• 依托单位: Massachusetts Institute of Technology
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-02-01 至 2018-01-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1153588&HistoricalAwards=false
• 关键词: Nitrate; Assimilation; Ecology; Prochlorococcus; Features

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assimilation genes in wild Prochlorococcus genomes and the isolation of an axenic strain capable of growth on nitrate (unpublished data).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/).

ProChorococus于1988年首次发现，现在被认为是海洋中最丰富的光合细胞，并且负责大量全球主要生产力。可以说，迄今为止，研究最熟悉的海洋微生物之一是，占地氯环菌是一种模型系统，可以促进我们对微生物生态学的理解。它由遗传和生理上不同种群的集合组成，这些种群共存并沿着可量化的光，温度和无机养分差异分布。早期使用培养的分离株的生理研究表明，这组蓝细菌无法吸收硝酸盐，通常是开阔的海洋中最丰富的无机氮来源。这一观察结果得到了前12个基因组序列的基因组序列，这些基因缺乏硝酸盐同化所需的基因。考虑到密切相关的，同时发生的，合子菌细胞具有它们，并且氮的可用性可能是海洋生态系统初级生产的重要限制因素，因此缺乏这些基因令人困惑。我们的理解在2009年发生了变化，随着野生核球菌基因组中硝酸盐同化基因的发现以及能够在硝酸盐上生长的轴突菌株的分离（未发表的数据）。这一发现导致了该项目的总体问题： - 野生中的核球菌元群体的哪个子集包含硝酸盐同化基因，并且该子群的动态在时间和空间上的动态如何有所不同？ - 这种功能性特征在环境中选择哪些环境特征？ - 硝酸盐同化基因的系统发育是否与局部环境或整体16S-23S更好地相关？他们告诉USABOUT哪些其他环境变量会影响硝酸盐相类似细胞的适应性？ - 特定菌株的损失或获得的损失或获得的生理方案是什么？这些问题将使用综合跨尺度方法来解决这些问题，以表征甲氯环球菌对种群，细胞和基因组水平的硝酸盐同化。具体而言，将在两个对比的开海时站（热和蝙蝠）以及沿大西洋（AMT）的纵向梯度（AMT）的两个对比的开海时站（AMT），在两个对比的开海时站（AMT）上测量硝酸盐的分布和丰度。 PI将检查硝酸盐同化，硝酸盐生长动力学的调节以及在氮限制条件下与氯环菌与综合赛竞争的能力。此外，他们将使用独立的培养单细胞基因组学方法来评估几种核糖型基因组环境中硝酸盐同化基因的系统发育多样性。这些研究将促进我们了解微生物中功能性状的生物地理学，如何通过选择来塑造它的作用以及物种内部功能多样性在prococcus的总体人口动力学中的作用。Boader的影响：PIS将利用MIT可用的几种途径来与不足的组合群体一起使用。其中包括：麻省理工学院夏季研究计划，汇聚（预览周末）；种子（星期六教育计划）； Keys（女孩计划）和MIT Edgerton中心，可促进当地K-12班的访问。 PI致力于向广泛的受众传达科学。例如，Chisholm出版了一本有关光合作用的儿童读物（Living Sunlight，Scholastic），目前正在续集有关海洋食品网。她的作品已在NPR，Mitworld和Microbeworld上发表。 Berube参加了Sea-It-Live项目的拍摄纪录片系列，旨在对公众进行有关船上海洋学研究的教育。 Berube将于2011年秋季参加指南针科学传播研讨会。该项目的提议主要由参与后的大多数人设计和撰写，这项工作将在其专业发展中发挥核心作用。该项目产生的数据将发布在公共网站上：ProChlorococus Portal（http://proportal.mit.edu/）。