Microbial ecology of coexisting ecotypes: Are all Prochlorococcus equal?

原氯球菌是一种光合作用有机体，在海洋中极其丰富，并影响全球范围内的生物地球化学循环。该项目旨在将原氯球菌群落结构与现场初级生产力联系起来。已知的12种原氯球菌生态型表现出广泛的多样性。据认为，这种多样性允许原氯球菌群在光线、营养物质和温度的梯度上保持数量优势，这些梯度伴随着深度、季节和纬度的变化。我们认识上的一个很大的差距在于，我们应该通过原氯球菌的丰度来评估它的生态系统价值，还是通过它的群落结构来评估它的生态价值，或者两者兼而有之。生态系统模型赋予所有生态型相同的角色。然而，来自栽培菌株和野生种群的基因组和生理证据初步表明，不同的基因类型可能通过光和营养生理的变化以及与其他微生物的相互作用而对生态系统做出不同的贡献。这些分子水平的差异对原位初级生产力的影响尚不清楚。该项目通过测量不同生态型对初级生产力的贡献来测试是否绝对丰度或群落结构决定了原氯球菌对生物地球化学动态的贡献。该项目的结果将为生态系统模型提供信息，以更好地表示气候和原氯球菌多样性的变化将如何影响全球营养循环、营养级联以及与其他细菌、病毒和食草动物的相互作用。这项工作所描述的见解和方法将普遍适用于开放海洋中丰富的微生物种群的生态，如有色和无色真核生物、异养细菌和其他蓝藻谱系。对共存生态型之间的差异的基本理解将有助于理解所有微生物生态系统中生态型之间的合作、竞争和协作机制。研究人员将建立一个教学模块，通过虚拟海洋探索让高中生接触微生物海洋学、大数据和系统生物学。主要目标将是让学生们深刻认识到海洋中“看不见的微生物森林”的重要性。学生将在大型公开数据库的海洋数据的背景下，研究丰富的微生物种群的分布模式。高中教师和学生实习生、一名研究生、研究人员和一名教育专家将为全国范围内的课堂设计、实施和测试该模块。这项工作将遵循以前开发的成功的教育模式(系统教育经验-参见)。研究人员将解决一个重要的假设，即原氯球菌生态型作为初级生产者对生态系统的贡献不同。更具体地说，研究人员假设，共存的生态型之间细胞分裂和固碳的模式不同，这些差异是基因组内容、基因表达、环境条件和群落组成的函数。技术方法将涉及两个基于现场的实验，将在阿罗哈海洋站的三个不同深度进行，这三个深度的原氯球菌群落组成不同。实验1将检验共存的生态型在细胞分裂中是否有所不同，使用16SRRNA测序来量化G1、S和G2细胞中的生态型丰度。实验2将使用RNA稳定同位素探测和13C-碳酸氢盐孵育后富含13C的RNA的16S rRNA测序，研究共存生态型之间的碳固定如何变化。这些实验将在原生氯球菌群落中进行，并在原地条件下改变条件，以模拟其他深度的光和温度。在这两个实验中，将检查一组选定的碳固定和细胞分裂基因的时间基因表达，以将基因表达模式与初级生产力联系起来。所有数据都将与海洋环境有关，包括其物理、化学和生物特征。

Prochlorococcus is a photosynthetic organism that is tremendously abundant in the ocean and influences biogeochemical cycles on global scales. This project aims to link Prochlorococcus community structure to primary productivity in situ. The twelve known Prochlorococcus ecotypes exhibit extensive diversity. It is thought that this diversity allows the Prochlorococcus "collective" to maintain numerical dominance across gradients in light, nutrients, and temperature that accompany changes in depth, season, and latitude. A large gap in our understanding lies in whether we should assess the ecosystem value of Prochlorococcus by its abundance or by its community structure or both. Ecosystem models assign all ecotypes the same role. However, genomic and physiological evidence from cultivated isolates and wild populations suggests tentatively that distinct genotypes may contribute differently to the ecosystem through variation in light and nutrient physiologies and interactions with other microorganisms. The consequences of these molecular-level differences to primary productivity in situ are unknown. This project tests whether absolute abundance, or community structure, determines the contributions of Prochlorococcus to biogeochemical dynamics by measuring the contributions of different ecotypes to primary productivity. The results of this project will inform ecosystem models towards better representation of how shifts in climate and Prochlorococcus diversity will affect global nutrient cycles, trophic cascades, and interactions with other bacteria, viruses, and grazers. The insights and approaches delineated by this work will be generally applicable to the ecology of abundant microbial populations in the open ocean such as pigmented and non-pigmented eukaryotes, heterotrophic bacteria, and other cyanobacterial lineages. A basic understanding of differences between coexisting ecotypes will provide inroads into understanding mechanisms of cooperation, competition, and collaboration among ecotypes in all microbial ecosystems. The investigators will build a teaching module to expose high school students to microbial oceanography, big data, and systems biology through virtual ocean exploration. The primary objective will be to impress upon students the importance of an "invisible forest" of microorganisms in the ocean. Students will examine the distribution patterns of abundant microbial groups in the context of oceanographic data from large publically available databases. High school teachers and student interns, a graduate student, the investigators, and an educational specialist will design, implement, and test the module for classrooms nationwide. This effort will follow a successful education model (Systems Education Experience - SEE) developed previously.The investigators will address an overarching hypothesis that Prochlorococcus ecotypes vary in their contribution to the ecosystem as primary producers. More specifically, the investigators hypothesize that patterns of cell division and carbon fixation vary between coexisting ecotypes, and these differences are a function of genome content, gene expression, environmental conditions, and community composition. The technical approach will involve two field-based experiments will be applied to three different depths, at the oceanographic Station ALOHA, that differ in Prochlorococcus community composition. Experiment 1 will examine whether coexisting ecotypes vary in cell division, using 16S rRNA sequencing to quantify ecotype abundance in G1, S, and G2 cells. Experiment 2 will examine how carbon fixation varies between coexisting ecotypes using RNA-stable isotope probing and 16S rRNA sequencing of RNA enriched in 13C after incubation with 13C-bicarbonate. These experiments will be performed with Prochlorococcus communities under native in situ conditions and shifts in conditions to mimic light and temperature of other depths. In both experiments, the temporal gene expression of a selected set of carbon fixation and cell division genes will be examined to link gene expression patterns to primary productivity. All data will be related to the oceanographic environment including its physical, chemical, and biological features.