Population genomics and ecotypic divergence in the most dominant lineage of marine bacteria

在地球沿海和开放海洋的上层水柱中，每毫升海水中大约有100万个微小的单细胞细菌，它们在推动营养循环和其他过程中发挥着重要作用，这些过程对这些系统对其他海洋生物的可居住性至关重要。有些海洋细菌与植物相似，因为它们利用来自太阳的能量将温室气体二氧化碳转化为有生命的物质，并产生氧气作为副产品，而另一些被称为化学异养生物的海洋细菌与人类和其他动物相似，因为它们消耗有机物和氧气，在生长过程中产生二氧化碳。虽然在显微镜下观察时，它们的大小和形状有限，但DNA测序等遗传技术已经揭示了海洋细菌自然群落中巨大的功能（即它们在做什么）和系统发育（即它们如何相关）生物多样性。尽管具有如此高的遗传多样性，但一组系统发育相关的化学异养细菌SAR11有时可以占全球海水系统中微生物细胞的50%以上；它被认为是地球上最丰富的生物之一，因此是海洋生态学的一个重要方面。虽然已知SAR11组由许多不同的“类型”组成，这些“类型”在位置、深度和时间上差异很大，但我们对区分不同类型的遗传编码特征知之甚少，也不知道遗传特征在组内是如何获得和失去的。本研究的目标是使用基因组学方法来理解形成我们星球上最丰富的生物群体之一的进化过程，并提高我们对形成自然微生物生物多样性的进化过程的理论理解。该项目将为一名博士后科学家和一名研究生提供先进的跨学科专业培训，并通过指导夏威夷原住民或太平洋岛屿血统的本科生进行实践研究和培训，增加代表性不足的群体在科学研究中的参与。研究结果将纳入一门关于比较基因组学和微生物进化的新大学课程。海洋微生物的培养收集也将扩大和保持，为其他海洋科学家提供宝贵的资源。该项目将利用最新的DNA测序技术和高通量灭绝培养方法来研究全球重要的海洋细菌谱系SAR11的同域种群的基因组进化特征。该项目的主要目标是了解在大型细菌种群（如SAR11）中形成基因组多样性的力量，并根据基因组学推断，确定这种多样性反映在种群之间功能差异的本质。SAR11细胞将从热带北太平洋和南太平洋以及亚极地北太平洋沿海的类似生态系统中分离出来，以研究地理距离与栖息地相似性对自由生活的浮游海洋细菌种群遗传学的影响。通过打开一个独特的基因组窗口，同时包含不同程度的遗传分化的SAR11谱系，本研究将有助于研究跨越宏观和微观进化过程之间连续体的进化动力学。关于本地SAR11种群遗传多样性产生、繁殖和去除机制的定量信息，也将有助于模拟SAR11和其他大型海洋浮游细菌种群在面对预测的气候引起的全球海洋变化时的命运。

In the upper water column of Earth's coastal and open oceans, roughly one million microscopic, single-celled bacteria inhabit each milliliter of seawater, where they play important roles in driving nutrient cycles and other processes that are vital to the habitability of these systems to other marine life. While some marine bacteria are similar to plants in that they use energy from the sun to transform the greenhouse gas carbon dioxide into living material and produce oxygen as a byproduct, other marine bacteria known as chemoheterotrophs are similar to humans and other animals in that they consume organic matter and oxygen, producing carbon dioxide as a consequence of their growth. Although they are limited in size and shape when observed under a microscope, genetic techniques such as DNA sequencing have revealed tremendous functional (i.e. what they are doing) and phylogenetic (i.e. how they are related) biodiversity in natural communities of marine bacteria. Despite this high genetic diversity, a single group of phylogenetically related chemoheterotrophic bacteria known as SAR11 can sometimes make up over 50% of the microscopic cells inhabiting seawater systems around the globe; it is considered one of the most abundant organisms on Earth and thus an important aspect of ocean ecology. While it is known that the SAR11 group consists of many distinct "types" that differ in abundance with location, depth and time, we know little about what genetically encoded features distinguish the different types, or how genetic characteristics are gained and lost within the group. The goal of this study is to use a genomics approach to understand the evolutionary processes that shape one of the most abundant groups of organisms on our planet, and to improve our theoretical understanding of the evolutionary processes that shape natural microbial biodiversity in general. This project will provide advanced, cross-disciplinary professional training for a postdoctoral scientist and a graduate student, and will increase the participation of underrepresented groups in scientific research by mentoring undergraduate students of native Hawaiian or Pacific Island ancestry in hands-on research and training. Results will be incorporated into a new university course offering on comparative genomics and microbial evolution. A culture collection of marine microorganisms will also be expanded and maintained, providing a valuable resource for other marine scientists.This project will take advantage of recent advances in DNA sequencing technology and a high throughput extinction culturing approach in order to investigate the evolutionary characteristics of genomes from sympatric populations of the globally important SAR11 marine bacterial lineage. The major objectives of this project are to understand the forces that shape genomic diversity in large bacterial populations such as SAR11, and to determine the nature by which this diversity is reflected in functional differences between populations, as inferred from genomics. SAR11 cells will be isolated from similar ecosystems in the tropical North and South Pacific, as well as the coastal ocean of the subpolar North Pacific, in order to investigate the effect of geographic distance versus habitat similarity on the population genetics of free-living, planktonic marine bacteria. By opening a unique genomic window that encompasses SAR11 lineages of varying degrees of genetic divergence simultaneously, this study will facilitate the investigation of evolutionary dynamics that spans a continuum between macro- and microevolutionary processes. Quantitative information regarding the mechanisms by which genetic diversity is generated, propagated, and removed from native SAR11 populations will also help efforts to model the fate of SAR11 and other large marine bacterioplankton populations in the face of predicted climate-induced changes to the global ocean.