The origins of bacterial species and pangenomes in the wild

细菌和其他微生物占地球上活性生物量的一半以上，控制着必需的营养物质通量，并编码着巨大的遗传多样性。尽管环境中有丰富的基因组和宏基因组测序，但细菌群体遗传学的基础知识仍然定义不清：什么是细菌物种，它是否值得定义？突变、重组和自然选择的速率是多少？这些力量是如何相互作用来构建细菌种群的？在这里，我提出了从自然环境和半自然围隔实验中采样细菌分离株和宏基因组的组合，以改善细菌种群遗传学的经验基础，提供理论，实验室进化实验和自然世界之间的联系。该提案旨在回答三大类问题： Q1：细菌进化的基本单位是什么？在什么条件下个体基因相对于物种（基因的集合）是基本单位？ 问题2：细菌物种形成（生态分化）的早期阶段在自然界中是如何在不同的环境和自然选择机制中进行的？ 问题3：是什么控制了自然界中细菌物种形成（或更广泛的多样化）的速度？ 我的团队（包括通过拟议项目培训的18名HQP）将结合使用（i）公开可用的序列数据来解决这些问题（例如，来自地球微生物组项目，以测试生物群落中相互竞争的多样化模型，以及斐济COMP的约40个，000个来自人类肠道的移动的基因，以测试群体遗传参数的变化是否主要由移动的基因家族或细菌宿主基因组驱动），（ii）在我的实验室中测序的时间序列种群基因组（例如，尚普兰湖中的水华形成蓝细菌和魁北克不同树种中的甲基杆菌），以跟踪自然界中的生态分化，以及（iii）受控的半自然围隔系统：麦吉尔大学高尔特自然保护区的大型实验性池塘阵列（LEAP），其中可以在已知的选择压力（例如杀虫剂）下用宏基因组学跟踪选择性扫描。 冲击物种通常被认为是进化的基本单位，但细菌和其他微生物很难归类为物种。在某些条件和时间尺度下，基因而不是物种可能是最相关的选择水平，这对如何最好地研究和设计微生物组具有影响。通过研究细菌在真实的时间和自然环境中的进化，这一提议将提高我们对细菌物种形成、其潜在机制以及促进细菌物种形成的生态因素的理解。在更应用的层面上，我们的结果将为重要生态系统的微生物基础如何预测模型提供信息。（例如淡水、森林、人类肠道）将对环境变化（例如酸化、农药污染、抗生素）作出反应。

Bacteria and other microbes account for over half the active biomass on Earth, control essential nutrient fluxes, and encode enormous genetic diversity. Despite an abundance of genomic and metagenomic sequencing from the environment, the basics of bacterial population genetics remain poorly defined: what is a bacterial species, and is it even worth defining? What are the rates of mutation, recombination, and natural selection in the wild and how do these forces interact to structure bacterial populations? Here I propose a combination of sampling bacterial isolates and metagenomes from natural environments and semi-natural mesocosm experiments to improve the empirical grounding of bacterial population genetics, providing a link between theory, laboratory evolution experiments, and the natural world. The proposal aims to answer three major sets of questions: Q1: What are the basic units of bacterial evolution? Under what conditions are individual genes versus species (ensembles of genes) the basic units? Q2: How do the early stages of bacterial speciation (ecological differentiation) proceed in nature, across different environments and regimes of natural selection? Q3: What controls rates of bacterial speciation (or diversification more broadly) in nature? My team (including 18 HQP to be trained through the proposed projects) will address these questions using a combination of (i) publicly available sequence data (e.g. from the Earth Microbiome Project to test competing diversification models across biomes, and the FijiCOMP set of ~40,000 mobile genes from the human gut to test whether variation in population genetic parameters is driven mainly by the mobile gene family or by the bacterial host genome), (ii) time series population genomes being sequenced in my lab (e.g. bloom-forming cyanobacteria in Lake Champlain and Methylobacterium across different tree species in Quebec) to track ecological differentiation in nature, and (iii) a controlled semi-natural mesocosm system: the Large Experimental Array of Ponds (LEAP) at the McGill University Gault Nature Reserve, where selective sweeps can be tracked with metagenomics under known selective pressures (e.g. pesticides). Impact. Species are generally considered the basic units of evolution, yet bacteria and other microbes are difficult to group into species. Under certain conditions and time scales, genes rather than species might be the most relevant level of selection, with implications for how best to study and engineer microbiomes. By studying bacterial evolution in real time and in natural setting, this proposal will improve our understanding of bacterial speciation, its underlying mechanisms, and the ecological factors that promote it. On a more applied level, our results will inform predictive models of how the microbial foundations of important ecosystems (e.g. freshwaters, forests, the human gut) will respond to environmental change (e.g. acidification, pesticide pollution, antibiotics).