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，控制必需的养分流动，并编码巨大的遗传多样性。尽管从环境中获得了大量的基因组和宏基因组测序，但细菌种群遗传学的基础仍然定义不清：什么是细菌物种，它是否值得定义？在野外，突变率、重组率和自然选择率是多少？这些力量是如何相互作用形成细菌种群的？在这里，我建议将从自然环境和半自然的中观实验中取样的细菌分离物和宏基因组相结合，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。该提案旨在回答三个主要问题：1 .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（基因集合）是基本单位？Q2：细菌物种形成的早期阶段（生态分化）是如何在自然界中，在不同的环境和自然选择制度下进行的？问题3：是什么控制着自然界中细菌物种形成（或更广泛地说，多样化）的速率？我的团队（包括将通过拟议项目培训的18名HQP）将使用以下组合来解决这些问题：(i)公开可用的序列数据（例如，来自地球微生物组项目的序列数据，用于测试跨生物群落的竞争性多样化模型，以及来自人类肠道的FijiCOMP约40,000个移动基因集，用于测试群体遗传参数的变化主要是由移动基因家族还是由细菌宿主基因组驱动）；（ii）在我的实验室中对时间序列种群基因组进行测序（例如，尚普兰湖的开花蓝藻和魁北克不同树种的甲基细菌），以跟踪自然界的生态分化；（iii）受控的半自然中游系统：麦吉尔大学高ult自然保护区的大型池塘实验阵列（LEAP），在已知的选择压力（例如农药）下，可以用宏基因组学跟踪选择性扫描。的影响。物种通常被认为是进化的基本单位，然而细菌和其他微生物很难归为物种。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，这意味着如何最好地研究和设计微生物组。通过在自然环境下实时研究细菌的进化，这一建议将提高我们对细菌物种形成、其潜在机制和促进它的生态因素的理解。在更实用的层面上，我们的结果将为重要生态系统（如淡水、森林、人类肠道）的微生物基础如何响应环境变化（如酸化、农药污染、抗生素）的预测模型提供信息。

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).