Maintenance and evolution of cooperation in synthetic microbial ecosystems

微生物种群中合作特性（如公共产品的生产）的出现，以及它们在搭便车者的存在下的维持，是进化生物学的一个核心问题。在第一个资助期，我们将实验与理论相结合，重点研究非选择性和选择性条件下人口统计学噪声对合作细菌种群生长动态和组成的影响。我们发现，在非选择条件下，不断增长的种群从不固定于一种特征，而是适应随机的稳定状态组成。在选择性条件下，我们通过实验验证了我们的理论预测，即人口噪声导致公共产品生产者在人口集合中的比例短暂增加。为此，我们建立了一个合成生态系统，并确定了假单胞菌群体合作行为的实验条件。此外，我们发现假单胞菌群体中pyoverdine合成基因的表达具有表型异质性，并受到铁有效性的调节。在即将到来的资助期内，我们打算扩大项目的范围，并沿着两条主要研究路线进行研究。(1)首先，我们将对pyoverdine生产和消费的基因调控机制及其对生产菌株和非生产菌株生长速度的影响进行更机械的分子理解。以往的理论模型部分忽略了累积吡啶和生长阶段对铁载体产生的影响。我们将扩展这些模型来解释这一特征，并对外部pyoverdine对生产者和非生产者菌株生长动态的影响进行定量分析。此外，我们计划揭示p.p putida产生和调控pyoverdine的分子机制。具体来说，我们将分析假定的个体调节回路，并将其活性与各种铁可用性条件下的代谢状态和吡啶生产联系起来。这些分析将提供调控网络的全面图景和不同环境下细胞行为的信息。(2)其次，我们将考虑空间扩展系统，以了解空间结构是否以及如何影响合作行为。我们将研究公共物品的动态和监管的额外效应，以及细菌流动性的异质性如何影响合作行为的出现。我们的理论研究将依赖于晶格气体模型，我们将采用随机模拟和分析方法进行分析。实验将在两种不同的环境中进行：一种是固定的空间环境，可以不间断地扩展到新的地点，另一种是允许公共物品和细胞持续传播的结构化环境。在不同的生态条件下，分析共培养在空间和时间上的发展。

The emergence of cooperative traits (like production of public goods) in microbial populations and their maintenance in the presence of free-riders is a central problem in evolutionary biology. In the first funding period, our focus was on the effect of demographic noise on growth dynamics and composition of cooperative bacterial populations under non-selective and selective conditions, combining experiments and theory. We showed that under non-selective conditions, growing populations never fixate to a trait, but adjust to a random steady state composition. In selective conditions, we experimentally validated our theoretical prediction that demographic noise leads to a transient increase in the fraction of public good producers in an ensemble of populations. To this end, we established a synthetic ecosystem and identified experimental conditions for cooperative behavior in Pseudomonas populations. Moreover, we showed that the expression of pyoverdine synthesis genes is phenotypically heterogeneous in a Pseudomonas population, and is modulated by iron availability. In the upcoming funding period, we intend to broaden the scope of the project and proceed along two main lines of research. (1) First, we will develop a more mechanistic molecular understanding of gene regulatory mechanisms underlying pyoverdine production and consumption, as well as its effect on the growth rate of producer and non-producer strains. Previous theoretical models partially neglected the effects of accumulated pyoverdine and growth phase on siderophore production. We will extend these models to account for this feature and perform a quantitative analysis of the impact of external pyoverdine on growth dynamics of producer and non-producer strains. Moreover, we plan to unravel the molecular mechanisms of pyoverdine production and regulation in P. putida. Specifically, we will analyze the presumed individual regulatory circuits and relate their activity to the metabolic state and pyoverdine production under various conditions of iron availability. These analyses will provide a comprehensive picture of the regulatory network and information on cell behavior in different environments. (2) Second, we will consider spatially extended systems to understand whether and how spatial structuring impacts cooperative behavior. We will investigate how the additional effects of dynamics and regulation of the public goods, and heterogeneity in bacterial mobility affect the emergence of cooperative behavior. Our theoretical studies will rely on lattice gas models, which we will analyze employing stochastic simulations and analytic approaches. Experiments will be performed with producer/non-producer co-cultures in two distinct settings: a fixed spatial environment with discontinuous expansion to new sites, and a structured environment allowing continuous spreading of public good and cells. The development of the co-culture in space and time will be analyzed in various ecological conditions.