Mant Dina, Orevi Tomer, Kashtan Nadav
Institute of Environmental Sciences, Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food, and Environment, Hebrew University, Rehovot 76100, Israel.
ISME J. 2025 Jan 2;19(1). doi: 10.1093/ismejo/wrae256.
Microbial communities thrive in virtually every habitat on Earth and are essential to the function of diverse ecosystems. Most microbial habitats are not spatially continuous and well-mixed, but rather composed, at the microscale, of many isolated or semi-isolated local patches of different sizes, resulting in partitioning of microbial populations into discrete local populations. The impact of this spatial fragmentation on population dynamics is not well-understood. Here, we study how such variably sized micro-habitat patches affect the growth dynamics of clonal microbial populations and how dynamics in individual patches dictate those of the metapopulation. To investigate this, we developed the μ-SPLASH, an ecology-on-a-chip platform, enabling the culture of microbes in microscopic landscapes comprised of thousands of microdroplets, with a wide range of sizes. Using the μ-SPLASH, we cultured the model bacteria Escherichia coli and based on time-lapse microscopy, analyzed the population dynamics within thousands of individual droplets. Our results reveal that growth curves substantially vary with droplet size. Although growth rates generally increase with drop size, reproductive success and the time to approach carrying capacity, display non-monotonic patterns. Combining μ-SPLASH experiments with computational modeling, we show that these patterns result from both stochastic and deterministic processes, and demonstrate the roles of initial population density, patchiness, and patch size distribution in dictating the local and metapopulation dynamics. This study reveals basic principles that elucidate the effects of habitat fragmentation and population partitioning on microbial population dynamics. These insights deepen our understanding of natural microbial communities and have significant implications for microbiome engineering.
微生物群落几乎在地球上的每一个栖息地都蓬勃发展，并且对于多样生态系统的功能至关重要。大多数微生物栖息地在空间上并非连续且充分混合，而是在微观尺度上由许多不同大小的孤立或半孤立的局部斑块组成，这导致微生物种群被分割成离散的局部种群。这种空间碎片化对种群动态的影响尚未得到充分理解。在此，我们研究这种大小可变的微生境斑块如何影响克隆微生物种群的生长动态，以及单个斑块中的动态如何决定集合种群的动态。为了研究这一点，我们开发了μ-SPLASH，一个芯片上的生态学平台，能够在由数千个具有广泛大小范围的微滴组成的微观景观中培养微生物。使用μ-SPLASH，我们培养了模式细菌大肠杆菌，并基于延时显微镜分析了数千个单个微滴内的种群动态。我们的结果表明，生长曲线随微滴大小显著变化。尽管生长速率通常随液滴大小增加，但繁殖成功率和接近承载能力的时间呈现非单调模式。将μ-SPLASH实验与计算建模相结合，我们表明这些模式是由随机和确定性过程共同导致的，并证明了初始种群密度、斑块性和斑块大小分布在决定局部和集合种群动态中的作用。这项研究揭示了阐明栖息地碎片化和种群分割对微生物种群动态影响的基本原理。这些见解加深了我们对自然微生物群落的理解，并对微生物组工程具有重要意义。
