Bacterial and Viral Predator-Prey Dynamics within Bacterial Biofilms at Cellular Resolution

项目摘要 纳德尔实验室研究细菌生物膜的空间力学和群落动态， 霍乱弧菌、副溶血性弧菌、大肠杆菌及其各自的细菌和病毒捕食者作为模型 系统.虽然一些海洋弧菌物种引起人类疾病，霍乱是历史上最严重的 重要的是，我的实验室不研究毒力机制或细菌致病机制。相反，我们利用这些物种 了解细胞分辨率下活生物膜的结构和群落动力学。大多数细菌 在自然界中产生表面结合的生物膜群落，但我们对细胞与细胞之间如何相互作用的了解少得惊人。 相互作用导致它们的更高层次的组成、架构和社区动态。由于生物膜结构 和组合物可以有助于它们在急性和慢性感染中的作用， 控制它们的结构和组成，特别是捕食性病毒和细菌如何攻击生物膜- 居住细胞，可能会导致新的方法来对抗临床感染。在未来五年，我们将专注于 因此，在生物膜领域中使用细胞分辨率成像的两个主要前沿领域受到的关注最少， 远了首先，迄今为止还没有研究如何在高分辨率下研究温带真菌与生物膜的相互作用; 温杆菌可以扩增并杀死易感细菌，但它们也可以整合到细菌基因组中 并随宿主细菌细胞沿着被动扩增。这种噬菌体生活史在自然界中非常重要， 在宿主微生物群中，确实经常影响细菌的毒力。我们将详细研究何时何地， 生物膜这些温和的细菌感染和杀死目标细菌，并在那里他们整合到宿主基因组。 此外，我们将严格比较温带和裂解性的繁殖动力学内 了解这些基本上不同的生活史策略如何影响噬菌体和细菌 在现实环境中的适应性。其次，绝大多数高分辨率生物膜研究都集中在 在营养培养基流动下在玻璃上生长的生物膜。许多现实的环境，包括海洋 弧菌不是这么简单的，它的生物膜生长在地形复杂的基质上， 直接从下面的表面而不是周围的液体介质中获得的营养物。我们将探讨 这些复杂的地形环境的后果，通过培养多物种生物膜的V。 霍乱弧菌和副溶血弧菌生长在虾壳甲壳素颗粒上并消耗这些颗粒。该系统将 使我们能够研究在自然基质上的多物种环境中生长如何影响群落 架构和动力学。最后，我们将严格测试现实的甲壳素环境如何影响能力， 噬菌蛭弧菌是一种普遍存在的细菌捕食者，它能够在一个小时内攻击并杀死弧菌猎物。 和多物种生物膜。我们的研究将沿着两个重要的新领域扩展，这两个领域都将产生 深入了解捕食性病毒和细菌物种如何杀死居住在其他受保护的生物膜中的猎物细菌。

PROJECT SUMMARY The Nadell lab studies the spatial mechanics and community dynamics of bacterial biofilms, using Vibrio cholerae, V. parahaemolyticus, Escherichia coli, and their respective bacterial and viral predators as model systems. While some marine Vibrio species cause human disease, with cholera being the most historically important, my lab does not study virulence mechanisms or bacterial pathogenesis. Rather, we use these species to understand the architectural and community dynamics of live biofilms at cellular resolution. Most bacteria produce surface-bound biofilm communities in nature, but we have strikingly little understanding of how cell-cell interactions lead to their higher order composition, architecture, and community dynamics. Since biofilm structure and composition can contribute to their role in acute and chronic infection, understanding the mechanisms controlling their structure and composition, and in particular how predatory viruses and bacteria attack biofilm- dwelling cells, may lead to novel approaches to fight clinical infections. Over the next five years we will focus on two major frontiers that have received minimal attention using cellular resolution imaging in the biofilm field thus far. First, no work thus far has examined how temperate phages interact with biofilms at high resolution; temperate phages can amplify and kill susceptible bacteria, but they can also integrate into the bacterial genome and amplify passively along with the host bacterial cell. This phage life history is widely important in nature and in host microbiota, and indeed often affects bacterial virulence. We will study in detail where and when within biofilms these temperate phages infect and kill target bacteria, and where they integrate into the host genome. Further, we will rigorously compare the propagation dynamics of temperate phages and lytic phages within biofilms to understand how these fundamentally distinct life history strategies influence phage and bacterial fitness in realistic environments. Second, the vast majority of high-resolution biofilm research has focused on biofilms grown on glass under flow of nutrient media. Many realistic environments, including those of marine Vibrio bacteria, are not this simple, with biofilms growing on topographically complex substrates, and with nutrients derived directly from the underlying surface rather than the surrounding liquid media. We will explore the consequences of these complex topographical environments by cultivating multispecies biofilms of V. cholerae and V. parahaemolyticus growing on and consuming particles of shrimp shell chitin. This system will permit us to study how growth in a multispecies context on naturalistic substrates influences community architecture and dynamics. Lastly, we will rigorously test how the realistic chitin environment influences the ability of a ubiquitous bacterial predator, Bdellovibrio bacteriovorus, is able to attack and kill Vibrio prey within single and multispecies biofilms. Our research will expand along two important new frontiers, both of which will yield insight into how predatory viral and bacterial species kill prey bacteria dwelling in otherwise protected biofilms.