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

项目总结 纳德尔实验室使用弧菌研究细菌生物膜的空间力学和群落动力学 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为模型 系统。虽然一些海洋弧菌物种会导致人类疾病，其中霍乱是历史上最常见的 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，我们用这些物种 了解活生物膜在细胞分辨率下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-细胞如何 互动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 而它们的组成有助于它们在急性和慢性感染中的作用，了解它们的机制 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，可能会导致对抗临床感染的新方法。在未来五年，我们将把重点放在 在生物膜领域中使用细胞分辨率成像得到最少关注的两个主要前沿 远远的。首先，到目前为止，还没有研究过温带噬菌体如何在高分辨率下与生物膜相互作用； 温带噬菌体可以放大和杀死敏感细菌，但它们也可以整合到细菌基因组中。 并与宿主细菌细胞一起被动扩增。这段噬菌体生活史在自然界和 在宿主微生物区系中，并且确实经常影响细菌的毒力。我们将在何时何地进行详细研究 这些温带噬菌体感染和杀死目标细菌，并在那里它们整合到宿主基因组中。 此外，我们将严格比较温带噬菌体和裂解噬菌体在 生物膜以了解这些根本不同的生活史策略如何影响噬菌体和细菌 适应现实环境。第二，绝大多数高分辨率生物膜研究都集中在 在营养介质流动下生长在玻璃上的生物膜。许多现实环境，包括海洋环境 弧菌并不是这么简单，生物膜生长在地形复杂的底物上，而且 营养物质直接来自下垫面，而不是周围的液体介质。我们将探索 这些复杂的地形环境通过培养多物种生物膜而产生的后果。 霍乱弧菌和副溶血性弧菌生长在虾壳几丁质颗粒上并消耗它们。这个系统将会 允许我们研究在自然基质上的多物种环境下的生长如何影响群落 建筑和动力学。最后，我们将严格测试现实的甲壳素环境对能力的影响 一种无处不在的细菌捕食者--细菌性蜈蚣弧菌，能够在一周内攻击和杀死猎物弧菌 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 洞察捕食性病毒和细菌物种如何杀死栖息在原本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.