Cell-cell interactions and the development of bacterial communities

项目摘要 在自然界中，细菌主要生活在群落中，特别是生物膜，其表面附着 包埋在细胞外基质中的细胞群落。细菌有很多优势 采用这种共同的生活方式，包括粘附表面，耐抗生素， 捕食和集体处理营养源。从人类的角度来看，生物膜可以是 有益的，例如在废水处理和生物修复的情况下。然而，生物膜可以 也是有问题的，例如生物膜在医学中引起重大问题，因为它们导致慢性感染， 并且在工业中生物膜污染表面并堵塞过滤装置。因为生物膜是三层 多维的，异质的，并随着时间的推移重新排列，迄今为止的调查已限于 当仅存在少数细胞时生物膜形成的光学研究或生物膜的总体表征 整个结构。我们最近取得了突破性进展，将单个细胞分解为活的、生长的生物膜 高达30微米的深度，使用定制的旋转盘共聚焦显微镜，荧光 报告员和自动细胞分割软件。生物膜可以从创始细胞克隆形成， 由许多独立的细胞聚集而成。在第一种情况下，我们对成熟生物膜的分析， 一个单一的创始人细胞的模式病原体霍乱弧菌，揭示了一个惊人的转变， 从无序的细胞发展到定向有序的细胞状态。第二种情况，我们 发现大肠杆菌的自动聚集依赖于对群体感应信号的趋化性 由细胞自身产生、检测和消耗。了解这些对比 发展过程及其对健康和工业的影响需要更深层次的机制 认识为此，我们将联合收割机生物物理建模与实验相结合，探讨其作用 在微生物群落的发展过程中，细胞与细胞之间的物理和化学相互作用。 在实验上，我们将扩展我们对霍乱弧菌和大肠杆菌的研究。包括工程信号 和基质生产突变体，我们将探索细胞异质性的殖民地内使用抗体 标记和荧光报告菌株。从理论上讲，我们的方法将联合收割机- 基础和连续模型。基于代理的建模将集中在订购过程中的单细胞行为 和聚合过程。连续体建模，包括线虫动力学的实质性扩展 理论来描述3D生物膜生长，将捕获长距离和长时间的行为。我们预计 从这项研究中获得的见解和我们开发的适用于细菌的建模工具， 在广泛的生物体和条件下的社区发展。

PROJECT ABSTRACT In nature, bacteria primarily live in communities, specifically biofilms, which are surface-attached communities of cells embedded in an extracellular matrix. There are many advantages for the bacteria that adopt this communal lifestyle including adhesion to surfaces, resistance to antibiotics and predation, and collective processing of nutrient sources. From a human perspective, biofilms can be beneficial, e.g. in the context of waste-water processing and bioremediation. However, biofilms can also be problematic, e.g. biofilms cause major problems in medicine as they lead to chronic infections, and in industry biofilms foul surfaces and clog filtration devices. Because biofilms are three dimensional, heterogeneous, and rearrange over time, to date investigations have been limited to optical studies of biofilm formation when only a few cells are present or to gross characterization of the entire structure. We recently made a breakthrough, resolving individual cells in living, growing biofilms up to a depth of 30 microns, using customized spinning-disk confocal microscopy, fluorescent reporters, and automated cell-segmentation software. Biofilms can form clonally from a founder cell or by aggregation of many independent cells. In the first case, our analysis of a mature biofilm, grown from a single founder cell of the model pathogen Vibrio cholerae, revealed a striking transition during biofilm development from disordered cells to an orientationally ordered nematic state. In the second case, we found that autoaggregation of Escherichia coli relies on chemotaxis to a quorum-sensing signal produced, detected, and consumed by the cells themselves. Understanding these contrasting developmental processes and their ramifications for health and industry requires deeper mechanistic understanding. To this end, we will combine biophysical modeling with experiments to explore the role of cell-cell interactions, both physical and chemical, in the development of microbial communities. Experimentally, we will extend our studies of both V. cholerae and E. coli to include engineered signal and matrix-production mutants, and we will explore cellular heterogeneity within colonies using antibody labeling and fluorescent-reporter strains. On the theoretical side, our approach will combine agent- based and continuum models. Agent-based modeling will focus on single-cell behavior during ordering and aggregation processes. Continuum modeling, including a substantial extension of nematodynamics theory to describe 3D biofilm growth, will capture behavior over long distances and times. We expect the insights gained from this study and the modeling tools we develop to be applicable to bacterial community development over a wide range of organisms and conditions.