It’s sweet to move on – bacteriophage infection and processing of glycan-based biofilms

在许多生态系统中，微生物以生物膜的形式组织起来，生物膜是蛋白质、DNA或多糖等生物聚合物的复杂混合物，即胞外聚合物（EPS）。EPS为包埋的细胞提供了有利的条件，并保护它们免受外部影响，例如抗生素。此外，细菌病毒（噬菌体）对它们的细菌宿主的访问受到生物膜的限制，这也对它们的感染率产生影响。尽管噬菌体介导的基因转移与形成生物膜的细菌群落的进化密切相关，但到目前为止，只有少数研究描述了噬菌体与生物膜的相互作用。在生物膜中，EPS形成了一个紧密的网络，减缓了颗粒扩散-也是噬菌体的扩散。特别是多糖组分负责生物膜的粘弹性稳定性和网络特征。我们的项目的目标是分析噬菌体感染聚糖为主的生物膜。许多噬菌体，作为其尾部的一部分，含有糖苷酶，这种酶切割EPS多糖（解聚酶），从而主动降低生物膜稳定性。迄今为止，还没有系统的研究这些解聚酶对噬菌体感染生物膜内的动力学的影响。amylovora，形成粘性聚糖为基础的生物膜，我们将在我们的研究中使用，以分析欧文氏菌的感染行为。荧光相关光谱（FCS）是一种非常适合的方法来跟踪噬菌体颗粒在生物膜中的扩散，具有高时空分辨率。我们将使用FCS研究噬菌体的流动性和感染率的欧文氏菌在生物膜，并将这些数据纳入人口动态的理论模型，特别是在解聚酶的存在下，消散的生物膜。解聚酶很可能也在生物膜中存在的不同底物的混合物中协同作用。为此，完全且可靠地鉴定病毒基因组中的聚糖-生物膜解聚酶是非常重要的。由于它们的模块化结构，这需要新的解聚酶注释算法，我们将在这个项目中开发。我们将使用它们来筛选新病毒解聚酶的宏基因组，以更深入地了解生物膜中的噬菌体-宿主关系。此外，新的生物膜解聚酶的发现对于生物技术作为抗生物膜形成病原体活性的抗微生物剂是高度期望的。

In many ecosystems, microorganisms organize themselves in biofilms, complex mixtures of biopolymers like proteins, DNA or polysaccharides, the extracellular, polymeric substance (EPS). The EPS offers advantageous conditions for the embedded cells and shields them against external influences, e.g. antibiotics. Also the access of bacterial viruses (bacteriophages) to their bacterial hosts is restricted by the biofilm that also has impact on their infection rate. However, so far only a few studies describe interactions of bacteriophages with biofilms, although phage-mediated gene transfer is intimately linked to the evolution of biofilm-forming bacterial communities.In the biofilm, the EPS forms a tight network that slows down particle diffusion – also that of bacteriophages. Especially the polysaccharide component is responsible for a biofilm’s viscoelastic stability and network character. Goal of our project is to analyze bacteriophage infection in glycan-dominated biofilms. Many bacteriophages, as part of their tails, contain glycosidases, enzymes that cleave the EPS polysaccharides (depolymerases) and thus actively reduce biofilm stability. So far, no systematic studies exist on the impact of these depolymerases on the dynamics of bacteriophage infection inside biofilms.Plant pathogens of the genus Erwinia, e.g. the causative agent of fire blight in apple trees, E. amylovora, form viscous glycan-based biofilms that we will use in our studies to analyze the infection behavior of Erwinia phages. Fluorescence correlation spectroscopy (FCS) is a well-suited method to follow diffusion of phage particles in biofilms with high spatiotemporal resolution. We will use FCS to study phage mobility and infection rates of Erwinia phages in biofilms and include this data into theoretical models of population dynamics, especially in the presence of depolymerases that dissipate the biofilm. Depolymerases most likely also act synergistically in mixtures of different phages present in a biofilm. For this it is highly important to completely and reliably identify glycan-biofilm depolymerases in viral genomes. Due to their modular architecture this necessitates new algorithm for depolymerase annotation which we will develop in this project. We will use them to screen metagenomes for new viral depolymerases, to gain a deeper understanding of phage-host relationships in biofilms. Moreover, the discovery of new biofilm depolymerases is highly desirable for biotechnology as antimicrobial agents active against biofilm-forming pathogens.