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

在许多生态系统中，微生物在生物膜中自我组织，生物膜是生物聚合物的复杂混合物，如蛋白质、DNA或多糖、胞外聚合物(EPS)。EPS为嵌入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)对其细菌宿主的访问也受到生物膜的限制，生物膜也对其感染率产生影响。然而，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，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。在生物膜中，EPS形成一个紧密的网络，减缓颗粒的扩散--也减缓噬菌体的扩散。尤其是多糖组分决定了生物膜的粘弹性稳定性和网络性。我们项目的目标是分析以多糖为主的生物膜中噬菌体的感染情况。许多噬菌体，作为其尾巴的一部分，含有糖苷酶，这种酶可以裂解EPS多糖(解聚酶)，从而主动降低生物膜的稳定性。到目前为止，还没有关于这些解聚酶对生物膜内噬菌体感染动态的影响的系统研究。欧文氏菌属的植物病原体，如苹果树上大火疫病的病原菌淀粉芽孢杆菌，形成了基于粘性多糖的生物膜，我们将在我们的研究中使用这些生物膜来分析欧文氏噬菌体的感染行为。荧光相关光谱(FCS)是一种很好地跟踪噬菌体颗粒在生物膜中扩散的高时空分辨率的方法。我们将使用FCS来研究欧文氏噬菌体在生物膜中的迁移率和感染率，并将这些数据纳入种群动力学的理论模型，特别是在解聚酶存在的情况下，分散生物膜。解聚酶很可能在生物膜中存在的不同噬菌体的混合物中发挥协同作用。为此，完整和可靠地鉴定病毒基因组中的糖-生物膜解聚酶是非常重要的。由于它们的模块化架构，这就需要我们将在本项目中开发的解聚酶注释的新算法。我们将利用它们来筛选新的病毒解聚酶的元基因组，以更深入地了解生物膜中噬菌体与宿主的关系。此外，新的生物膜解聚酶的发现对于生物技术来说是非常可取的，因为它是有效地对抗生物膜形成病原体的抗菌剂。

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.