Abstract：
The bacterial diseases black leg and soft rot in potatoes cause heavy losses of potatoes worldwide. Bacteria within the genus Pectobacteriaceae are the causative agents of black leg and soft rot. The use of antibiotics in agriculture is heavily regulated and no other effective treatment currently exists, but bacteriophages (phages) have shown promise as potential biocontrol agents. In this study we isolated soft rot bacteria from potato tubers and plant tissue displaying soft rot or black leg symptoms collected in Danish fields. We then used the isolated bacterial strains as hosts for phage isolation. Using organic waste, we isolated phages targeting different species within Pectobacterium. Here we focus on seven of these phages representing a new genus primarily targeting P. brasiliense; phage Ymer, Amona, Sabo, Abuela, Koroua, Taid and Pappous. TEM image of phage Ymer showed siphovirus morphotype, and the proposed Ymer genus belongs to the class Caudoviricetes, with double-stranded DNA genomes varying from 39 kb to 43 kb. In silico host range prediction using a CRISPR-Cas spacer database suggested both P. brasiliense, P. polaris and P. versatile as natural hosts for phages within the proposed Ymer genus. A following host range experiment, using 47 bacterial isolates from Danish tubers and plants symptomatic with soft rot or black leg disease verified the in silico host range prediction, as the genus as a group were able to infect all three Pectobacterium species. Phages did, however, primarily target P. brasiliense isolates and displayed differences in host range even within the species level. Two of the phages were able to infect two or more Pectobacterium species. Despite no nucleotide similarity with any phages in the NCBI database, the proposed Ymer genus did share some similarity at the protein level, as well as gene synteny, with currently known phages. None of the phages encoded integrases or other genes typically associated with lysogeny. Similarly, no virulence factors nor antimicrobial resistance genes were found, and combined with their ability to infect several soft rot-causing Pectobacterium species from Danish fields, demonstrates their potential as biocontrol agents against soft rot and black leg diseases in potatoes.
摘要：
马铃薯中的细菌性疾病黑腿和软腐病导致全世界马铃薯的重大损失。鸡杆菌属中的细菌是黑腿和软腐病的病原体。抗生素在农业中的使用受到严格管制，目前没有其他有效的治疗方法存在，但是噬菌体（噬菌体）已显示出作为潜在生物控制剂的希望。在这项研究中，我们从丹麦田地中收集的马铃薯块茎和植物组织中分离出软腐病菌，这些细菌表现出软腐病或黑腿症状。然后我们使用分离的细菌菌株作为噬菌体分离的宿主。使用有机废物，我们分离了针对感染杆菌内不同物种的噬菌体。在这里，我们专注于这些噬菌体中的七个，这些噬菌体代表了主要针对巴西疟原虫的新属；噬菌体Ymer，阿莫纳,萨博,Abuela,Koroua,Taid和Pappous。噬菌体Ymer的透射电镜图像显示，拟议的Ymer属属于Caudoviricetes类，双链DNA基因组从39kb到43kb不等。在使用CRISPR-Cas间隔区数据库进行的计算机宿主范围预测中，两种情况都表明了巴西假单胞菌，P.polris和P.P.作为拟建Ymer属内噬菌体的天然宿主。以下主机范围实验，使用来自丹麦块茎和有软腐病或黑腿病症状的植物的47种细菌分离株，验证了计算机寄主范围的预测，作为一个群体，该属能够感染所有三个感染杆菌属物种。噬菌体确实如此，然而,主要针对巴西假单胞菌分离株，即使在物种水平上也显示出宿主范围的差异。其中两个噬菌体能够感染两个或更多个感染细菌物种。尽管与NCBI数据库中的任何噬菌体没有核苷酸相似性，提出的Ymer属在蛋白质水平上确实有一些相似性，以及基因同质性，目前已知的噬菌体。没有噬菌体编码整合酶或其他通常与溶源性相关的基因。同样，没有发现毒力因子或抗菌素耐药基因，并结合它们感染丹麦田地中几种软腐烂的淋病杆菌的能力，证明了它们作为抗马铃薯软腐病和黑腿病的生物防治剂的潜力。
