Table_2_Harnessing the genomic diversity of Pseudomonas strains against lettuce bacterial pathogens.XLSX

Lettuce is a major vegetable crop worldwide that is affected by numerous bacterial pathogens, including Xanthomonas hortorum pv. vitians, Pseudomonas cichorii, and Pectobacterium carotovorum. Control methods are scarce and not always effective. To develop new and sustainable approaches to contain these pathogens, we screened more than 1,200 plant-associated Pseudomonas strains retrieved from agricultural soils for their in vitro antagonistic capabilities against the three bacterial pathogens under study. Thirty-five Pseudomonas strains significantly inhibited some or all three pathogens. Their genomes were fully sequenced and annotated. These strains belong to the P. fluorescens and P. putida phylogenomic groups and are distributed in at least 27 species, including 15 validly described species. They harbor numerous genes and clusters of genes known to be involved in plant-bacteria interactions, microbial competition, and biocontrol. Strains in the P. putida group displayed on average better inhibition abilities than strains in the P. fluorescens group. They carry genes and biosynthetic clusters mostly absent in the latter strains that are involved in the production of secondary metabolites such as 7-hydroxytropolone, putisolvins, pyochelin, and xantholysin-like and pseudomonine-like compounds. The presence of genes involved in the biosynthesis of type VI secretion systems, tailocins, and hydrogen cyanide also positively correlated with the strains’ overall inhibition abilities observed against the three pathogens. These results show promise for the development of biocontrol products against lettuce bacterial pathogens, provide insights on some of the potential biocontrol mechanisms involved, and contribute to public Pseudomonas genome databases, including quality genome sequences on some poorly represented species.

生菜是全球范围内的重要蔬菜作物，可受到多种细菌性病原菌的侵染，包括莴苣黄单胞菌生菜致病变种（Xanthomonas hortorum pv. vitians）、菊苣假单胞菌（Pseudomonas cichorii）以及胡萝卜软腐果胶杆菌（Pectobacterium carotovorum）。目前针对该类病害的防治手段匮乏且效果往往不佳。为开发新型可持续的病原菌防控策略，本研究从农业土壤中分离得到1200余株植物相关假单胞菌（Pseudomonas）菌株，并针对它们对上述三种供试细菌性病原菌的体外拮抗活性进行了筛选。其中35株假单胞菌可显著抑制部分或全部三种病原菌，研究人员对这些菌株的基因组完成了全测序与注释。这些菌株隶属于荧光假单胞菌（P. fluorescens）和恶臭假单胞菌（P. putida）系统发育类群，分属至少27个物种，其中15个为已有效发表的物种。它们携带大量已知参与植物-细菌互作、微生物竞争及生物防治的基因及基因簇。相较于荧光假单胞菌类群菌株，恶臭假单胞菌类群菌株的平均拮抗活性更强。此类菌株携带有多数在荧光假单胞菌类群菌株中缺失的基因与生物合成基因簇，这些基因簇参与合成7-羟基托酚酮（7-hydroxytropolone）、假单胞溶菌素（putisolvins）、吡咯菌素（pyochelin）以及黄溶菌素类（xantholysin-like）、假单胞菌素类（pseudomonine-like）次生代谢产物。参与VI型分泌系统（type VI secretion systems）、尾菌素（tailocins）及氰化氢生物合成的基因的存在，也与菌株对三种病原菌的综合拮抗活性呈显著正相关。本研究结果为开发针对生菜细菌性病害的生物防治产品提供了潜在可能，阐明了部分潜在的生物防治机制，同时也为公共假单胞菌基因组数据库（涵盖部分代表性不足物种的高质量基因组序列）提供了宝贵的数据支撑。