Data_Sheet_1_Functional and Genomic Analysis of Rouxiella badensis SER3 as a Novel Biocontrol Agent of Fungal Pathogens.PDF

In recent decades, various bacterial species have been characterized as biocontrol agents for plant crop diseases; however, only a few genera have been predominantly reported in the literature. Therefore, the identification of new antagonists against phytopathogens is essential for boosting sustainable food production systems. In this study, we evaluated the role of strain SER3 from the recently discovered Rouxiella badensis as a biocontrol agent. SER3 was isolated from the phyllosphere of decaying strawberry fruit (Fragaria × ananassa) and showed different grades of antagonism against 20 fungal pathogens of berries, based on confrontation assays, due to the action of its diffusible and volatile compounds. These fungal pathogens were isolated from decayed strawberry, blackberry, and blueberry fruit and were characterized through internal transcribed spacer (ITS) sequencing and homology searches, exhibiting similarity with well-known postharvest pathogens such as Botrytis, Fusarium, Geotrichum, Mucor, Penicillium, Alternaria, and Botryosphaeria. Koch’s postulates were confirmed for most pathogens by reinfecting berry fruit. SER3 showed good capacity to inhibit the growth of Botrytis cinerea and Fusarium brachygibbosum in strawberry fruit, affecting mycelial development. To gain better understanding of the genetic and metabolic capacities of the SER3 strain, its draft genome was determined and was found to comprise a single chromosome of 5.08 Mb, 52.8% G + C content, and 4,545 protein-coding genes. Phylogenetic analysis indicated that the SER3 strain is affiliated with the R. badensis species, with an average nucleotide identity >96% and a genome-to-genome distance >70%. A comparison of the genomic properties of R. badensis SER3 and other close bacterial relatives showed several genes with potential functions in biocontrol activities, such as those encoding siderophores, non-ribosomal peptide synthetases, and polyketide synthases. This is the first study to demonstrate a novel role of the recently discovered R. badensis species (and any other species of the genus Rouxiella) as a biocontrol agent against postharvest fungal pathogens.

近数十年来，诸多细菌菌种已被鉴定为植物作物病害的生防剂（biocontrol agents），但现有文献中仅报道了少数几个菌属。因此，鉴定可拮抗植物病原菌（phytopathogens）的新型拮抗菌株，对于推动可持续粮食生产体系至关重要。本研究评估了新发现的巴登斯罗氏菌（Rouxiella badensis）菌株SER3的生防功能。该菌株分离自腐烂草莓果实（Fragaria × ananassa）的叶围（phyllosphere），经对峙试验（confrontation assays）证实，其产生的扩散性与挥发性代谢物可对20种浆果真菌病原菌产生不同程度的拮抗作用。这些真菌病原菌分离自腐烂的草莓、黑莓与蓝莓果实，通过内部转录间隔区（internal transcribed spacer, ITS）测序与同源性搜索完成鉴定，与灰葡萄孢属（Botrytis）、镰刀菌属（Fusarium）、地霉属（Geotrichum）、毛霉属（Mucor）、青霉属（Penicillium）、链格孢属（Alternaria）以及葡萄座腔菌属（Botryosphaeria）等常见采后病原菌具有高度同源性。通过对浆果果实进行人工再侵染，证实了大多数病原菌符合科赫氏法则（Koch’s postulates）。菌株SER3可有效抑制草莓果实内灰葡萄孢（Botrytis cinerea）与短胖镰刀菌（Fusarium brachygibbosum）的生长，干扰其菌丝发育。为深入解析菌株SER3的遗传与代谢潜能，本研究完成了其草图基因组（draft genome）测序，结果显示该菌株包含一条5.08 Mb的单一染色体，G+C含量为52.8%，共编码4545个蛋白质编码基因。系统发育分析表明，菌株SER3隶属于巴登斯罗氏菌物种，平均核苷酸一致性（average nucleotide identity, ANI）>96%，基因组间距离（genome-to-genome distance）>70%。通过对比巴登斯罗氏菌SER3与其他近缘细菌的基因组特征，发现多个具备生防功能潜力的基因，例如编码铁载体（siderophores）、非核糖体肽合成酶（non-ribosomal peptide synthetases）与聚酮合酶（polyketide synthases）的基因。本研究首次证实，新发现的巴登斯罗氏菌物种（以及罗氏菌属的任何其他物种）可作为采后真菌病原菌的生防剂，这也是罗氏菌属相关物种生防功能的首次报道。