Ehau-Taumaunu Hanareia, Bell Terrence H, Sadeghi Javad, Hockett Kevin L
Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA.
Department of Physical and Environmental Sciences, University of Toronto - Scarborough, Toronto, ON, Canada.
Environ Microbiome. 2025 Jul 1;20(1):77. doi: 10.1186/s40793-025-00734-1.
BACKGROUND: Microbial-based treatments to protect plants against phytopathogens typically focus on soil-borne disease or the aboveground application of one or a few biocontrol microorganisms. However, diverse microbiomes may provide unique benefits to phytoprotection in the phyllosphere, by restricting pathogen access to niche space and/or through multiple forms of direct antagonism. We previously showed that successive experimental passaging of phyllosphere microbiomes along with the phytopathogen Pseudomonas syringae pv. tomato (Pto), which causes bacterial speck in tomato, led to the development of a disease suppressive microbial community. Here, we used amplicon sequencing to assess bacterial and fungal composition at the end of each passage, as well as shotgun metagenomics at key passages based on observed disease-suppressive phenotypes, to assess differences in functional potential between suppressive and non-suppressive communities. RESULTS: Bacterial composition changed and diversity declined quickly due to passaging and remained low, particularly in treatments with Pto present, whereas fungal diversity did not. Pseudomonas and Xanthomonas populations were particularily enriched in disease-suppressive microbiomes compared to conducive microbiomes. The relative abundance of Pseudomonas syringae group gemonosp. 3 (the clade to which the introduced pathogen belongs) in shotgun metagenomic data was similar to what we observed for Pseudomonas ASVs in the 16S rRNA gene dataset. We also observed an increase in the abundance of genes associated with microbial antagonism at Passage 4, corresponding to the highest observed disease severity. CONCLUSIONS: Taxonomic richness and evenness were low within samples, with clustering occurring for suppressive or non-suppressive microbiomes. The relative abundance of genes associated with antagonism was higher for disease-suppressive phyllosphere microbiomes. This work is an important step towards understanding the microbe-microbe interactions within disease-suppressive phyllosphere communities.
背景：基于微生物的植物病害防治方法通常聚焦于土壤传播病害或地上部分施用一种或几种生物防治微生物。然而，多样化的微生物群落可能通过限制病原体进入生态位空间和/或通过多种直接拮抗形式，为叶际的植物保护提供独特的益处。我们之前表明，叶际微生物群落与引起番茄细菌性斑点病的番茄丁香假单胞菌致病型（Pto）连续进行实验传代，导致了一个病害抑制性微生物群落的形成。在此，我们使用扩增子测序来评估每一代传代结束时的细菌和真菌组成，以及基于观察到的病害抑制表型在关键传代时进行鸟枪法宏基因组学分析，以评估抑制性和非抑制性群落之间功能潜力的差异。 结果：由于传代，细菌组成发生变化且多样性迅速下降并维持在低水平，特别是在存在Pto的处理中，而真菌多样性则没有。与有利于病害发生的微生物群落相比，假单胞菌属和黄单胞菌属种群在病害抑制性微生物群落中特别富集。在鸟枪法宏基因组数据中，丁香假单胞菌gemonosp. 3组（引入病原体所属的进化枝）的相对丰度与我们在16S rRNA基因数据集中观察到的假单胞菌扩增子序列变异（ASV）相似。我们还观察到在第4代时与微生物拮抗相关的基因丰度增加，这与观察到的最高病害严重程度相对应。 结论：样本内的分类丰富度和均匀度较低，抑制性或非抑制性微生物群落出现聚类。病害抑制性叶际微生物群落中与拮抗相关的基因相对丰度更高。这项工作是朝着理解病害抑制性叶际群落内微生物-微生物相互作用迈出的重要一步。
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