Data underlying publication: Spinach Seed Microbiome Characteristics Linked to Suppressiveness Against Pythium ultimum Damping-Off

Using a bioassay setup, we recently demonstrated that eliminating the seed microbiota of certain spinach (<em>Spinacia oleracea</em>) seed lots makes them more susceptible to damping-off caused by <em>Pythium ultimum</em>. This indicates that the presence of an intact seed microbiome can confer disease suppression against this pathogen which attacks seedlings during germination. This study aimed at identifying the key actors associated with seed microbiome suppressiveness by correlating the bioassay results with the taxonomy and relative abundance of bacteria and fungi present in eight spinach seed lots differing in suppressive potential. Seed lots shared core taxa, but 81 % of all taxa were rare and a large proportion of variance between samples was explained by seed lot identity. Additionally, 7.1 % of bacterial and 6.2 % of fungal community variance between samples correlated with the trait of disease suppression. High fungal diversity was a characteristic of highly suppressive seed lots. More specifically, a higher relative abundance of basidiomycetous dimorphic yeasts such as <em>Vishniacozyma</em>, <em>Papiliotrema</em> and <em>Filobasidium</em> was a key feature of suppressive seed microbiomes. The same was true for the bacterial genera <em>Massilia</em> and <em>Paenibacillus</em> which are known for their antagonistic properties. Consequently, we suggest for the abundance of these genera to be used as an indicator of seed lot suppressive potential. As a result, seed processing and treatment can become more targeted with indicator taxa being used to evaluate the presence of beneficial seed-associated microbial functions. This process in turn would contribute to the sustainable management of seedling diseases. Finally, this study highlights the ubiquity of yeasts in spinach seed microbiota and their potential beneficial roles for seed health.

我们近期借助生物测定（bioassay）体系证实，去除部分菠菜（Spinacia oleracea）种子批次的种子微生物组（seed microbiota）后，这些种子更易受终极腐霉（Pythium ultimum）引发的猝倒病（damping-off）侵染。这表明完整的种子微生物组可赋予种子抵御该病原菌的病害抑制能力——该病原菌会在种子萌发阶段侵染幼苗。本研究旨在通过将生物测定结果与8个病害抑制潜力存在差异的菠菜种子批次中细菌和真菌的分类学组成及相对丰度进行关联分析，以鉴定与种子微生物组病害抑制活性相关的关键类群。各菠菜种子批次共享部分核心类群（core taxa），但全部类群中有81%为稀有类群，且样本间的大部分群落变异可归因于种子批次本身的属性。此外，样本间7.1%的细菌群落变异与6.2%的真菌群落变异与病害抑制性状存在相关性。真菌多样性较高是病害抑制能力较强的种子批次的典型特征。更具体地说，担子菌门二态酵母（basidiomycetous dimorphic yeasts）的相对丰度较高，是具备病害抑制活性的种子微生物组的关键特征，这类酵母涵盖维什尼奇酵母属（Vishniacozyma）、帕皮利奥酵母属（Papiliotrema）与丝孢酵母属（Filobasidium）。同样具备拮抗特性的细菌属——马西利亚菌属（Massilia）与类芽孢杆菌属（Paenibacillus）也呈现出类似的丰度模式。据此，我们建议将上述菌属的丰度作为评估种子批次病害抑制潜力的指示指标。通过利用指示类群评估种子相关有益微生物功能的存在情况，可使种子加工与处理流程更具靶向性，进而助力幼苗病害的可持续防控。本研究最后还阐明了酵母在菠菜种子微生物组中的普遍存在性，及其对种子健康的潜在有益作用。