Bziuk Nina, Maccario Lorrie, Straube Benjamin, Wehner Gwendolin, Sørensen Søren J, Schikora Adam, Smalla Kornelia
Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Messeweg 11-12, 38104, Braunschweig, Germany.
Section of Microbiology, Copenhagen University, Universitetsparken 15, 2100, Copenhagen, Denmark.
Environ Microbiome. 2021 Oct 28;16(1):20. doi: 10.1186/s40793-021-00389-8.
Bacteria associated with plants can enhance the plants' growth and resistance against phytopathogens. Today, growers aim to reduce the use of mineral fertilizers and pesticides. Since phytopathogens cause severe yield losses in crop production systems, biological alternatives gain more attention. Plant and also seed endophytes have the potential to influence the plant, especially seed-borne bacteria may express their beneficiary impact at initial plant developmental stages. In the current study, we assessed the endophytic seed microbiome of seven genetically diverse barley accessions by 16S rRNA gene amplicon sequencing and verified the in vitro plant beneficial potential of isolated seed endophytes. Furthermore, we investigated the impact of the barley genotype and its seed microbiome on the rhizosphere microbiome at an early growth stage by 16S rRNA gene amplicon sequencing.
The plant genotype displayed a significant impact on the microbiota in both barley seed and rhizosphere. Consequently, the microbial alpha- and beta-diversity of the endophytic seed microbiome was highly influenced by the genotype. Interestingly, no correlation was observed between the endophytic seed microbiome and the single nucleotide polymorphisms of the seven genotypes. Unclassified members of Enterobacteriaceae were by far most dominant. Other abundant genera in the seed microbiome belonged to Curtobacterium, Paenibacillus, Pantoea, Sanguibacter and Saccharibacillus. Endophytes isolated from barley seeds were affiliated to dominant genera of the core seed microbiome, based on their 16S rRNA gene sequence. Most of these endophytic isolates produced in vitro plant beneficial secondary metabolites known to induce plant resistance.
Although barley accessions representing high genetic diversity displayed a genotype-dependent endophytic seed microbiome, a core seed microbiome with high relative abundances was identified. Endophytic isolates were affiliated to members of the core seed microbiome and many of them showed plant beneficial properties. We propose therefore that new breeding strategies should consider genotypes with high abundance of beneficial microbes.
与植物相关的细菌可促进植物生长并增强其对植物病原体的抗性。如今，种植者旨在减少矿物肥料和农药的使用。由于植物病原体在作物生产系统中会导致严重的产量损失，生物替代方案受到了更多关注。植物以及种子内生菌有可能影响植物，尤其是种子携带的细菌可能在植物发育初期发挥有益作用。在本研究中，我们通过16S rRNA基因扩增子测序评估了7个遗传多样性不同的大麦品种的内生种子微生物组，并验证了分离出的种子内生菌在体外对植物的有益潜力。此外，我们通过16S rRNA基因扩增子测序研究了大麦基因型及其种子微生物组在早期生长阶段对根际微生物组的影响。
植物基因型对大麦种子和根际的微生物群均有显著影响。因此，内生种子微生物组的微生物α多样性和β多样性受基因型的影响很大。有趣的是，在七个基因型的内生种子微生物组与单核苷酸多态性之间未观察到相关性。肠杆菌科未分类成员是迄今为止最主要的。种子微生物组中的其他丰富属包括短小杆菌属、芽孢杆菌属、泛菌属、血杆菌属和糖杆菌属。根据其16S rRNA基因序列，从大麦种子中分离出的内生菌隶属于核心种子微生物组的优势属。这些内生分离株中的大多数在体外产生已知可诱导植物抗性的有益植物次生代谢产物。
尽管代表高遗传多样性的大麦品种显示出基因型依赖性的内生种子微生物组，但仍鉴定出了具有高相对丰度的核心种子微生物组。内生分离株隶属于核心种子微生物组的成员，其中许多具有对植物有益的特性。因此，我们建议新的育种策略应考虑有益微生物丰度高的基因型。
