Kampouris Ioannis D, Kuhl-Nagel Theresa, Behr Jan Helge, Sommermann Loreen, Babin Doreen, Francioli Davide, Zrenner Rita, Kublik Susanne, Schloter Michael, Ludewig Uwe, Smalla Kornelia, Neumann Günter, Grosch Rita, Geistlinger Joerg
Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany.
Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Germany.
Environ Microbiome. 2025 Jun 12;20(1):69. doi: 10.1186/s40793-025-00729-y.
Plant beneficial microorganisms as inoculants can improve crop performance, but factors affecting their impact on plant performance under field conditions remain unclear, thereby limiting their use in farming. Here, we investigated how farming practices (e.g., tillage and N-fertilization intensity) and growing seasons influenced the impact of a beneficial microorganism consortium (BMc: Trichoderma, Bacillus, and Pseudomonas strains) in maize and affected the rhizosphere competence of each BMc strain. In addition, we tested whether the consortium affects the resident rhizosphere microbiome and crop performance. In two growing seasons (2020 and 2021), we assessed how BMc inoculation affects maize growth, nutritional status, gene expression, and rhizosphere microbiome under different farming practices at the flowering stage.
Inoculated strains successfully colonized the maize rhizosphere independently of farming practice. BMc inoculation improved plant growth and iron uptake in 2020, regardless of farming practice. These effects co-occurred with lower precipitation levels in 2020 compared to 2021. BMc inoculation reduced the expression of several stress-related genes in maize in 2020 under drought. An increased iron uptake by the BMc-inoculated plants was observed in 2020 and was associated with the upregulation of the gene ZmNAS3, which is linked to iron uptake. Therefore, BMc inoculation mitigated the drought impact on maize. The microbial rhizosphere communities were altered by BMc inoculation in both years, but patterns of responder taxa differed between seasons. Metagenome analysis revealed that more genes (e.g., genes encoding biosurfactants and siderophores) were enriched in the rhizosphere of BMc-inoculated plants in 2020 than in 2021. Moreover, we identified bacterial and fungal taxa positively associated with maize iron uptake. The relative abundance of these iron uptake-associated bacterial and fungal taxa significantly increased due to BMc inoculation in 2020, while they showed overall higher relative abundances in 2021, independently of BMc inoculation. We mapped the sequences of these iron-associated taxa to publicly available genomes and verified the occurrence of various plant beneficial traits in several mapped genomes.
Overall, we show that the growing season determined the effect of BMc inoculation on maize plants by shaping microbiome composition and function in the maize rhizosphere more than farming practice. These findings highlight the importance of the complex interplay between microbial inoculants and the resident rhizosphere microorganisms under abiotic stress conditions.
作为接种剂的植物有益微生物可改善作物生长表现，但在田间条件下影响其对植物生长表现作用的因素仍不清楚，这限制了它们在农业中的应用。在此，我们研究了耕作方式（如耕作和氮肥施用量）和生长季节如何影响有益微生物联合体（BMc：木霉菌、芽孢杆菌和假单胞菌菌株）对玉米的作用，并影响每个BMc菌株的根际竞争力。此外，我们测试了该联合体是否会影响根际常驻微生物群落和作物生长表现。在两个生长季节（2020年和2021年），我们评估了在开花期不同耕作方式下，接种BMc如何影响玉米生长、营养状况、基因表达和根际微生物群落。
接种菌株成功定殖于玉米根际，与耕作方式无关。在2020年，无论耕作方式如何，接种BMc均能改善植物生长和铁吸收。与2021年相比，这些效果在2020年伴随着较低的降水量出现。在2020年干旱条件下，接种BMc降低了玉米中几个与胁迫相关基因的表达。2020年观察到接种BMc的植物铁吸收增加，这与与铁吸收相关的ZmNAS3基因上调有关。因此，接种BMc减轻了干旱对玉米的影响。两年中接种BMc均改变了微生物根际群落，但不同季节响应类群的模式不同。宏基因组分析表明，2020年接种BMc的植物根际中富集的基因（如编码生物表面活性剂和铁载体的基因）比2021年更多。此外，我们鉴定出与玉米铁吸收呈正相关的细菌和真菌类群。2020年，由于接种BMc，这些与铁吸收相关的细菌和真菌类群的相对丰度显著增加，而在2021年，无论是否接种BMc，它们的相对丰度总体上更高。我们将这些与铁相关类群的序列映射到公开可用的基因组上，并在几个映射基因组中验证了各种植物有益性状的存在。
总体而言，我们表明生长季节比耕作方式更能通过塑造玉米根际微生物群落组成和功能来决定接种BMc对玉米植株的影响。这些发现突出了在非生物胁迫条件下微生物接种剂与根际常驻微生物之间复杂相互作用的重要性。
