Fertilization influences the substrate, rhizosphere, and endosphere bacteriome of Petunia × hybrida

Authors: QUIJA-PILLAJO, JUAN - The Ohio State University; CHAPIN, LAURA - The Ohio State University; OWEN, JAMES - Former ARS Employee; Altland, James; JONES, MICHELLE - The Ohio State University

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/10/2025
Publication Date: 12/5/2025
Citation: Quija-Pillajo, J., Chapin, L., Owen, J., Altland, J.E., Jones, M. 2025. Fertilization influences the substrate, rhizosphere, and endosphere bacteriome of Petunia × hybrida. Frontiers in Microbiology. 16. Article 1719754. https://doi.org/10.3389/fmicb.2025.1719754.
DOI: https://doi.org/10.3389/fmicb.2025.1719754

Interpretive Summary: In greenhouse production, plants are often grown in soilless substrates, such as peat mixes, where the role of beneficial microbes is not well understood. The problem addressed in this study was the lack of knowledge about how fertilization rates and plant types influence the microbial communities (bacteriome) in these substrates and around plant roots. To investigate this, petunia plants were grown in peat-based substrate under three different fertilizer levels. Plant growth and health were measured, and advanced genetic sequencing was used to analyze the bacteria present in the substrate, around the roots (rhizosphere), and inside the roots (endosphere). It was found that higher fertilizer rates led to larger and healthier plants, but also caused changes in the types and diversity of bacteria present. Fertilization was shown to strongly affect the bacterial communities, especially by lowering the pH of the substrate, which in turn reduced bacterial diversity in the rhizosphere. The plant variety also influenced which bacteria were present. The substrate itself was found to be the main source of microbial diversity, and most bacteria found in the roots could also be found in the substrate. However, only a few types of bacteria were consistently found inside the roots, suggesting selective recruitment by the plant. This demonstrates that fertilization and plant type are key factors shaping the microbial environment in soilless greenhouse systems. This shows that nutrient management and substrate selection can be used to influence beneficial microbial communities, potentially improving plant growth and fertilizer efficiency. The findings encourage further research to optimize microbial interactions for healthier and more productive greenhouse crops.

Technical Abstract: In controlled environment agriculture (CEA), soil is replaced with soilless substrates that have poorly understood microbiome dynamics. We investigated the rhizosphere and endosphere bacteriome of Petunia × hybrida ‘Picobella Blue’ (Picobella) and ‘Wave Purple’ (Wave) grown in a soilless substrate (80% sphagnum peat and 20% perlite) under three fertilization rates (25, 100, and 200 mg·L–1 N). Plant growth was assessed with the TraitFinder phenotyping platform, shoot dry weight, and nutrient analysis. Bacteriomes were profiled by 16S rRNA amplicon sequencing from unplanted substrate, bulk substrate, rhizosphere, and endosphere samples. Both cultivars grew largest and healthiest at 200 mg·L–1 N. Picobella fertilized with 100 and 200 mg·L–1 N were equally green, whereas Wave was greenest at 200 mg·L–1 N. Distinct bacteriomes were observed across unplanted substrate, rhizosphere, and endosphere. In unplanted substrate, fertilizer rate shaped bacterial community composition but not alpha diversity. In the rhizosphere, pH changes driven by fertilization strongly influenced bacterial community structure and reduced diversity. Endosphere and rhizosphere communities were further shaped by cultivar and fertilization rate. These findings highlight nutrient management as a key driver of bacteriome dynamics across the substrate–plant continuum, underscoring the complex interactions between fertilization, plant genotype, and microbial communities in soilless culture.