Abstract
Strawberry is cultivated in both soil-based field and substrate-based soilless hydroponic systems, yet how cultivation context shapes root-associated bacterial communities and their interaction architecture remains unclear. We compared root-associated bacterial communities from field root-associated soil and hydroponic root-adhering substrate under asymptomatic and symptomatic conditions using 16S rRNA gene amplicon sequencing. Cultivation system was the primary driver of community structure, clearly separating field and hydroponic samples. Field communities were enriched in Firmicutes and Actinobacteria, such as Bacillaceae and Nocardioidaceae, whereas hydroponic communities showed higher relative abundances of Proteobacteria, Bacteroidetes, Planctomycetes, and Verrucomicrobia, including Chitinophagaceae and Sphingomonadaceae. Differential abundance and Random Forest analyses revealed consistent enrichment of Bacillus-associated ASVs in field samples, whereas asymptomatic and symptomatic communities showed greater compositional differentiation in hydroponic than in field samples.. Co-occurrence network analysis further demonstrated that hydroponic communities contained more taxa and interactions but exhibited lower density and clustering compared to field communities, indicating reduced structural cohesion. These findings demonstrate that cultivation system strongly influences both the composition and structural organization of strawberry root-associated bacterial communities, with implications for microbiome-informed disease management in intensive production systems.
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Data availability
The raw paired-end FASTQ sequencing reads are publicly available at the NCBI Sequence Read Archive (SRA) under BioProject accession number PRJNA1260172. The data can be downloaded using the SRA Toolkit (fasterq-dump) or via the European Nucleotide Archive (ENA) mirror.
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Funding
This research was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (RS-2023-00251252 and 2020R1A6A1A03047729), Rural Development Administration (RS-2025-02613089), and Biomaterials Specialized Graduate Program through the Korea Environmental Industry & Technology Institute (KEITI), funded by the Ministry of Climate, Energy and Environment (MCEE).
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M.R. conceived the study and contributed to conceptualization, methodology, investigation, formal analysis, data curation, visualization, and writing of the original draft, as well as review and editing of the manuscript. D.H., D.L., and B.K. contributed to the development and refinement of the methodology. K.C. contributed to conceptualization, supervised the project, provided resources, acquired funding, and was responsible for project administration and manuscript review and editing. All authors contributed to the article and approved the submitted version.
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Roy, M., Han, D., Lee, D. et al. Cultivation system and plant health influence root-associated bacterial community structure and interaction networks in strawberry.
Sci Rep (2026). https://doi.org/10.1038/s41598-026-45642-7
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DOI: https://doi.org/10.1038/s41598-026-45642-7
Keywords
- Root-associated microbiome
- Strawberry
- Hydroponic cultivation
- Co-occurrence network
- Plant health
Source: Ecology - nature.com
