Cube-based screening identifies a quinoa-derived synthetic microbial community that promotes plant growth and modulates root epidermal responses under salt stress
4 affiliations
- 1Graduate School of Science and Technology, University of Tsukuba
- 2Japan International Research Center for Agricultural Sciences (JIRCAS)
- 3Rice Department, Ministry of Agriculture and Cooperatives (MOAC)
- 4Institute of Life and Environmental Sciences, University of Tsukuba
Abstract
Plant-associated bacteria can improve plant performance under abiotic stress, but beneficial functions in plant microbiomes may depend on defined combinations of microorganisms rather than individual isolates alone. Here, we developed a cube-based screening strategy to identify functional synthetic microbial communities (SynComs) from 135 quinoa-associated bacterial isolates while preserving combinatorial diversity and traceability of isolate-level contributions. The isolates were divided into five 27-isolate sets, each arranged as a 3 × 3 × 3 cube in which each 3 × 3 layer was defined as a 9-isolate SynCom, generating 45 SynComs in total. Screening under 100 mM NaCl identified SynCom DY1 (SCDY1) as a candidate salt stress-mitigating consortium. SCDY1 consisted of nine taxonomically diverse isolates and exhibited a multifunctional profile, including siderophore production, phosphate solubilization, carboxymethyl cellulose degradation, indole compound production, and growth under saline conditions. In Arabidopsis thaliana , SCDY1 promoted primary root elongation in a salinity-dependent manner and increased biomass under moderate salinity conditions, with the clearest overall effects observed at 120 mM NaCl. At least a subset of the constituent bacteria was recoverable from inoculated seedlings. RNA sequencing and targeted RT-qPCR indicated that SCDY1 modulated host gene expression under moderate salinity stress, with responsive genes associated with oxidative stress, water- and oxygen-related processes, phenylpropanoid biosynthesis, glutathione metabolism, and root epidermis-related processes. Root hair phenotyping further showed that SCDY1 enhanced root hair-related traits and shifted visible root hair formation closer to the root apex. These findings identify a quinoa-derived SynCom that improves Arabidopsis performance under salinity stress and provide a practical, traceable framework for discovering beneficial microbial consortia from plant-associated bacterial collections.
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BibTeX
@article{dangjarean2026cubebased,
title = {{Cube-based screening identifies a quinoa-derived synthetic microbial community that promotes plant growth and modulates root epidermal responses under salt stress}},
author = {Hatairat Dangjarean and Yoshinori Murata and Yasufumi Kobayashi and Sara Neyrot and Takuya Ogata and Yasunari Fujita},
journal = {Frontiers in Plant Science},
year = {2026},
month = oct,
doi = {10.3389/fpls.2026.1934646},
url = {https://www.frontiersin.org/articles/10.3389/fpls.2026.1934646/full},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Cube-based screening identifies a quinoa-derived synthetic microbial community that promotes plant growth and modulates root epidermal responses under salt stress
AU - Hatairat Dangjarean
AU - Yoshinori Murata
AU - Yasufumi Kobayashi
AU - Sara Neyrot
AU - Takuya Ogata
AU - Yasunari Fujita
PY - 2026
DA - 2026/10/20
JO - Frontiers in Plant Science
DO - 10.3389/fpls.2026.1934646
UR - https://www.frontiersin.org/articles/10.3389/fpls.2026.1934646/full
AB - Plant-associated bacteria can improve plant performance under abiotic stress, but beneficial functions in plant microbiomes may depend on defined combinations of microorganisms rather than individual isolates alone. Here, we developed a cube-based screening strategy to identify functional synthetic microbial communities (SynComs) from 135 quinoa-associated bacterial isolates while preserving combinatorial diversity and traceability of isolate-level contributions. The isolates were divided into five 27-isolate sets, each arranged as a 3 × 3 × 3 cube in which each 3 × 3 layer was defined as a 9-isolate SynCom, generating 45 SynComs in total. Screening under 100 mM NaCl identified SynCom DY1 (SCDY1) as a candidate salt stress-mitigating consortium. SCDY1 consisted of nine taxonomically diverse isolates and exhibited a multifunctional profile, including siderophore production, phosphate solubilization, carboxymethyl cellulose degradation, indole compound production, and growth under saline conditions. In Arabidopsis thaliana , SCDY1 promoted primary root elongation in a salinity-dependent manner and increased biomass under moderate salinity conditions, with the clearest overall effects observed at 120 mM NaCl. At least a subset of the constituent bacteria was recoverable from inoculated seedlings. RNA sequencing and targeted RT-qPCR indicated that SCDY1 modulated host gene expression under moderate salinity stress, with responsive genes associated with oxidative stress, water- and oxygen-related processes, phenylpropanoid biosynthesis, glutathione metabolism, and root epidermis-related processes. Root hair phenotyping further showed that SCDY1 enhanced root hair-related traits and shifted visible root hair formation closer to the root apex. These findings identify a quinoa-derived SynCom that improves Arabidopsis performance under salinity stress and provide a practical, traceable framework for discovering beneficial microbial consortia from plant-associated bacterial collections.
SN - 1664-462X
ER -