Cube-based screening identifies a quinoa-derived synthetic microbial community that promotes plant growth and modulates root epidermal responses under salt stress.

Authors

Hatairat Dangjarean, Yoshinori Murata, Yasufumi Kobayashi, Sara Neyrot, Takuya Ogata, Yasunari Fujita

Published in

Frontiers in plant science. Volume 17. Pages 1934646. Epub Oct 20, 2026.

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.

PMID:
42978678
Bibliographic data and abstract were imported from PubMed on 04 Nov 2026.

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