A stable 15-member bacterial SynCom promotes Brachypodium growth under drought stress
IntroductionRhizosphere microbiomes are known to drive soil nutrient cycling and influence plant fitness during adverse environmental conditions. Field-derived robust Synthetic Communities (SynComs) of microbes mimicking the diversity of rhizosphere microbiomes can greatly advance a deeper understan...
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Frontiers Media S.A.
2025-08-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1649750/full |
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| author | Archana Yadav Mingfei Chen Shwetha M. Acharya Grace Kim Yuguo Yang Tiffany Z. Zhao Eunice Tsang Romy Chakraborty |
| author_facet | Archana Yadav Mingfei Chen Shwetha M. Acharya Grace Kim Yuguo Yang Tiffany Z. Zhao Eunice Tsang Romy Chakraborty |
| author_sort | Archana Yadav |
| collection | DOAJ |
| description | IntroductionRhizosphere microbiomes are known to drive soil nutrient cycling and influence plant fitness during adverse environmental conditions. Field-derived robust Synthetic Communities (SynComs) of microbes mimicking the diversity of rhizosphere microbiomes can greatly advance a deeper understanding of such processes. However, assembling stable, genetically tractable, reproducible, and scalable SynComs remains challenging.MethodsHere, we present a systematic approach using a combination of network analysis and cultivation-guided methods to construct a 15-member SynCom from the rhizobiome of Brachypodium distachyon. This SynCom incorporates diverse strains from five bacterial phyla. Genomic analysis of the individual strains was performed to reveal encoded plant growth-promoting traits, including genes for the synthesis of osmoprotectants (trehalose and betaine) and Na+/K+ transporters, and some predicted traits were validated by laboratory phenotypic assays.ResultsThe SynCom demonstrates strong stability both in vitro and in planta. Most strains encoded multiple plant growth-promoting functions, and several of these were confirmed experimentally. The presence of osmoprotectant and ion transporter genes likely contributed to the observed resilience of Brachypodium to drought stress, where plants amended with the SynCom recovered better than those without. We further observed preferential colonization of SynCom strains around root tips under stress, likely due to active interactions between plant root metabolites and bacteria.DiscussionOur results demonstrate that trait-informed construction of synthetic communities can yield stable, functionally diverse consortia that enhance plant resilience under drought. Preferential colonization near root tips points to active, localized plant–microbe signaling as a component of stress-responsive recruitment. This stable SynCom provides a scalable platform for probing mechanisms of plant-microbe interaction and for developing microbiome-based strategies to improve soil and crop performance in variable environments. |
| format | Article |
| id | doaj-art-c170bcab9b8c41fe9170675715d92c5f |
| institution | Kabale University |
| issn | 1664-302X |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj-art-c170bcab9b8c41fe9170675715d92c5f2025-08-20T03:39:26ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2025-08-011610.3389/fmicb.2025.16497501649750A stable 15-member bacterial SynCom promotes Brachypodium growth under drought stressArchana Yadav0Mingfei Chen1Shwetha M. Acharya2Grace Kim3Yuguo Yang4Tiffany Z. Zhao5Eunice Tsang6Romy Chakraborty7Climate and Ecosystem Sciences Division, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesClimate and Ecosystem Sciences Division, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesClimate and Ecosystem Sciences Division, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, United StatesClimate and Ecosystem Sciences Division, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesClimate and Ecosystem Sciences Division, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesClimate and Ecosystem Sciences Division, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesClimate and Ecosystem Sciences Division, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesIntroductionRhizosphere microbiomes are known to drive soil nutrient cycling and influence plant fitness during adverse environmental conditions. Field-derived robust Synthetic Communities (SynComs) of microbes mimicking the diversity of rhizosphere microbiomes can greatly advance a deeper understanding of such processes. However, assembling stable, genetically tractable, reproducible, and scalable SynComs remains challenging.MethodsHere, we present a systematic approach using a combination of network analysis and cultivation-guided methods to construct a 15-member SynCom from the rhizobiome of Brachypodium distachyon. This SynCom incorporates diverse strains from five bacterial phyla. Genomic analysis of the individual strains was performed to reveal encoded plant growth-promoting traits, including genes for the synthesis of osmoprotectants (trehalose and betaine) and Na+/K+ transporters, and some predicted traits were validated by laboratory phenotypic assays.ResultsThe SynCom demonstrates strong stability both in vitro and in planta. Most strains encoded multiple plant growth-promoting functions, and several of these were confirmed experimentally. The presence of osmoprotectant and ion transporter genes likely contributed to the observed resilience of Brachypodium to drought stress, where plants amended with the SynCom recovered better than those without. We further observed preferential colonization of SynCom strains around root tips under stress, likely due to active interactions between plant root metabolites and bacteria.DiscussionOur results demonstrate that trait-informed construction of synthetic communities can yield stable, functionally diverse consortia that enhance plant resilience under drought. Preferential colonization near root tips points to active, localized plant–microbe signaling as a component of stress-responsive recruitment. This stable SynCom provides a scalable platform for probing mechanisms of plant-microbe interaction and for developing microbiome-based strategies to improve soil and crop performance in variable environments.https://www.frontiersin.org/articles/10.3389/fmicb.2025.1649750/fullmicrobiomerhizosphereBrachypodiumdroughtSynComplant growth promotion (PGP) |
| spellingShingle | Archana Yadav Mingfei Chen Shwetha M. Acharya Grace Kim Yuguo Yang Tiffany Z. Zhao Eunice Tsang Romy Chakraborty A stable 15-member bacterial SynCom promotes Brachypodium growth under drought stress Frontiers in Microbiology microbiome rhizosphere Brachypodium drought SynCom plant growth promotion (PGP) |
| title | A stable 15-member bacterial SynCom promotes Brachypodium growth under drought stress |
| title_full | A stable 15-member bacterial SynCom promotes Brachypodium growth under drought stress |
| title_fullStr | A stable 15-member bacterial SynCom promotes Brachypodium growth under drought stress |
| title_full_unstemmed | A stable 15-member bacterial SynCom promotes Brachypodium growth under drought stress |
| title_short | A stable 15-member bacterial SynCom promotes Brachypodium growth under drought stress |
| title_sort | stable 15 member bacterial syncom promotes brachypodium growth under drought stress |
| topic | microbiome rhizosphere Brachypodium drought SynCom plant growth promotion (PGP) |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1649750/full |
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