Omics-driven insights into plant growth-promoting microorganisms for sustainable agriculture
Abstract Plant growth-promoting microorganisms (PGPMs) are pivotal to advancing sustainable agriculture, offering eco-friendly solutions for nutrient acquisition, stress tolerance, and disease suppression. Integrating multi-omics approaches, genomics, transcriptomics, proteomics, and metabolomics ha...
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| Format: | Article |
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Springer
2025-07-01
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| Series: | Discover Sustainability |
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| Online Access: | https://doi.org/10.1007/s43621-025-01582-2 |
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| author | Abhishek Sahoo Garima Yadav Tushar Mehta Mukesh Meena Prashant Swapnil |
| author_facet | Abhishek Sahoo Garima Yadav Tushar Mehta Mukesh Meena Prashant Swapnil |
| author_sort | Abhishek Sahoo |
| collection | DOAJ |
| description | Abstract Plant growth-promoting microorganisms (PGPMs) are pivotal to advancing sustainable agriculture, offering eco-friendly solutions for nutrient acquisition, stress tolerance, and disease suppression. Integrating multi-omics approaches, genomics, transcriptomics, proteomics, and metabolomics has substantially deepened our understanding of plant–microbe interactions at molecular and system levels. Genomic studies have identified key PGPM traits such as nitrogen fixation, siderophore biosynthesis, and stress-responsive gene clusters. At the same time, transcriptomic profiling has illuminated plant immune priming and hormonal modulation under microbial influence. Proteomics analysis have revealed protein networks underpinning microbial colonization, stress adaptation, and metabolite exchange, with specific markers such as ACC deaminase and antioxidant enzymes linked to growth promotion. Metabolomics further elucidates biochemical pathways shaped by PGPMs, including increased levels of flavonoids, osmoprotectants, and signalling molecules in host plants. The application of omics-guided microbial consortia shows enhanced efficacy compared to single-strain inoculants, promoting greater biomass, yield, and stress resilience. Case studies highlight the successful deployment of PGPMs in ameliorating salinity and drought stress, enhancing phytoremediation, and improving nutrient uptake in diverse crops. Despite these advances, challenges persist, including limited omics resolution in complex soil environments, a lack of standardised data integration pipelines, and ecological variability affecting microbial persistence. Emerging technologies like CRISPR-based genome editing and AI-driven consortia design promise to overcome these barriers by tailoring microbial interventions to crop-specific and environmental contexts. This comprehensive review underscores the transformative potential of multi-omics in PGPM research while emphasizing the need for interdisciplinary collaboration to translate molecular insights into field-level agricultural innovations. |
| format | Article |
| id | doaj-art-c580324b7d3b4697b6a11bc1ffa401aa |
| institution | Kabale University |
| issn | 2662-9984 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Springer |
| record_format | Article |
| series | Discover Sustainability |
| spelling | doaj-art-c580324b7d3b4697b6a11bc1ffa401aa2025-08-20T04:01:42ZengSpringerDiscover Sustainability2662-99842025-07-016112310.1007/s43621-025-01582-2Omics-driven insights into plant growth-promoting microorganisms for sustainable agricultureAbhishek Sahoo0Garima Yadav1Tushar Mehta2Mukesh Meena3Prashant Swapnil4Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia UniversityLaboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia UniversityLaboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia UniversityLaboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia UniversityDepartment of Botany, School of Basic Sciences, Central University of PunjabAbstract Plant growth-promoting microorganisms (PGPMs) are pivotal to advancing sustainable agriculture, offering eco-friendly solutions for nutrient acquisition, stress tolerance, and disease suppression. Integrating multi-omics approaches, genomics, transcriptomics, proteomics, and metabolomics has substantially deepened our understanding of plant–microbe interactions at molecular and system levels. Genomic studies have identified key PGPM traits such as nitrogen fixation, siderophore biosynthesis, and stress-responsive gene clusters. At the same time, transcriptomic profiling has illuminated plant immune priming and hormonal modulation under microbial influence. Proteomics analysis have revealed protein networks underpinning microbial colonization, stress adaptation, and metabolite exchange, with specific markers such as ACC deaminase and antioxidant enzymes linked to growth promotion. Metabolomics further elucidates biochemical pathways shaped by PGPMs, including increased levels of flavonoids, osmoprotectants, and signalling molecules in host plants. The application of omics-guided microbial consortia shows enhanced efficacy compared to single-strain inoculants, promoting greater biomass, yield, and stress resilience. Case studies highlight the successful deployment of PGPMs in ameliorating salinity and drought stress, enhancing phytoremediation, and improving nutrient uptake in diverse crops. Despite these advances, challenges persist, including limited omics resolution in complex soil environments, a lack of standardised data integration pipelines, and ecological variability affecting microbial persistence. Emerging technologies like CRISPR-based genome editing and AI-driven consortia design promise to overcome these barriers by tailoring microbial interventions to crop-specific and environmental contexts. This comprehensive review underscores the transformative potential of multi-omics in PGPM research while emphasizing the need for interdisciplinary collaboration to translate molecular insights into field-level agricultural innovations.https://doi.org/10.1007/s43621-025-01582-2Plant growth-promoting microorganisms (PGPMs)Multi-omics approachesPlant–microbe interactionsSustainable agricultureBioinoculants |
| spellingShingle | Abhishek Sahoo Garima Yadav Tushar Mehta Mukesh Meena Prashant Swapnil Omics-driven insights into plant growth-promoting microorganisms for sustainable agriculture Discover Sustainability Plant growth-promoting microorganisms (PGPMs) Multi-omics approaches Plant–microbe interactions Sustainable agriculture Bioinoculants |
| title | Omics-driven insights into plant growth-promoting microorganisms for sustainable agriculture |
| title_full | Omics-driven insights into plant growth-promoting microorganisms for sustainable agriculture |
| title_fullStr | Omics-driven insights into plant growth-promoting microorganisms for sustainable agriculture |
| title_full_unstemmed | Omics-driven insights into plant growth-promoting microorganisms for sustainable agriculture |
| title_short | Omics-driven insights into plant growth-promoting microorganisms for sustainable agriculture |
| title_sort | omics driven insights into plant growth promoting microorganisms for sustainable agriculture |
| topic | Plant growth-promoting microorganisms (PGPMs) Multi-omics approaches Plant–microbe interactions Sustainable agriculture Bioinoculants |
| url | https://doi.org/10.1007/s43621-025-01582-2 |
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