Abstract
Abstract Aim The study explores the functional plasticity of rhizosphere microbiomes in response to microbial inoculants, a topic not yet fully explored in open-field agroecosystems. Specifically, it assesses the lasting impact of nursery-stage inoculation with the arbuscular mycorrhizal fungus (AMF) Rhizophagus irregularis and symbiosis-stimulating compounds on the rhizosphere microbiome of Solanum lycopersicum . Methods Tomato seedlings were inoculated with R. irregularis in a commercial nursery. During this period, seedlings were irrigated weekly with strigolactone analogues and the flavonoid quercetin, both with and without AMF inoculation. At harvest, five months post-transplanting, rhizosphere samples were collected for mycorrhizal colonization assessment and predictive metagenomic profiling. Results Nursery AMF inoculation, especially when combined with the strigolactone mimic SL-M2 and quercetin, significantly enhanced mycorrhizal colonization. Although all plants became colonized, early inoculation did not affect bacterial or fungal taxonomic composition at harvest. However, it induced substantial shifts in predicted bacterial metabolic functions, affecting 137 of 154 KEGG modules. These changes, which included key metabolic shifts—such as reduced energy metabolism, increased carbohydrate degradation over lipid or amino acid metabolism, and enriched biosynthesis of stress-responsive metabolites—occurred independently of later colonization or signalling molecule application. Conclusions Early AMF inoculation primes the rhizosphere bacteriome toward a stress-adapted functional state, likely mediated by altered root exudation during early symbiosis. The application of SL-M2 and quercetin further supports their role as prebiotics in sustaining inoculant efficacy. This study provides mechanistic insight into how nursery-stage microbial interventions can shape rhizosphere functionality, offering promising strategies for microbiome-driven improvements in sustainable agriculture. Graphical Abstract
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Claims 7
Claim · model-written summary
Nursery AMF inoculation combined with SL-M2 and quercetin significantly enhanced mycorrhizal colonization of tomato.
- Taxon
- Solanum lycopersicum
Solanum lycopersicume3 - Treatment
- Nursery AMF inoculation, especially when combined with the strigolactone mimic SL-M2 and quercetine1
- Interactor
- R. irregularis
Rhizophagus irregularise2symbiont - Outcome
- mycorrhizal colonizatione1
- Direction
- enhancede1
- Setting
- commercial nurserye2
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Nursery AMF inoculation, especially when combined with the strigolactone mimic SL-M2 and quercetin, significantly enhanced mycorrhizal colonization”
e2“Tomato seedlings were inoculated with R. irregularis in a commercial nursery”
e3“rhizosphere microbiome of Solanum lycopersicum”
Claim · model-written summary
Early inoculation did not affect bacterial or fungal taxonomic composition of the tomato rhizosphere at harvest.
- Taxon
- Solanum lycopersicumSolanum lycopersicume3
- Treatment
- early inoculatione4
- Outcome
- bacterial or fungal taxonomic compositione4
- Direction
- did not affecte4
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e4“early inoculation did not affect bacterial or fungal taxonomic composition at harvest”
e3“rhizosphere microbiome of Solanum lycopersicum”
Claim · model-written summary
Early inoculation induced substantial shifts in predicted bacterial metabolic functions, affecting 137 of 154 KEGG modules.
- Taxon
- Solanum lycopersicumSolanum lycopersicume3
- Treatment
- early inoculatione4
- Outcome
- predicted bacterial metabolic functionse5
- Direction
- shiftse5
- Value
- 137 of 154 KEGG modulese5
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e5“it induced substantial shifts in predicted bacterial metabolic functions, affecting 137 of 154 KEGG modules”
e4“early inoculation did not affect bacterial or fungal taxonomic composition at harvest”
e3“rhizosphere microbiome of Solanum lycopersicum”
Claim · model-written summary
Early inoculation shifted predicted bacterial metabolism toward reduced energy metabolism.
- Taxon
- Solanum lycopersicumSolanum lycopersicume3
- Treatment
- early inoculatione4
- Outcome
- energy metabolisme6
- Direction
- reducede6
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e6“reduced energy metabolism”
e4“early inoculation did not affect bacterial or fungal taxonomic composition at harvest”
e3“rhizosphere microbiome of Solanum lycopersicum”
Claim · model-written summary
Early inoculation shifted predicted bacterial metabolism toward increased carbohydrate degradation over lipid or amino acid metabolism.
- Taxon
- Solanum lycopersicumSolanum lycopersicume3
- Treatment
- early inoculatione4
- Outcome
- carbohydrate degradatione7
- Direction
- increasede7
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e7“increased carbohydrate degradation over lipid or amino acid metabolism”
e4“early inoculation did not affect bacterial or fungal taxonomic composition at harvest”
e3“rhizosphere microbiome of Solanum lycopersicum”
Claim · model-written summary
Early inoculation enriched predicted bacterial biosynthesis of stress-responsive metabolites.
- Taxon
- Solanum lycopersicumSolanum lycopersicume3
- Treatment
- early inoculatione4
- Outcome
- biosynthesis of stress-responsive metabolitese6
- Direction
- enrichede6
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e6“enriched biosynthesis of stress-responsive metabolites”
e4“early inoculation did not affect bacterial or fungal taxonomic composition at harvest”
e3“rhizosphere microbiome of Solanum lycopersicum”
Claim · model-written summary
Early AMF inoculation likely primes the tomato rhizosphere bacteriome toward a stress-adapted functional state through altered root exudation.
- Taxon
- Solanum lycopersicumSolanum lycopersicume3
- Treatment
- Early AMF inoculatione5
- Outcome
- stress-adapted functional statee5
- Qualifier
- altered root exudation during early symbiosise5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e5“Early AMF inoculation primes the rhizosphere bacteriome toward a stress-adapted functional state, likely mediated by altered root exudation during early symbiosis”
e3“rhizosphere microbiome of Solanum lycopersicum”
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