References

Principles for rigorous design and application of synthetic microbial communities.

10.1002/advs.202514750 · ExternalCitation · doi-reference

Microbial diversity and function in the rhizosphere microbiome: Driving forces and monitoring approaches.

10.1002/agg2.70169 · ExternalCitation · doi-reference

Synergistic biocontrol of Bacillus subtilis and Pseudomonas fluorescens against early blight disease in tomato.

10.1007/s00253-023-12642-w · ExternalCitation · doi-reference

Development of a chemotactic SynCom bioorganic fertilizer for biocontrol of bacterial wilt in tobacco fields.

10.1007/s00253-025-13547-6 · ExternalCitation · doi-reference

Biochar reshapes soil bacterial community composition and survival strategies: A meta-analysis revealing trade-offs between microbial stability and functional complexity.

10.1007/s00374-025-01971-9 · ExternalCitation · doi-reference

Plant microbiome structure and benefits for sustainable agriculture.

10.1016/j.cpb.2021.100198 · ExternalCitation · doi-reference

Deciphering and designing microbial communities by genome-scale metabolic modelling.

10.1016/j.csbj.2024.04.055 · ExternalCitation · doi-reference

L-asparaginase-driven antibiosis in Pseudomonas fluorescens EK007: A promising biocontrol strategy against fire blight.

10.1016/j.ijbiomac.2024.136402 · ExternalCitation · doi-reference

Synthetic microbial communities rescues strawberry from soil-borne disease by enhancing soil functional microbial abundance and multifunctionality.

10.1016/j.jare.2025.08.040 · ExternalCitation · doi-reference

Microbial communities associated with plants: Learning from nature to apply it in agriculture.

10.1016/j.mib.2017.03.011 · ExternalCitation · doi-reference

Mitigating maize stalk rot disease: Harnessing Bacillus subtilis PM57 and Bacillus cereus PM38 as biocontrol allies against Erwiniacarotovora.

10.1016/j.micpath.2025.107556 · ExternalCitation · doi-reference

The relevance of biochar and co-applied SynComs on maize quality and sustainability: Evidence from field experiments.

10.1016/j.scitotenv.2025.178872 · ExternalCitation · doi-reference

Design, analysis and application of synthetic microbial consortia.

10.1016/j.synbio.2016.02.001 · ExternalCitation · doi-reference

A systematic discussion and comparison of the construction methods of synthetic microbial community.

10.1016/j.synbio.2024.06.006 · ExternalCitation · doi-reference

Enhancing sourdough fermentation with AI and multi-omics: From natural diversity to synthetic microbial community.

10.1016/j.tifs.2025.105233 · ExternalCitation · doi-reference

The rhizosphere microbiome and plant health.

10.1016/j.tplants.2012.04.001 · ExternalCitation · doi-reference

Protists: Puppet masters of the rhizosphere microbiome.

10.1016/j.tplants.2018.10.011 · ExternalCitation · doi-reference

Rational management of the plant microbiome for the Second Green Revolution.

10.1016/j.xplc.2024.100812 · ExternalCitation · doi-reference

Synthetic communities and metabolite-driven enrichment of keystone rhizosphere microbial taxa suppress bacterial wilt disease in peanut.

10.1016/j.xplc.2026.101790 · ExternalCitation · doi-reference

Machine learning-guided synthetic microbial communities enable functional and sustainable degradation of persistent environmental pollutants.

10.1021/acs.est.6c01112 · ExternalCitation · doi-reference

A synthetic microbial community of plant core microbiome can be a potential biocontrol tool.

10.1021/acs.jafc.2c08017 · ExternalCitation · doi-reference

Citrate synthase GltA modulates the 2,4-Diacetylphloroglucinol biosynthesis of Pseudomonas fluorescens 2P24 and is essential for the biocontrol capacity.

10.1021/acs.jafc.3c03051 · ExternalCitation · doi-reference

Cross-Kingdom synthetic microbiota suppresses wheat fusarium crown rot by remodeling the rhizosphere microbiome and metabolome.

10.1021/acs.jafc.5c11786 · ExternalCitation · doi-reference

A strategy for stable, on-seed application of a nitrogen-fixing microbial inoculant by microencapsulation in spray-dried cross-linked alginates.

10.1021/acsagscitech.2c00107 · ExternalCitation · doi-reference

Rhizosphere microbiome structure alters to enable wilt resistance in tomato.

10.1038/nbt.4232 · ExternalCitation · doi-reference

Going back to the roots: The microbial ecology of the rhizosphere.

10.1038/nrmicro3109 · ExternalCitation · doi-reference

Persistent microbiome members in the common bean rhizosphere: An integrated analysis of space, time, and plant genotype.

10.1038/s41396-021-00955-5 · ExternalCitation · doi-reference

Sucrose triggers a novel signaling cascade promoting Bacillus subtilis rhizosphere colonization.

10.1038/s41396-021-00966-2 · ExternalCitation · doi-reference

Synthetic bacterial community derived from a desert rhizosphere confers salt stress resilience to tomato in the presence of a soil microbiome.

10.1038/s41396-022-01238-3 · ExternalCitation · doi-reference

Cross-kingdom synthetic microbiota supports tomato suppression of Fusarium wilt disease.

10.1038/s41467-022-35452-6 · ExternalCitation · doi-reference

Tapping the rhizosphere metabolites for the prebiotic control of soil-borne bacterial wilt disease.

10.1038/s41467-023-40184-2 · ExternalCitation · doi-reference

Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease.

10.1038/s41467-023-43926-4 · ExternalCitation · doi-reference

Fusaric acid mediates the assembly of disease-suppressive rhizosphere microbiota via induced shifts in plant root exudates.

10.1038/s41467-024-49218-9 · ExternalCitation · doi-reference

Superiority of native soil core microbiomes in supporting plant growth.

10.1038/s41467-024-50685-3 · ExternalCitation · doi-reference

From “synthetic” to defined microbial communities for clearer terminology.

10.1038/s41467-026-74251-1 · ExternalCitation · doi-reference

Data-driven synthetic microbes for sustainable future.

10.1038/s41540-025-00556-4 · ExternalCitation · doi-reference

A cross-systems primer for synthetic microbial communities.

10.1038/s41564-024-01827-2 · ExternalCitation · doi-reference

Community standards and future opportunities for synthetic communities in plant–microbiota research.

10.1038/s41564-024-01833-4 · ExternalCitation · doi-reference

Plant-microbiome interactions: From community assembly to plant health.

10.1038/s41579-020-0412-1 · ExternalCitation · doi-reference

Harnessing the plant microbiome for sustainable crop production.

10.1038/s41579-024-01079-1 · ExternalCitation · doi-reference

Changes in microbial community and enzyme activity in soil under continuous pepper cropping in response to Trichoderma hamatum MHT1134 application.

10.1038/s41598-021-00951-x · ExternalCitation · doi-reference

Co-inoculation of rhizobacteria promotes growth, yield, and nutrient contents in soybean and improves soil enzymes and nutrients under drought conditions.

10.1038/s41598-021-01337-9 · ExternalCitation · doi-reference

Effects of long-term continuous cultivation on the structure and function of soil bacterial and fungal communities of Fritillaria Cirrhosa on the Qinghai-Tibetan Plateau.

10.1038/s41598-024-70625-x · ExternalCitation · doi-reference

Impact of microbial consortia and fertilization regimes on the soil microbiome in maize field trials.

10.1038/s41598-026-47528-0 · ExternalCitation · doi-reference

Root microbiota confers rice resistance to aluminium toxicity and phosphorus deficiency in acidic soils.

10.1038/s43016-023-00848-0 · ExternalCitation · doi-reference

Synthetic microbial communities for sustainable hydroponic tomato production.

10.1038/s44264-026-00147-8 · ExternalCitation · doi-reference

High bacterial diversity drives the suppression of a soilborne plant disease.

10.1073/pnas.2509303123 · ExternalCitation · doi-reference

Scale-up of industrial microbial processes.

10.1093/femsle/fny138 · ExternalCitation · doi-reference

Synthetic microbial communities (SynComs) of the human gut: Design, assembly, and applications.

10.1093/femsre/fuad012 · ExternalCitation · doi-reference

Siderophore interactions drive the ability of Pseudomonas spp. consortia to protect tomato against Ralstonia solanacearum.

10.1093/hr/uhae186 · ExternalCitation · doi-reference

Decoding endophytic microbiome dynamics: Engineering antagonistic synthetic consortia for targeted fusarium suppression in monoculture regimes.

10.1093/hr/uhaf286 · ExternalCitation · doi-reference

Ecological design of high-performance synthetic microbial communities: From theoretical foundations to functional optimization.

10.1093/ismeco/ycaf133 · ExternalCitation · doi-reference

Strategies for tailoring functional microbial synthetic communities.

10.1093/ismejo/wrae049 · ExternalCitation · doi-reference

Defined synthetic microbial communities colonize and benefit field-grown sorghum.

10.1093/ismejo/wrae126 · ExternalCitation · doi-reference

Plant growth-promotion triggered by extracellular polymer is associated with facilitation of bacterial cross-feeding networks of the rhizosphere.

10.1093/ismejo/wraf040 · ExternalCitation · doi-reference

Decoding emergent properties of microbial community functions through subcommunity observations and interpretable machine learning.

10.1093/ismejo/wraf236 · ExternalCitation · doi-reference

Offensive role of the Bacillus extracellular matrix in driving metabolite-mediated dialog and adaptive strategies with the fungus Botrytis.

10.1093/ismejo/wraf277 · ExternalCitation · doi-reference

Stress-induced keystone species facilitate functional microbial community assembly to suppress root-knot nematodes for susceptible plants.

10.1093/ismejo/wrag022 · ExternalCitation · doi-reference

Unraveling plant-microbe interactions: Can integrated omics approaches offer concrete answers?

10.1093/jxb/erad448 · ExternalCitation · doi-reference

Tomato roots secrete tomatine to modulate the bacterial assemblage of the rhizosphere.

10.1093/plphys/kiab069 · ExternalCitation · doi-reference

Biocontrol of bacterial wilt disease using plant-associated bacterial communities in tomato.

10.1094/mpmi-09-24-0114-r · ExternalCitation · doi-reference

Emergence and spread of new races of wheat stem rust fungus: Continued threat to food security and prospects of genetic control.

10.1094/phyto-01-15-0030-fi · ExternalCitation · doi-reference

Phenazines in plant-beneficial Pseudomonas spp.: Biosynthesis, regulation, function and genomics.

10.1111/1462-2920.14395 · ExternalCitation · doi-reference

The complex extracellular biology of Streptomyces.

10.1111/j.1574-6976.2009.00206.x · ExternalCitation · doi-reference

The rhizosphere microbiome: Plant-microbial interactions for resource acquisition.

10.1111/jam.15686 · ExternalCitation · doi-reference

Combating biotic stresses in plants by synthetic microbial communities: Principles, applications and challenges.

10.1111/jam.15799 · ExternalCitation · doi-reference

Fusaric acid contributes to virulence of Fusarium oxysporum on plant and mammalian hosts.

10.1111/mpp.12536 · ExternalCitation · doi-reference

The importance of the microbiome of the plant holobiont.

10.1111/nph.13312 · ExternalCitation · doi-reference

Plant growth-promoting rhizobacterium Bacillus cereus AR156 induced systemic resistance against multiple pathogens by priming of camalexin synthesis.

10.1111/pce.14729 · ExternalCitation · doi-reference

Turning antagonists into allies: Bacterial-fungal interactions enhance the efficacy of controlling Fusarium wilt disease.

10.1126/sciadv.ads5089 · ExternalCitation · doi-reference

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome.

10.1126/science.aaw9285 · ExternalCitation · doi-reference

Rewilding plant microbiomes.

10.1126/science.abn6350 · ExternalCitation · doi-reference

Requirement of siderophore biosynthesis for plant colonization by Salmonella enterica.

10.1128/aem.07867-11 · ExternalCitation · doi-reference

Probiotic diversity enhances rhizosphere microbiome function and plant disease suppression.

10.1128/mbio.01790-16 · ExternalCitation · doi-reference

Cross-Feedings, competition, and positive and negative synergies in a four-species synthetic community for anaerobic degradation of cellulose to methane.

10.1128/mbio.03189-22 · ExternalCitation · doi-reference

The role of plant host genetics in shaping the composition and functionality of rhizosphere microbiomes.

10.1128/msystems.00041-24 · ExternalCitation · doi-reference

Metabolic interactions affect the biomass of synthetic bacterial biofilm communities.

10.1128/msystems.01045-23 · ExternalCitation · doi-reference

Precision probiotics in agroecosystems: Multiple strategies of native soil microbiotas for conquering the competitor Ralstonia solanacearum.

10.1128/msystems.01159-21 · ExternalCitation · doi-reference

Deep roots and splendid boughs of the global plant virome.

10.1146/annurev-phyto-030320-041346 · ExternalCitation · doi-reference

Bacterial community structure and co-occurrence networks in the rhizosphere and root endosphere of the grafted apple.

10.1186/s12866-024-03210-x · ExternalCitation · doi-reference

Plant growth promotion and biocontrol properties of a synthetic community in the control of apple disease.

10.1186/s12870-024-05253-8 · ExternalCitation · doi-reference

Biochar-based organic fertilizer application promotes the alleviation of tobacco (Nicotiana tabacum L.) continuous cropping obstacles by improving soil chemical properties and microbial community structure.

10.1186/s12870-025-06266-7 · ExternalCitation · doi-reference

Multi-genome metabolic modeling predicts functional inter-dependencies in the Arabidopsis root microbiome.

10.1186/s40168-022-01383-z · ExternalCitation · doi-reference

Synthetic community derived from grafted watermelon rhizosphere provides protection for ungrafted watermelon against Fusarium oxysporum via microbial synergistic effects.

10.1186/s40168-024-01814-z · ExternalCitation · doi-reference

Interactions with native microbial keystone taxa enhance the biocontrol efficiency of Streptomyces.

10.1186/s40168-025-02120-y · ExternalCitation · doi-reference

Long-term continuous cropping reshapes soybean rhizosphere microbiome and metabolome to alleviate allelopathic stress and enhance disease suppression.

10.1186/s40168-025-02311-7 · ExternalCitation · doi-reference

Ecology-guided Bacillus SynCom from a rice-duckweed core reveals division of labor for concurrent growth promotion and sheath blight suppression.

10.1186/s40168-026-02360-6 · ExternalCitation · doi-reference

The genotype of barley cultivars influences multiple aspects of their associated microbiota via differential root exudate secretion.

10.1371/journal.pbio.3002232 · ExternalCitation · doi-reference

Compatible bacterial mixture, tolerant to desiccation, improves maize plant growth.

10.1371/journal.pone.0187913 · ExternalCitation · doi-reference

Functional redundancy as a stabilizing principle in bacterial communities under antibiotic perturbation: Mechanisms, trade-offs, and emerging frameworks.

10.3389/fmed.2026.1834295 · ExternalCitation · doi-reference

Current insights into the role of rhizosphere bacteria in disease suppressive soils.

10.3389/fmicb.2017.02529 · ExternalCitation · doi-reference

Perspectives of microbial inoculation for sustainable development and environmental management.

10.3389/fmicb.2018.02992 · ExternalCitation · doi-reference

ACC deaminase producing bacteria with multifarious plant growth promoting traits alleviates salinity stress in french bean (Phaseolus vulgaris) Plants.

10.3389/fmicb.2019.01506 · ExternalCitation · doi-reference

Antifungal, plant growth-promoting, and genomic properties of an endophytic actinobacterium Streptomyces sp. NEAU-S7GS2.

10.3389/fmicb.2019.02077 · ExternalCitation · doi-reference

Modulating drought stress response of maize by a synthetic bacterial community.

10.3389/fmicb.2021.747541 · ExternalCitation · doi-reference

Interactions between phenolic acids and microorganisms in rhizospheric soil from continuous cropping of Panax notoginseng.

10.3389/fmicb.2022.791603 · ExternalCitation · doi-reference

Construction of environmental synthetic microbial consortia: Based on engineering and ecological principles.

10.3389/fmicb.2022.829717 · ExternalCitation · doi-reference

Synthetic microbial consortia derived from rhizosphere soil protect wheat against a soilborne fungal pathogen.

10.3389/fmicb.2022.908981 · ExternalCitation · doi-reference

Designing a synthetic microbial community devoted to biological control: The case study of Fusarium wilt of banana.

10.3389/fmicb.2022.967885 · ExternalCitation · doi-reference

Promotion of the growth and yield of Zea mays by synthetic microbial communities from Jala maize.

10.3389/fmicb.2023.1167839 · ExternalCitation · doi-reference

An antibiotic produced by Pseudomonas fluorescens CFBP2392 with antifungal activity against Rhizoctonia solani.

10.3389/fmicb.2023.1286926 · ExternalCitation · doi-reference

Biocontrol of citrus fungal pathogens by lipopeptides produced by Bacillus velezensis TZ01.

10.3389/fmicb.2024.1471305 · ExternalCitation · doi-reference

Plant microbiome technology for sustainable agriculture.

10.3389/fmicb.2024.1500260 · ExternalCitation · doi-reference

Teosinte-derived SynCom and precision biofertilization modulate the maize microbiome, enhancing growth, yield, and soil functionality in a Mexican field.

10.3389/fmicb.2025.1534327 · ExternalCitation · doi-reference

Soil microbiome dysbiosis and rhizosphere metabolic dysfunction drive continuous cropping obstacles of Codonopsis tangshen.

10.3389/fmicb.2025.1628234 · ExternalCitation · doi-reference

A stable 15-member bacterial SynCom promotes Brachypodium growth under drought stress.

10.3389/fmicb.2025.1649750 · ExternalCitation · doi-reference

Features and rhizosphere colonization strategies of Lactobacillus plantarum 0308 in soil-tomato systems.

10.3389/fmicb.2025.1652881 · ExternalCitation · doi-reference

Synthetic microbiomes in bioengineered rhizospheres: New frontiers for climate-resilient agriculture.

10.3389/fmicb.2026.1780132 · ExternalCitation · doi-reference

Plant microbiome engineering: From inoculation to genome editing.

10.3389/fmicb.2026.1781381 · ExternalCitation · doi-reference

Strategies for transferring resistance into wheat: From wide crosses to GM cassettes.

10.3389/fpls.2014.00692 · ExternalCitation · doi-reference

Microbial consortia for effective biocontrol of root and foliar diseases in tomato.

10.3389/fpls.2021.756368 · ExternalCitation · doi-reference

Triple interactions for induced systemic resistance in plants.

10.3389/fpls.2024.1464710 · ExternalCitation · doi-reference

Isolation and characterization of Stenotrophomonas rhizophila T3E: A multifunctional rhizobacterium enhancing tomato growth and soil health.

10.3389/fpls.2025.1692957 · ExternalCitation · doi-reference

Engineering the plant microbiome: Synthetic community approaches to enhance crop protection.

10.3389/fpls.2025.1705289 · ExternalCitation · doi-reference

A minimal cross-kingdom SynCom promotes plant growth and suppresses wheat crown rot via coordinated rhizosphere microbiome remodeling.

10.3389/fpls.2026.1758273 · ExternalCitation · doi-reference

Differential modulation of tomato root exudates by Streptomyces strains underlies contrasting control of Fusarium oxysporum f. sp. lycopersici.

10.3389/fpls.2026.1759226 · ExternalCitation · doi-reference

Soil-borne diseases in medicinal plants: Linking allelopathy and host immunity to microbiome-based interventions.

10.3389/fpls.2026.1797910 · ExternalCitation · doi-reference

A systematic review on the continuous cropping obstacles and control strategies in medicinal plants.

10.3390/ijms241512470 · ExternalCitation · doi-reference

Actinobacteria as effective biocontrol agents against plant pathogens, an overview on their role in eliciting plant defense.

10.3390/microorganisms10091739 · ExternalCitation · doi-reference

Synthetic microbial community promotes bacterial communities leading to soil multifunctionality in desertified land.

10.3390/microorganisms12061117 · ExternalCitation · doi-reference

The colonization of synthetic microbial communities carried by bio-organic fertilizers in continuous cropping soil for potato plants.

10.3390/microorganisms12112371 · ExternalCitation · doi-reference

Formation of a novel antagonistic bacterial combination to enhance biocontrol for cucumber Fusarium wilt.

10.3390/microorganisms13010133 · ExternalCitation · doi-reference

Pathogen identification, antagonistic microbe screening, and biocontrol strategies for Aconitum carmichaelii root rot.

10.3390/microorganisms13092202 · ExternalCitation · doi-reference

Evaluation of biocontrol efficacy of Bacillus velezensis HAB-2 combined with Pseudomonas hunanensis and Enterobacter soli against cowpea fusarium wilt.

10.3390/microorganisms13112578 · ExternalCitation · doi-reference

Rhizosphere microbiome engineering for climate-smart agriculture: From synthetic consortia to precision decision support.

10.3390/microorganisms14051138 · ExternalCitation · doi-reference

Allelochemicals from the Rhizosphere Soil of Potato (Solanum tuberosum L.) and Their Interactions with the Soilborne Pathogens.

10.3390/plants11151934 · ExternalCitation · doi-reference

Plant growth-promoting soil bacteria: Nitrogen fixation, phosphate solubilization, siderophore production, and other biological activities.

10.3390/plants12244074 · ExternalCitation · doi-reference

Microbiome-Mediated strategies to manage major soil-borne diseases of tomato.

10.3390/plants13030364 · ExternalCitation · doi-reference

Characterizing wheat rhizosphere bacterial microbiome dynamics under salinity stress: Insights from 16S rRNA metagenomics for enhancing stress tolerance.

10.3390/plants14071033 · ExternalCitation · doi-reference

Application of a synthetic microbial community to enhance pepper resistance against Phytophthora capsici.

10.3390/plants14111625 · ExternalCitation · doi-reference

Meta-analysis reveals that the genus Pseudomonas can be a better choice of biological control agent against bacterial wilt disease caused by Ralstonia solanacearum.

10.5423/ppj.oa.11.2015.0235 · ExternalCitation · doi-reference

Take-all of wheat and natural disease suppression: A review.

10.5423/ppj.si.07.2012.0112 · ExternalCitation · doi-reference