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Plant stress caused by abiotic and biotic factors poses a significant threat to global agricultural productivity and food security. Beneficial soil microorganisms, particularly plant growth-promoting rhizobacteria (PGPR), mycorrhizal fungi, and endophytic microbes, play a critical role in enhancing plant stress tolerance through diverse functional mechanisms. This review provides a comprehensive analysis of the functional profiling of beneficial soil microbes and their contributions to improving plant resilience under stress conditions such as drought, salinity, temperature extremes, and pathogen attack. Key mechanisms include phytohormone modulation, osmolyte accumulation, antioxidant enzyme activation, induced systemic resistance, and nutrient acquisition enhancement. Advances in omics technologies, including metagenomics, transcriptomics, and metabolomics, have facilitated deeper insights into microbial functions and plant–microbe interactions. Emerging approaches such as microbiome engineering, biofertilizer development, and precision agriculture are discussed for their potential to mitigate stress impacts sustainably. Furthermore, the implications of microbial-based stress management strategies for environmental sustainability and public health are highlighted, particularly in reducing agrochemical use and improving food quality. Despite promising developments, challenges related to field variability, microbial survival, and large-scale application remain. Future research directions emphasize the integration of multi-disciplinary approaches to optimize microbial interventions for sustainable agriculture and global health
Keywords: Beneficial soil microbes; Plant stress tolerance; Plant growth-promoting rhizobacteria (PGPR); Mycorrhiza; Abiotic stress; Biotic stress; Biofertilizers; Microbiome engineering; Sustainable agriculture; Plant–microbe interactions; Beneficialsoilmicrobes; Plantstresstolerance; Plantgrowth-promotingrhizobacteria(PGPR); Plant–microbeinteractions
Mycorrhiza; Abiotic stress; Biotic stress; Biofertilizers; Microbiome engineering; Sustainable agriculture; Plant–microbeinteractions.
1.Introduction croorganismsreleaseorganicacidsandenzymesthat increase phosphorus availability in soils [26,27]. In Plantgrowthandproductivityareincreasinglythreat- addition,AMFformsymbioticassociationswithplant enedbyawiderangeofabioticandbioticstressfac- roots, extending the effective root surface area and tors,includingdrought,salinity,temperatureextremes, enhancingtheuptakeofwaterandnutrients,partic- heavymetals,andpathogenicinfections.Thesestres- ularlyunderdroughtconditions[28,29]. Apartfrom sorssignificantlyreducecropyieldandquality,posing abioticstressmitigation,beneficialsoilmicrobesalso serious challenges to global food security and pub- playavitalroleinprotectingplantsagainstbioticstress lic health [1,2]. Climate change has further intensi- causedbypathogens. Mechanismssuchasinduced fiedthefrequencyandseverityofthesestresses,ne- systemicresistance(ISR),productionofantimicrobial cessitatingthedevelopmentofsustainableandenvi- compounds,andcompetitiveexclusioncontributeto ronmentally friendly strategies to enhance plant re- disease suppression [30–32]. Microorganisms such silience[3,4].Therhizosphere,definedasthenarrow asPseudomonasandTrichodermahavebeenexten- zone of soil influenced by plant roots, is a dynamic sivelystudiedfortheirbiocontrolpropertiesandability andbiologicallyactiveinterfacewherecomplexinter- toenhanceplantimmunity[33,34].Recentadvances actionsoccurbetweenplantsandmicroorganisms[5]. inhigh-throughputsequencingandomicstechnolo- Thisregionhostsadiversecommunityofbeneficial gies, includingmetagenomics, transcriptomics, and soilmicrobes,includingplantgrowth-promotingrhi- metabolomics,havesignificantlyimprovedourunder- zobacteria(PGPR),arbuscularmycorrhizalfungi(AMF), standingofplant–microbeinteractions[35–37].These andendophytes,whichplayacrucialroleinimprov- technologiesprovideinsightsintomicrobialdiversity, ing plant stress tolerance [6–8]. Early work by Hilt- functional capabilities, and metabolic pathways in- nerestablishedtheconceptoftherhizosphere,while volvedinstresstolerance.Plantsactivelyshapetheir subsequentstudiesdemonstratedtheabilityofPGPR rhizospheremicrobiomethroughthereleaseofroot toenhanceplantgrowthandmitigatestresseffects exudates,whichserveassignalingmoleculesandnu- [9–11].Beneficialsoilmicroorganismsemploymultiple trientsourcesforbeneficialmicrobes[38,39]. Micro- functionalmechanismstoimproveplanttoleranceto biome engineering has emerged as a promising ap- stressconditions.Oneofthekeymechanismsinvolves proachtoenhanceplantstresstolerancebymanipulat- the production of phytohormones such as indole-3- ingmicrobialcommunities[40].Thedevelopmentof acetic acid, gibberellins, and cytokinins, which reg- syntheticmicrobialconsortiaandbiofertilizersoffers ulateplantgrowthanddevelopmentunderadverse newopportunitiesforsustainableagricultureandre- conditions[12,13].Inaddition,severalPGPRproduce duceddependenceonchemicalinputs[41,42].These 1-aminocyclopropane-1-carboxylate(ACC)deaminase, strategiesareparticularlyimportantinthecontextof whichreducesstress-inducedethylenelevelsinplants, climatechangeandenvironmentalsustainability.The therebyalleviatinggrowthinhibition[14,15]. These applicationofbeneficialsoilmicrobesalsohasimpor- mechanismshavebeenwidelyreportedtoenhance tantimplicationsforpublichealth.Reducingtheuse planttolerancetodrought,salinity,andotherabiotic ofchemicalfertilizersandpesticidesminimizesenvi- stresses[16,17].Anotherimportantadaptiveresponse ronmentalcontamination,improvessoilhealth,and involvestheaccumulationofosmolytessuchaspro- enhancesfoodsafety[43,44].Microbial-basedagricul- line,glycinebetaine,andsolublesugars,whichhelp turalpracticescontributetosustainablefoodproduc- maintaincellularosmoticbalanceduringstress[18,19]. tionsystemsandsupportglobaleffortstomitigatecli- Microbialinoculationhasbeenshowntoenhanceos- matechange[45].Despitethepromisingpotentialof molyteaccumulationandimprovewaterretentionca- beneficialsoilmicrobes,severalchallengesremainin pacityinplantssubjectedtodroughtandsalinitycon- theirpracticalapplication.Environmentalvariability, ditions[20]. Furthermore, beneficialmicrobesstim- soilheterogeneity,andcompetitionwithnativemicro- ulateantioxidantdefensesystems,increasingtheac- bialcommunitiescanaffectthesurvivalandeffective- tivityofenzymessuchassuperoxidedismutase,cata- nessofintroducedmicrobes[46,47].Additionally,the lase,andperoxidase,therebyreducingoxidativedam- lackofstandardizedformulationsanddeliverysystems agecausedbystress[21–23]. Nutrientacquisitionis limitslarge-scaleadoptionofmicrobialtechnologies alsosignificantlyenhancedbysoilmicrobes,contribut- [48]. Inconclusion,functionalprofilingofbeneficial ingtoimprovedplanthealthunderstressconditions. soilmicrobesprovidescriticalinsightsintotheirrolein Nitrogen-fixingbacteriasuchasRhizobium,Azotobac- enhancingplantstresstolerance.Harnessingthesemi- ter, and Azospirillum convert atmospheric nitrogen crobialfunctionsthroughinnovativeandsustainable into plant-available forms, thereby improving nitro- approachescansignificantlyimproveagriculturalpro- genuseefficiency[24,25].Phosphate-solubilizingmi- ductivitywhileensuringenvironmentalsustainability 2.3 ActivationofAntioxidantDefenseSystems andpublichealthsafety.
Environmentalstressesoftenresultinexcessivepro- ductionofreactiveoxygenspecies(ROS),whichcause 2.MechanismsofBeneficialSoilMicrobesin oxidativedamagetolipids,proteins,andnucleicacids. EnhancingPlantStressTolerance Beneficialsoilmicrobesenhancetheplant’santioxi- dantdefensesystembyincreasingtheactivityofkey Beneficialsoilmicroorganismsplayacriticalrolein enzymessuchassuperoxidedismutase,catalase,per- enhancingplantresiliencetoenvironmentalstresses oxidase, andascorbateperoxidase[67–70]. Thisen- through complex physiological, biochemical, and hancedantioxidantactivityreducesoxidativestress molecularinteractionswithintherhizosphere.These andprotectscellularcomponents,therebyimproving microbes,includingplantgrowth-promotingrhizobac- plantresilience.Studieshavealsoshownthatmicro- teria(PGPR),arbuscularmycorrhizalfungi(AMF),and bialinoculationcanupregulategenesassociatedwith endophytes,contributetostresstolerancebymodulat- antioxidantpathways,furtherstrengtheningplantde- ingplantmetabolism,improvingnutrientacquisition, fensemechanisms[71,72].
andactivatingdefensepathways.Recentadvancesin plant–microbeinteractionstudieshavedemonstrated 2.4 NutrientAcquisitionandRhizosphereEngineer- thatthesemechanismsfunctionsynergisticallytomiti- ing gatetheeffectsofabioticandbioticstresses[49–52]. Nutrient limitation is a major factor affecting plant stresstolerance. Beneficialmicrobesenhancenutri- 2.1 PhytohormoneModulationandEthyleneRegu- entavailabilitythroughvariousprocesses,includingni- lation trogenfixation,phosphorussolubilization,potassium Oneofthemostsignificantmechanismsemployedby mobilization, and micronutrient chelation [73–76]. beneficialmicrobesisthemodulationofplantphyto- Nitrogen-fixingbacteriasuchasRhizobium,Azotobac- hormones.PGPRsynthesizehormonessuchasindole- ter, and Azospirillum convert atmospheric nitrogen 3-aceticacid(IAA),cytokinins,andgibberellins,which into plant-available forms, thereby improving nitro- regulaterootarchitecture,enhancelateralrootforma- genuseefficiency[77,78].Phosphate-solubilizingbac- tion, andimprovenutrientuptakeunderstresscon- teriareleaseorganicacidsandenzymesthatconvert ditions[49–53]. Akeymicrobialadaptationinvolves insolublephosphorusintoaccessibleforms[79,80].Ar- theproductionofACCdeaminase,whichlowersthe buscularmycorrhizalfungi(AMF)establishsymbiotic levelsofstress-inducedethyleneinplants. Elevated associationswithplantroots, extendinghyphalnet- ethylenelevelsareknowntoinhibitrootelongation worksintothesoilandenhancingtheuptakeofwater andoverallplantgrowthunderstressconditions.By andnutrients,particularlyunderdroughtconditions degradingACC,theprecursorofethylene,microbesal- [81–83]. Additionally, microbial activity contributes leviatestress-inducedgrowthinhibitionandenhance toimprovedsoilstructure,organicmatterdecompo- planttolerancetodrought,salinity,andtemperature sition,andenhancedmicrobialbiomass,collectively extremes[54–57]. Furthermore, microbialsignaling referredtoasrhizosphereengineering[84–86]. moleculesinfluencehormonalcross-talkwithinplants, enablingbetteradaptationtoenvironmentalstressors [58,59].
2.5 InducedSystemicResistance(ISR)andBiocon- trolMechanisms 2.2 OsmoticAdjustmentandCellularHomeostasis Beneficialmicrobesplayacrucialroleinprotecting Abioticstressessuchasdroughtandsalinitydisrupt plantsagainstpathogensthroughinducedsystemic cellularosmoticbalance,leadingtodehydrationand resistance(ISR).Thismechanisminvolvestheactiva- reducedmetabolicactivity. Beneficialmicrobespro- tion of plant defense pathways mediated by signal- motetheaccumulationofcompatiblesolutes,includ- ing molecules such as jasmonic acid, salicylic acid, ingproline,glycinebetaine,trehalose,andsolublesug- andethylene[87–89]. MicroorganismssuchasPseu- ars,whichplayacrucialroleinosmoticadjustment domonas,Bacillus,andTrichodermaproduceantimi- [60–63].Theseosmolytesstabilizecellularmembranes, crobialcompounds,siderophores,andlyticenzymes protectproteinsfromdenaturation,andmaintainen- thatsuppresspathogengrowth[90–92]. Inaddition, zymeactivityunderstressconditions.Microbialinocu- competitiveexclusionandnicheoccupationbybenefi- lationhasbeenshowntosignificantlyenhancewater- cialmicrobesreducepathogencolonizationintherhi- useefficiencyandmaintaincellularturgorpressure, zosphere.Thesebiocontrolmechanismsareessential therebyimprovingplantsurvivalunderwater-deficit formanagingbioticstressinasustainableandenviron- conditions[64–66].
2.6 Molecular Signaling and Plant–Microbe Com- cropproductivityandstressresilience. Theseappli- munication cations are increasingly important in the context of Recent studies have highlighted the importance of climatechange,soildegradation,andtheneedtore- molecular signaling in plant–microbe interactions. ducedependenceonchemicalinputs.Microbial-based Root exudates act as chemical signals that attract technologiesoffersustainablesolutionsthatintegrate beneficialmicrobesandregulatemicrobialcoloniza- plant health, soil fertility, and environmental safety tion[96–98].Microbialsignalingmolecules,including [102].
quorum-sensingcompoundsandvolatileorganiccom- pounds(VOCs),influenceplantgeneexpressionand 3.1 BiofertilizersandMicrobialInoculants stressresponses[99–101].Thisbidirectionalcommuni- Biofertilizers containing beneficial microorganisms cationbetweenplantsandmicrobesplaysacrucialrole suchasplantgrowth-promotingrhizobacteria(PGPR), inestablishingsymbioticrelationshipsandenhancing phosphate-solubilizingbacteria(PSB),andarbuscular stresstolerance.
mycorrhizalfungi(AMF)arewidelyusedtoenhance nutrientavailabilityandplantgrowth. Theseinocu- lantsimprovenitrogenfixation,phosphorussolubiliza- tion,andoverallnutrientcycling,leadingtoincreased crop productivity under stress conditions [103,104]. Theuseofmicrobialconsortiahasbeenshowntobe more effective than single-strain inoculants, as syn- ergistic interactions among microbes enhance their functionalefficiencyandadaptabilityindiversesoil environments [105–107]. Additionally, biofertilizers contributetoimprovedsoilorganiccarbonandmicro- bialbiomass,whicharecriticalindicatorsofsoilhealth [108].
3.2 MicrobiomeEngineeringandSyntheticMicro- bialCommunities Microbiomeengineeringinvolvesthemanipulationof
cificenvironmentalconditionsandcroprequirements [109,110]. Theseengineeredmicrobialcommunities canenhancenutrientacquisition,regulateplanthor- mone levels, and improve stress resilience through coordinatedfunctionalactivities[111–113]. Thisap- proachrepresentsapromisingfrontierinsustainable agriculture,allowingprecisetargetingofbeneficialmi- crobialfunctions.
3.3 Climate-ResilientAgriculture Beneficial soil microbes play a vital role in climate-
3.ApplicationsofBeneficialSoilMicrobesin useefficiency,maintainsplantphysiologicalstability, Sustainable Agriculture and Stress Manage- andreducesyieldlossesunderadverseclimaticcon- ment ditions[114–116].Inregionswithfragileecosystems, The functional understanding of beneficial soil mi- suchasrainfedandsemi-aridareas,microbialinterven- crobeshasledtotheirwidespreadapplicationinmod- tionshavebeenshowntosignificantlyimprovecrop ern agriculture as eco-friendly tools for improving survivalandproductivity[117].Theseapproachesare MicrobialGroup RepresentativeGenera FunctionalRole StressTypeMitigated Hormoneproduction, PGPR Pseudomonas,Bacillus Drought,salinity ACCdeaminase Nitrogen-fixers Rhizobium,Azotobacter Nitrogenfixation Nutrientstress PSB Bacillus,Pseudomonas Phosphorussolubilization Nutrientdeficiency AMF Glomusspp. Nutrient&wateruptake Drought Biocontrolagents Trichoderma Pathogensuppression Bioticstress
ISRactivation Defensesignalingpathways Diseaseresistance essentialforensuringfoodsecurityunderchanging climatescenarios.
3.4 IntegrationwithPrecisionAgriculture Theintegrationofmicrobialtechnologieswithpreci- sionagriculturesystemshasopenednewavenuesfor efficientresourcemanagement.Precisionapplication ofmicrobialinoculantsusingadvancedtoolssuchas remotesensing,soilsensors,andGPS-basedsystems ensuresoptimaldeliveryandeffectiveness[118,119]. Thisapproachminimizesinputwastage,enhancesnu- trientuseefficiency,andimprovescropperformance undervariablefieldconditions.Moreover,data-driven decision-makingallowsforsite-specificmanagement ofsoilmicrobialpopulations,leadingtomoresustain- ableagriculturalpractices[120–122].
3.5 Biocontrol and Integrated Pest Management SustainableAgriculture (IPM) Beneficial microbes are widely used as biocontrol carbonsequestrationbystabilizingsoilorganiccarbon agentsinintegratedpestmanagement(IPM)systems. andimprovingsoilaggregation[128–130].Thesepro- MicroorganismssuchasTrichoderma,Pseudomonas, cessesnotonlyimprovesoilfertilitybutalsocontribute andBacillussuppressplantpathogensthroughmecha- toclimatechangemitigationbyreducinggreenhouse nismsincludingantibioticproduction,competitionfor gasemissionsassociatedwithintensiveagricultural nutrients,andinducedsystemicresistance[123–125]. practices[131].
Theuseofmicrobialbiocontrolagentsreducesreliance onchemicalpesticides,therebyminimizingenviron- 3.7 RoleinFoodQualityandNutritionalSecurity mentalcontaminationandpromotingecologicalbal- ance[126,127].Thesestrategiesareparticularlyimpor- Theapplicationofbeneficialsoilmicrobeshasbeen tantforsustainablecropprotectionandreducingthe linkedtoimprovementsincropqualityandnutritional emergenceofpesticide-resistantpathogens. content. Enhancednutrientuptakeresultsinhigher concentrationsofessentialmineralsandvitaminsin 3.6 SoilHealthRestorationandCarbonSequestra- crops,contributingtobetterhumannutrition[132,133]. tion Furthermore,reduceduseofchemicalfertilizersand Microbial-basedapproachescontributesignificantly pesticideslowerstheriskofharmfulresiduesinfood tosoilhealthrestorationbyenhancingsoilstructure, products, therebyimprovingfoodsafetyandpublic increasingorganicmattercontent,andpromotingnu- healthoutcomes[134–136].
trientcycling. Beneficialmicrobesplayakeyrolein Process MicrobialAgents NutrientImpact AgriculturalBenefit IncreasesN Nitrogenfixation Rhizobium,Azotobacter Reducedfertilizeruse availability ImprovesP Phosphorussolubilization PSB Enhancedgrowth availability Organicmatter Soilmicrobes Nutrientrelease Soilfertility decomposition Mycorrhizalsymbiosis AMF Nutrientuptake Stresstolerance
Biocontrol/IPM Pathogensuppression Reducedpesticideuse Soilrestoration Carbonsequestration Improvedsoilhealth playacrucialroleinmaintainingsoilandenvironmen- talhealth,whicharefundamentalcomponentsofthe OneHealthframeworkthatintegrateshuman,animal, and ecosystem health [141–143]. By improving soil fertility,reducinggreenhousegasemissions,andmini- mizingwatercontamination,beneficialsoilmicrobes contributetosustainableecosystemsandlong-term publichealthbenefits[144].
5.ChallengesandFuturePerspectives .Despitethepromisingpotentialofbeneficialsoilmi- crobes, several challenges hinder their large-scale
4.PublicHealthImplications othermajorlimitationisthecompetitionbetweenin- Theapplicationofbeneficialsoilmicrobesinagricul- troducedmicrobialinoculantsandnativesoilmicro- ture extends beyond crop productivity and environ- bialcommunities,whichcanreducetheestablishment mentalsustainability,withsignificantimplicationsfor and persistence of beneficial strains [147]. Further- publichealth. Theexcessiveuseofchemicalfertiliz- more,thelackofstandardizedformulations,storage ersandpesticideshasbeenlinkedtoenvironmental stability, and efficient delivery systems poses chal- pollution,foodcontamination,andadversehealthef- lengesforcommercialapplication[148,149]. Future fectsinhumans.Microbial-basedagriculturalpractices researchshouldfocusonthedevelopmentofrobust, offeraviablealternativebyreducingdependencyon stress-tolerantmicrobialstrainswithenhancedadapt- syntheticinputsandpromotingeco-friendlyfarming abilitytodiverseenvironmentalconditions.Advances systems[137].Theuseofbiofertilizersandmicrobialin- inmulti-omicstechnologies,includingmetagenomics, oculantsminimizestheaccumulationoftoxicresidues transcriptomics,andmetabolomics,offeropportuni- infoodproducts,therebyimprovingfoodsafetyandre- tiestobetterunderstandplant–microbeinteractions ducinghealthrisksassociatedwithlong-termexposure andoptimizemicrobialinterventions[150–152].The toagrochemicals[138,139].Additionally,enhancednu- integrationofmicrobialtechnologieswithprecision trientuptakefacilitatedbybeneficialmicrobesleadsto agricultureanddigitalfarmingtoolsisanotherpromis- improvedcropnutritionalquality,contributingtobet- ingdirection.Suchintegrationcanenablesite-specific terhumanhealthoutcomesandaddressingmicronu- applicationofmicrobialinoculants,improvingtheiref- trientdeficiencies[140].Microbialinterventionsalso ficiencyandscalability.Long-termfieldstudiesacross differentagroecologicalzonesareessentialtovalidate environmentalvariability,andscalability.Continued laboratory findings and promote wider adoption of research,technologicalinnovation,andpolicysupport microbial-basedsolutions.
areessentialtofullyrealizethepotentialofrhizosphere microbiomerestructuring.
6.Conclusion 8.FuturePerspectives Beneficialsoilmicrobesrepresentasustainableand innovativeapproachtoenhancingplantstresstoler- Future research should focus on developing site- ance,improvingcropproductivity,andensuringenvi- specific microbiome solutions tailored to different ronmentalandpublichealthsafety.Throughdiverse crops,soiltypes,andclimaticconditions.Advancesin mechanisms such as phytohormone regulation, os- artificialintelligenceandmachinelearningcanplay motic adjustment, antioxidant defense, nutrient ac- a crucial role in predicting microbial behavior and quisition,andinducedsystemicresistance,thesemi- optimizingmicrobiomeinterventions[120]. Thede- croorganisms significantly enhance plant resilience velopmentofnext-generationbiofertilizers,including underbothabioticandbioticstressconditions. The syntheticmicrobialconsortia,offerssignificantpoten- functionalprofilingofsoilmicrobialcommunities,sup- tialfor enhancingnutrientefficiencyand cropyield ported by advances in omics technologies, has pro- [121]. Theseformulationsshouldbedesignedtoen- vided deeper insights into the complex interactions surestability,compatibility,andlong-termeffective- between plants and microbes. These insights have nessunderfieldconditions.Integrationofmulti-omics facilitatedthedevelopmentofpracticalapplications approaches with ecological modeling will enable a such as biofertilizers, microbiome engineering, and deeperunderstandingofplant–microbeinteractions climate-resilientagriculturalsystems.Importantly,the andfacilitatethedesignoftargetedinterventions[122]. adoptionofmicrobial-basedagriculturalpracticescon- Additionally, researchshouldexploretheroleofmi- tributestoreducedagrochemicaluse,improvedfood crobiomesinmitigatingclimatechangethroughcar- quality, andenhancedenvironmentalsustainability, bonsequestrationandreductionofgreenhousegas therebysupportingglobalpublichealthgoals. How- emissions [123]. From a public health perspective, ever,challengesrelatedtofieldvariability,microbial microbiome-basedagriculturecancontributetosafe survival,andlarge-scaleimplementationmustbead- and sustainable food production systems, reducing dressedtofullyrealizetheirpotential. Inconclusion, exposuretoharmfulagrochemicalsandimprovingnu- integratingbeneficialsoilmicrobesintomodernagri- tritionalquality[124].Policymakersshouldprioritize culturalsystemsoffersapromisingpathwaytoward thedevelopmentofregulatoryframeworksandincen- sustainablefoodproduction,ecologicalbalance,and tivestosupporttheadoptionofthesetechnologies. improvedhumanhealth.Continuedinterdisciplinary Finally,interdisciplinarycollaborationamongmicro- researchandinnovationwillbecriticalinharnessing biologists,agronomists,environmentalscientists,and thefullpotentialofthesemicrobialresourcesforfuture publichealthexpertsisessentialtoaddressthecom- agriculturalandpublichealthadvancements. plexchallengesassociatedwithsustainableagriculture andglobalfoodsecurity[125–130].