Public Health · Vol. 11, No. 1 · 2026 · pp. 192–202 · e-ISSN 2472-3878

Rhizosphere Microbiome Restructuring Enhances Nutrient Use Efficiency and Crop Yield: Mechanisms, Innovations, and Future Perspectives

Lahar Jyoti Bordoloi, Chakpram Birendrajit, Mahua Banerjee, Abhijit Debnath, Ratan Das

Department of Soil Science, KVK Kiphire (Nagaland), ICAR Research Complex for NEH Region, Nagaland Centre, Nagaland-798611, IndiaIndia
Department of Directorate of Extension Education, CAU, Imphal- 795004, Manipur, IndiaIndia
Department of Agronomy, Institute of Agriculture, Visva-Bharati, Sriniketan, Birbhum 731236, West Bengal, IndiaIndia
Department of Horticulture, KVK Dhalai, Salema-799278, Tripura, IndiaIndia
Department of Horticulture, KVK Unakoti-799279, Tripura, IndiaIndia

DOI: https://doi.org/10.17140/phoj.11.01.192 · Published 2026-03-21 · Licence: https://creativecommons.org/licenses/by/4.0 · © 2026 The Author(s)

Also available as PDF (figures and tables appear in the PDF).

Abstract

The rhizosphere microbiome plays a crucial role in regulating plant health, nutrient acquisition, and overall agricultural productivity. Recent advances in microbial ecology and biotechnology have highlighted the importance of restructuring rhizosphere microbial communities to enhance nutrient use efficiency (NUE) and crop yield. This review synthesizes current knowledge on the mechanisms through which beneficial soil microorganisms, including plant growth-promoting rhizobacteria (PGPR), mycorrhizal fungi, and endophytes, influence nutrient cycling, root architecture, and stress resilience. Key mechanisms such as biological nitrogen fixation, phosphorus solubilization, phytohormone production, and microbial signaling are discussed in detail. Emerging innovations, including microbiome engineering, biofertilizers, and precision agriculture approaches, are evaluated for their potential to sustainably improve crop productivity under changing climatic conditions. Additionally, the role of multi-omics tools in understanding plant–microbe interactions and guiding targeted microbiome interventions is emphasized. Despite promising advancements, challenges such as field variability, microbial survival, and scalability remain significant barriers to widespread adoption. Future perspectives focus on integrating microbiome-based strategies with conventional agronomic practices to achieve sustainable intensification of agriculture while ensuring environmental and public health safety. This review underscores the critical importance of rhizosphere microbiome restructuring as a viable approach to improving nutrient efficiency and ensuring global food security.Rhizosphere microbiome;

Keywords: Rhizosphere microbiome; Nutrient use efficiency; Plant growth-promoting rhizobacteria (PGPR); Biofertilizers; Sustainable agriculture; Microbiome engineering; Crop productivity; Soil health; Mycorrhiza; Plant–microbe interactions; Rhizospheremicrobiome; Nutrientuseefficiency; Plantgrowth-promotingrhizobacteria(PGPR); Sustainableagriculture; Microbiomeengineering; Cropproductivity; Soilhealth; Plant–microbeinteractions

Discussion

Thefindingssynthesizedinthisreviewclearlydemonstratethatrhizospheremicrobiomerestructuringisa powerfulandmultifacetedapproachtoenhancingnutrientuseefficiency(NUE)andcropproductivity.The integrationofmicrobialecologywithagronomicpracticeshasprovidednewinsightsintosustainableagriculturalintensification,aligningcloselywithglobalfood securityandpublichealthobjectives.Oneofthemost significant observations is the central role of microbialdiversityandcommunitystructureindetermining soilfunctionality.Highmicrobialdiversitycontributes toecosystemstability,efficientnutrientcycling,and resilienceagainstenvironmentalstressors[101,102]. Thisalignswithglobalstudiesindicatingthatbiodiversitylossinagriculturalsoilsleadstoreducedecosystem services and increased vulnerability to climate change[103].Theidentificationofkeystonetaxafurtheremphasizestheimportanceofmaintainingfunctional microbial networks for sustained soil fertility [104].ThemechanismsunderlyingNUEenhancement areprimarilydrivenbymicrobialprocessessuchasbiologicalnitrogenfixation,phosphorussolubilization, andmicronutrientmobilization.Thesefindingscorroborateearlierstudiesthathighlighttheinefficienciesof syntheticfertilizersandtheneedforbiologicallymediatednutrientmanagementsystems[105,106].Thesynergisticinteractionsbetweenplantgrowth-promoting rhizobacteria(PGPR)andarbuscularmycorrhizalfungi (AMF)furtherstrengthennutrientacquisitionandplant resilience,reinforcingtheconceptofaholobiontsystemwhereplantsandmicrobesfunctionasanintegratedunit[107,108]. Advancementsinmulti-omics technologieshavesignificantlyimprovedourunderseveralconstraintslimitthewidespreadadoptionof microbiome-basedtechnologies.Oneoftheprimary challengesistheinconsistencyofmicrobialinoculants underfieldconditions. FactorssuchassoilpH,temperature,moisture,andnativemicrobialcompetition cansignificantlyinfluencetheeffectivenessofintroducedmicroorganisms[116,117].Moreover,thelackof standardizedprotocolsformicrobialformulationand applicationfurthercomplicateslarge-scaleimplementation[118]. Anotherimportantconsiderationisthe socio-economicaspectofadoptingmicrobiome-based practices.Farmersmaybehesitanttoadoptnewtechnologieswithoutclearevidenceofcost-effectiveness andlong-termbenefits[119]. Therefore, policysupport,extensionservices,andfarmereducationareessentialtopromotetheadoptionofsustainableagriculturalpractices.

4.Conclusion

Thepresentreviewhighlightsthatrhizospheremicrobiomerestructuringisapromisingandsustainableapproachtoimprovingnutrientuseefficiencyandcrop productivity.TheintegrationofbeneficialmicroorganismssuchasPGPR,AMF,andotherfunctionalmicrobialgroupsenhancesnutrientavailability,improves planthealth,andincreasesresiliencetoenvironmentalstresses.Theevidencesuggeststhatmicrobiomebasedinterventionscansignificantlyreducereliance on chemical fertilizers, thereby minimizing environmentalpollutionandpromotingsustainableagriculture.Thishasdirectimplicationsforpublichealth,as improvedsoilandcrophealthcontributetosaferfood systemsandreducedecologicalrisks. However,the successfulimplementationofthesestrategiesrequires overcomingchallengesrelatedtomicrobialsurvival, environmentalvariability,andscalability.Continued research,technologicalinnovation,andpolicysupport areessentialtofullyrealizethepotentialofrhizosphere microbiomerestructuring.

5.FuturePerspectives

Future research should focus on developing sitespecific microbiome solutions tailored to different crops,soiltypes,andclimaticconditions.Advancesin artificialintelligenceandmachinelearningcanplay a crucial role in predicting microbial behavior and optimizingmicrobiomeinterventions[120]. Thedevelopmentofnext-generationbiofertilizers,including syntheticmicrobialconsortia,offerssignificantpotentialfor enhancingnutrientefficiencyand cropyield [121]. Theseformulationsshouldbedesignedtoensurestability,compatibility,andlong-termeffectivenessunderfieldconditions.Integrationofmulti-omics approaches with ecological modeling will enable a deeperunderstandingofplant–microbeinteractions andfacilitatethedesignoftargetedinterventions[122]. Additionally, researchshouldexploretheroleofmicrobiomesinmitigatingclimatechangethroughcarbonsequestrationandreductionofgreenhousegas emissions [123]. From a public health perspective, microbiome-basedagriculturecancontributetosafe and sustainable food production systems, reducing exposuretoharmfulagrochemicalsandimprovingnutritionalquality[124].Policymakersshouldprioritize thedevelopmentofregulatoryframeworksandincentivestosupporttheadoptionofthesetechnologies. Finally,interdisciplinarycollaborationamongmicrobiologists,agronomists,environmentalscientists,and publichealthexpertsisessentialtoaddressthecomplexchallengesassociatedwithsustainableagriculture andglobalfoodsecurity[125–130].

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