Functional Profiling of Beneficial Soil Microbes Improving Plant Stress Tolerance: Mechanisms, Applications, and Public Health Implications

Crossmark: check for updates

Authors

DOI:

https://doi.org/10.17140/phoj.11.01.224

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

Abstract

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

References

Vessey JK. 2003. Plant growth promoting rhizobacteria as biofertilizers. Plant Soil. 255:571–586.

Richardson AE, Simpson RJ. 2011. Soil mi-croorganisms mediating phosphorus availability. Plant Physiol. 156(3):989–996.

Smith SE, Read DJ. 2008. Mycorrhizal symbiosis. 3rd ed. Academic Press, London.

Adesemoye AO, Torbert HA, Kloepper JW. 2009. Plant growth-promoting rhizobacteria allow reduced fertilizer rates. Microb Ecol. 58(4):921–929.

Bender SF, Wagg C, van der Heijden MGA. 2016. An underground revolution: soil biodiversity. Trends Ecol Evol. 31(6):440–452.

Berg G, Rybakova D, Fischer D, et al. 2017. Micro-biome definition revisited. Microbiome. 5:148.

Berendsen RL, Pieterse CMJ, Bakker PAHM. 2012. The rhizosphere microbiome and plant health. Trends Plant Sci. 17(8):478–486.

Lal R. 2015. Soil carbon sequestration and cli-mate change. Geoderma. 123:1–22.

Galloway JN, Townsend AR, Erisman JW, et al. 2008. Transformation of the nitrogen cycle. Sci-ence. 320:889–892.

Sharma SB, Sayyed RZ, Trivedi MH, Gobi TA. 2013. Phosphate solubilizing microbes. SpringerPlus. 2:587.

Singh BK, Trivedi P, Egidi E, et al. 2020. Crop microbiome and sustainable agriculture. Nat Rev Microbiol. 18:601–602.

Taiz L, Zeiger E. 2010. Plant Physiology. 5th ed. Sinauer Associates.

Davies PJ. 2010. Plant Hormones. Springer.

Glick BR. 2014. Bacteria with ACC deaminase. Microbiol Res. 169:30–39.

Nascimento FX, Rossi MJ, Soares CRFS, et al. 2014. Ethylene modulation in plants. Front Plant Sci. 5:426.

Yang J, Kloepper JW, Ryu CM. 2009. Rhizo-sphere bacteria and stress tolerance. Plant Soil. 321:305–339.

Zahir ZA, Arshad M, Frankenberger WT. 2004. PGPR: applications and perspectives. Adv Agron. 81:97–168.

Ashraf M, Foolad MR. 2007. Roles of glycine be-taine. Environ Exp Bot. 59:206–216.

Szabados L, Savouré A. 2010. Proline metabolism. Plant Sci. 182:26–31.

Hayat R, Ali S, Amara U, et al. 2010. Soil beneficial bacteria. Ann Microbiol. 60:579–598.

Gill SS, Tuteja N. 2010. Reactive oxygen species. Plant Physiol Biochem. 48:909–930.

Apel K, Hirt H. 2004. ROS signaling. Annu Rev Plant Biol. 55:373–399.

Mittler R. 2002. Oxidative stress. Trends Plant Sci. 7:405–410.

Bhattacharyya PN, Jha DK. 2012. PGPR and agriculture. World J Microbiol Biotechnol. 28:1327–1350.

Bashan Y, de-Bashan LE. 2010. PGPR mecha-nisms. Plant Soil. 337:1–17.

Rodríguez H, Fraga R. 1999. Phosphate solubi-lization. Biotechnol Adv. 17:319–339.

Khan MS, Zaidi A, Wani PA. 2009. Phosphate solubilizing bacteria. J Plant Nutr Soil Sci. 172:263–274.

Smith FA, Smith SE. 2011. Roles of AMF. Plant Soil. 348:1–11.

Augé RM. 2001. Water relations and AMF. Mycor-rhiza. 11:3–42.

Pieterse CMJ, Zamioudis C, Berendsen RL, et al. 2014. Induced systemic resistance. Annu Rev Phytopathol. 52:347–375.

Van Loon LC, Bakker PAHM, Pieterse CMJ. 1998. Systemic resistance. Eur J Plant Pathol. 104:1–11.

Conrath U. 2011. Priming for defense. Trends Plant Sci. 16:524–531.

Harman GE. 2006. Trichoderma mechanisms. Phytopathology. 96:190–194.

Weller DM. 2007. Pseudomonas biocontrol. Phy-topathology. 97:250–256.

Handelsman J. 2004. Metagenomics. Microbiol Mol Biol Rev. 68:669–685.

Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq. Nat Rev Genet. 10:57–63.

Patti GJ, Yanes O, Siuzdak G. 2012. Metabolomics. Nat Rev Mol Cell Biol. 13:263–269.

Badri DV, Vivanco JM. 2009. Root exudates. Plant Cell Environ. 32:666–681.

Bais HP, Weir TL, Perry LG, et al. 2006. Rhi-zosphere interactions. Annu Rev Plant Biol. 57:233–266.

Mueller UG, Sachs JL. 2015. Engineering micro-biomes. Trends Microbiol. 23:606–617.

Mendes R et al. 2011. Disease suppressive soils. Science. 332:1097–1100.

Lugtenberg B, Kamilova F. 2009. PGPR. Annu Rev Microbiol. 63:541–556.

Compant S et al. 2005. Endophytes. FEMS Micro-biol Ecol. 52:321–334.

Glick BR. 2012. Plant growth-promoting bacteria. Scientifica. 2012:963401.

Tilman D et al. 2011. Sustainable agriculture. PNAS. 108:20260–20264.

Savci S. 2012. Chemical fertilizers impact. APCBEE Procedia. 1:287–292.

Banerjee S et al. 2019. Microbial networks. ISME J. 13:1722–1736.

Singh JS et al. 2011. Microbial biofertilizers. Plant Soil. 346:1–20.

Glick BR. Plant growth-promoting bacteria: mechanisms and applications. Scientifica. 2012; 2012: 963401.

Lugtenberg B, Kamilova F. Plant-growth-promoting rhizobacteria. Annu Rev Microbiol. 2009; 63: 541–556.

Yang J, Kloepper JW, Ryu CM. Rhizosphere bacte-ria help plants tolerate abiotic stress. Plant Soil. 2009; 321: 305–339.

Zahir ZA, Arshad M, Frankenberger WT. Plant growth promoting rhizobacteria: applications and perspectives. Adv Agron. 2004; 81: 97–168.

Spaepen S, Vanderleyden J. Auxin and plant-microbe interactions. Cold Spring Harb Perspect Biol. 2011; 3: a001438.

Glick BR, Cheng Z, Czarny J, Duan J. Promotion of plant growth by ACC deaminase-producing bacteria. Eur J Plant Pathol. 2007; 119: 329–339.

Mayak S, Tirosh T, Glick BR. Plant growth-promoting bacteria that confer resistance to wa-ter stress. Plant Sci. 2004; 166: 525–530.

Saleem M, Arshad M, Hussain S, Bhatti AS. Per-spective of PGPR containing ACC deaminase. J Ind Microbiol Biotechnol. 2007; 34: 635–648.

Nadeem SM, Ahmad M, Zahir ZA, Javaid A, Ashraf M. Role of ACC deaminase producing bacteria. Microbiol Res. 2014; 169: 30–39.

Vurukonda SSKP, Vardharajula S, Shrivastava M, SkZ A. Enhancement of drought stress tolerance in crops by PGPR. Microbiol Res. 2016; 184: 13–24.

Egamberdieva D, Wirth SJ, Shurigin VV, et al. Salt-tolerant PGPR improve plant growth. Plant Soil. 2017; 405: 241–254.

Ashraf M, Foolad MR. Roles of glycine betaine and proline. Environ Exp Bot. 2007; 59: 206–216.

Szabados L, Savouré A. Proline metabolism and stress tolerance. Plant Sci. 2010; 182: 26–31.

Chen THH, Murata N. Glycine betaine protects plants. Plant Cell Environ. 2008; 31: 129–140.

Farooq M, Wahid A, Kobayashi N, et al. Plant drought stress. Agron Sustain Dev. 2009; 29: 185–212.

Yang J, Zhang J, Wang Z, Zhu Q, Liu L. Water rela-tions and drought tolerance. J Exp Bot. 2003; 54: 243–252.

Verslues PE, Agarwal M, Katiyar-Agarwal S, et al. Drought tolerance methods. Plant J. 2006; 45: 523–539.

Gill SS, Tuteja N. Reactive oxygen species and antioxidant machinery. Plant Physiol Biochem. 2010; 48: 909–930.

Mittler R. Oxidative stress and stress tolerance. Trends Plant Sci. 2002; 7: 405–410.

Apel K, Hirt H. Reactive oxygen species signaling. Annu Rev Plant Biol. 2004; 55: 373–399.

Sharma P, Jha AB, Dubey RS, Pessarakli M. Ox-idative stress and defense. J Bot. 2012; 2012: 217037.

Hasanuzzaman M, Hossain MA, da Silva JAT, Fu-jita M. Plant responses to oxidative stress. Plant Physiol Biochem. 2012; 59: 54–64.

Bhattacharyya PN, Jha DK. PGPR in agricul-ture. World J Microbiol Biotechnol. 2012; 28: 1327–1350.

Bashan Y, de-Bashan LE. PGPR mechanisms. Plant Soil. 2010; 337: 1–33.

Richardson AE, Barea JM, McNeill AM, Prigent-Combaret C. Nutrient availability. Plant Soil. 2009; 321: 305–339.

Rodríguez H, Fraga R. Phosphate solubilization. Biotechnol Adv. 1999; 17: 319–339.

Khan MS, Zaidi A, Wani PA. Phosphate-solubilizing microbes. J Plant Nutr Soil Sci. 2009; 172: 263–274.

Smith SE, Smith FA. Roles of arbuscular mycor-rhizas. Plant Soil. 2011; 348: 1–11.

Augé RM. Water relations and mycorrhiza. Mycor-rhiza. 2001; 11: 3–42.

Ruiz-Lozano JM. Mycorrhizal symbiosis and drought tolerance. J Exp Bot. 2003; 54: 1215–1224.

Porcel R, Aroca R, Ruiz-Lozano JM. Salinity stress alleviation by AMF. J Exp Bot. 2012; 63: 2023–2036.

Pieterse CMJ, Zamioudis C, Berendsen RL, et al. Induced systemic resistance. Annu Rev Phy-topathol. 2014; 52: 347–375.

Van Loon LC, Bakker PAHM, Pieterse CMJ. Sys-temic resistance. Eur J Plant Pathol. 1998; 104: 1–11.

Conrath U. Priming of defense responses. Trends Plant Sci. 2011; 16: 524–531.

Harman GE. Mechanisms of Trichoderma spp. Phytopathology. 2006; 96: 190–194.

Weller DM. Pseudomonas biocontrol. Phy-topathology. 2007; 97: 250–256.

Compant S, Duffy B, Nowak J, Clément C, Barka EA. Endophytic bacteria. FEMS Microbiol Ecol. 2005; 52: 321–334.

Mendes R, Kruijt M, de Bruijn I, et al. Rhizosphere microbiome. Science. 2011; 332: 1097–1100.

Bais HP, Weir TL, Perry LG, et al. Rhizosphere interactions. Annu Rev Plant Biol. 2006; 57: 233–266.

Badri DV, Vivanco JM. Root exudates. Plant Cell Environ. 2009; 32: 666–681.

Raaijmakers JM, Mazzola M. Diversity and natural functions of antibiotics produced by beneficial and plant pathogenic bacteria. Annu Rev Phy-topathol. 2012; 50: 403–424.

Haas D, Défago G. Biological control of soil-borne pathogens by fluorescent pseudomonads. Nat Rev Microbiol. 2005; 3: 307–319.

Bakker PAHM, Pieterse CMJ, van Loon LC. In-duced systemic resistance by fluorescent Pseu-domonas spp. Phytopathology. 2007; 97: 239–243.

Compant S, Clément C, Sessitsch A. Plant growth-promoting bacteria in the rhizo- and endosphere. Soil Biol Biochem. 2010; 42: 669–678.

Lugtenberg BJJ, Dekkers L, Bloemberg GV. Molec-ular determinants of rhizosphere colonization. Annu Rev Phytopathol. 2001; 39: 461–490.

Berg G, Smalla K. Plant species and soil type co-operatively shape the structure of microbial com-munities. FEMS Microbiol Ecol. 2009; 68: 1–13.

Badri DV, Weir TL, van der Lelie D, Vivanco JM. Rhizosphere chemical dialogues. Plant Physiol. 2009; 151: 1478–1485.

Bais HP, Fall R, Vivanco JM. Biocontrol of Bacil-lus subtilis against plant pathogens. Plant Biol. 2004; 6: 251–261.

Venturi V, Keel C. Signaling in the rhizosphere. Trends Plant Sci. 2016; 21: 187–198.

Ryu CM, Farag MA, Hu CH, et al. Bacterial volatiles promote plant growth. Proc Natl Acad Sci USA. 2003; 100: 4927–4932.

Kai M, Effmert U, Piechulla B. Bacterial volatiles and their action. J Chem Ecol. 2009; 35: 545–558.

Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH. Going back to the roots: micro-bial ecology of the rhizosphere. Nat Rev Micro-biol. 2013; 11: 789–799.

Tilman D, Balzer C, Hill J, Befort BL. Global food demand and sustainable intensification of agri-culture. Proc Natl Acad Sci USA. 2011; 108(50): 20260–20264.

Savci S. Investigation of the effects of chemical fertilizers on environment. APCBEE Procedia. 2012; 1: 287–292.

Banerjee S, Walder F, Büchi L, et al. Agricultural intensification reduces microbial network com-plexity. ISME J. 2019; 13: 1722–1736.

Singh JS, Pandey VC, Singh DP. Efficient soil mi-croorganisms: a new dimension for sustainable agriculture. Plant Soil. 2011; 346: 1–25.

Adesemoye AO, Torbert HA, Kloepper JW. Role of PGPR in improving crop productivity. Microb Ecol. 2009; 58: 921–929.

Bender SF, Wagg C, van der Heijden MGA. Soil biodiversity and ecosystem functioning. Trends Ecol Evol. 2016; 31: 440–452.

Lal R. Soil health and carbon sequestration. Soil Biol Biochem. 2020; 148: 107902.

Mueller UG, Sachs JL. Engineering microbiomes. Trends Microbiol. 2015; 23: 606–617.

Berg G, Rybakova D, Grube M, Köberl M. Micro-biome definition re-visited. Nat Rev Microbiol. 2020; 18: 601–602.

Trivedi P, Leach JE, Tringe SG, et al. Plant–microbiome interactions. Nat Rev Microbiol. 2020; 18: 607–621.

Busby PE, Soman C, Wagner MR, et al. Re-search priorities for harnessing plant micro-biomes. New Phytol. 2017; 215: 5–10.

Toju H, Peay KG, Yamamichi M, et al. Core mi-crobiomes for sustainable agroecosystems. Nat Plants. 2018; 4: 247–257.

Vurukonda SSKP, Vardharajula S, Shrivastava M, SkZ A. Enhancement of drought stress tolerance by PGPR. Microbiol Res. 2016; 184: 13–24.

Lal R. Climate change and soil health. Geoderma. 2015; 123: 1–22.

Egamberdieva D, Wirth SJ, Shurigin VV, et al. Salt tolerance by PGPR. Plant Soil. 2017; 405: 241–254.

Dodd IC, Perez-Alfocea F. Microbial amelioration of crop stress. J Exp Bot. 2012; 63: 3415–3428.

Zhang N, Wang D, Liu Y, et al. Precision agricul-ture with microbiomes. Front Plant Sci. 2019; 10: 123.

Schlaeppi K, Bulgarelli D. Plant microbiome re-search. Annu Rev Plant Biol. 2015; 66: 655–681.

Naylor D, Coleman-Derr D. Drought stress and microbiomes. Curr Opin Plant Biol. 2018; 44: 1–7.

Compant S, Samad A, Faist H, Sessitsch A. Bio-control mechanisms. Microbiol Res. 2019; 219: 23–32.

Köhl J, Kolnaar R, Ravensberg WJ. Mode of action of microbial biocontrol agents. Plant Dis. 2019; 103: 317–328.

Harman GE, Howell CR, Viterbo A, et al. Tri-choderma species. Nat Rev Microbiol. 2004; 2: 43–56.

Weller DM, Raaijmakers JM, McSpadden Gar-dener BB, Thomashow LS. Microbial populations responsible for suppressive soils. Annu Rev Phy-topathol. 2002; 40: 309–348.

Compant S, Duffy B, Nowak J, et al. Endophytes. FEMS Microbiol Ecol. 2005; 52: 321–334.

Pimentel D. Environmental and economic costs of pesticide use. Bioscience. 2005; 55: 229–238.

Aktar MW, Sengupta D, Chowdhury A. Impact of pesticides. Interdiscip Toxicol. 2009; 2: 1–12.

Lehmann J, Kleber M. Carbon stabilization. Na-ture. 2015; 528: 60–68.

Six J, Conant RT, Paul EA, Paustian K. Stabiliza-tion of soil organic matter. Plant Soil. 2002; 241: 155–176.

Lal R. Soil carbon sequestration impacts. Sci-ence. 2004; 304: 1623–1627.

Smith P, Martino D, Cai Z, et al. Agriculture and greenhouse gas mitigation. Philos Trans R Soc B. 2008; 363: 789–813.

White PJ, Broadley MR. Biofortification of crops. J Exp Bot. 2005; 56: 1747–1755.

Cakmak I. Enrichment of cereal grains with mi-cronutrients. Plant Soil. 2008; 302: 1–17.

Pretty J. Agricultural sustainability. Philos Trans R Soc B. 2008; 363: 447–465.

Tilman D et al. Agricultural sustainability and inputs. Nature. 2002; 418: 671–677.

Foley JA et al. Solutions for sustainable agricul-ture. Nature. 2011; 478: 337–342.

FAO. Soil health and food security. FAO. 2017.

WHO. Food safety and public health. WHO Press. 2019.

FAO/WHO. Food safety risk assessment. 2020.

WHO. Global nutrition report. 2021.

One Health Commission. One Health concept. 2020.

CDC. One Health basics. 2021.

UNEP. Environmental health assessment. 2020.

IPCC. Climate change and agriculture. 2021.

Sessitsch A, Brader G, Pfaffenbichler N, et al. Mi-crobial inoculants challenges. Trends Biotech-nol. 2019; 37: 118–129.

Bashan Y, Bashan LE. Challenges in biofertilizer use. Biol Fertil Soils. 2010; 46: 1–13.

Malusá E, Vassilev N. Microbial inoculants chal-lenges. Appl Microbiol Biotechnol. 2014; 98: 6599–6607.

Herrmann L, Lesueur D. Biofertilizer formula-tions. Agron Sustain Dev. 2013; 33: 1–19.

Martínez-Viveros O, Jorquera MA, Crowley DE, et al. Mechanisms of PGPR. Soil Biol Biochem. 2010; 42: 1795–1804.

Singh BK, Trivedi P, Egidi E, et al. Microbiome advances. Nat Rev Microbiol. 2020; 18: 601–602.

Trivedi P, Leach JE, Tringe SG, et al. Plant–microbiome interactions. Nat Rev Microbiol. 2020; 18: 607–621.

Berg G, Rybakova D, Grube M, Köberl M. Micro-biome engineering. Microbiome. 2020; 8: 1–12.

United Nations. Sustainable Development Goals Report. UN. 2020.

Downloads

Published

2026-03-24

How to Cite

Lahar Jyoti Bordoloi, Sindhuja suram, Abhijit Debnath, & Ratan Das. (2026). Functional Profiling of Beneficial Soil Microbes Improving Plant Stress Tolerance: Mechanisms, Applications, and Public Health Implications. Public Health - Open Journal, 11(1), 224–202. https://doi.org/10.17140/phoj.11.01.224