Evaluating PGPR traits coupling under mutagenesis: A phenotypic and statistical framework for targeted improvement

Hakim Hamoum; Hiba Rahman Chibani; Ahcen Bouznad; Mehdi Naimi; Abdelouaheb Chibani

doi:10.15832/ankutbd.1812966

Evaluating PGPR traits coupling under mutagenesis: A phenotypic and statistical framework for targeted improvement

Abstract

Understanding the functional coupling between key PGP traits is crucial as PGPR use multiple mechanisms to promote plant growth and nutrition. This study uses UV mutagenesis to generate diversity in Stenotrophomonas maltophilia GZB27, applying a phenotypic statistical framework to evaluate coupling between indole-3-acetic acid production and phosphate solubilization for targeted improvement. UV exposure time inversely correlated with survival; 8.4 minutes achieved the target 5% viability threshold. Significant variation in IAA production occurred among 19 mutants compared to the wild type (18.19 µg/mL): nine hyperproducers (peak in M6, +33.5%; 24.28 µg/mL) and three strains with reduced biosynthesis (e.g., M16, −31.1%; 12.54 µg/mL) were identified. Significant variation in phosphate solubilization was observed among 19 mutants versus wild type (249.00 µg/mL): seven hyper efficient solubilizers (peak in M14: +62.1%; 403.67 µg/mL) and two with reduced capacity (e.g., M6: -50.1%; 124.33 µg/mL) were identified. Three integrated statistical methods were used to evaluate metabolic coupling between phosphate solubilization and IAA production in PGPR mutants. Spearman's correlation (ρ=0.213, p=0.368) revealed no significant population-level relationship, visually confirmed by dispersed data points indicating strain-specific autonomy. Antagonistic profiling quantified a strong functional trade-off via the Antagonism Index (AI), with mutants specializing in high PS (e.g., M3, M17) exhibiting reduced IAA, and vice-versa (e.g., M6, M10); only rare strains such as M4 showed balanced traits. Phenotypic Pleiotropy Modelling found predominantly neutral indices (41% of strains) and no significant trait correlation (Pearson r=0.245, p=0.2983), indicating minimal genetic constraint between traits. This multi-scale evaluation suggested genetically distinct bases governing PS and IAA

Keywords

References

Achal V, Savant V V & Reddy M S (2007). Phosphate solubilization by a wild type strain and UV-induced mutants of Aspergillus tubingensis. Soil Biology and Biochemistry 39(2): 695–699. https://doi.org/10.1016/j.soilbio.2006.09.003
Adrio J L & Demain A L (2006). Genetic improvement of processes yielding microbial products. FEMS Microbiology Reviews 30(2): 187 214. https://doi.org/10.1111/j.1574-6976.2005.00009.x
Alapati P S N T & Saharan B S (2025). Identification and functional characterization of plant growth-promoting rhizobacteria enhancing growth and nutritional quality of Sorghum bicolor. Discover Plants 2(1): 191. https://doi.org/10.1007/s44372-025-00284-3
Almario J, Gobbin D, Défago G, Moënne-Loccoz Y & Rezzonico F (2014). Prevalence of type III secretion system in effective biocontrol pseudomonads. Research in Microbiology 165(4): 300–304. https://doi.org/10.1016/j.resmic.2014.03.008
Altaf M A, Shahid R, Kumar R, Altaf M M, Kumar A, Khan L U, Saqib M, Nawaz M A, Saddiq B & Bahadur S (2023). Phytohormones mediated modulation of abiotic stress tolerance and potential crosstalk in horticultural crops. Journal of Plant Growth Regulation 42(8): 4724–4750. https://doi.org/10.1007/s00344-022-10812-0
Amy C, Avice J C, Laval K, Trinsoutrot-Gattin I & Bressan M (2024). The importance of considering levels of P and N fertilization to promote beneficial interaction between rapeseed https://doi.org/10.3390/agronomy14020334 an Anthropogenic and phosphate-solubilizing bacteria. Agronomy 14(2): 334.
Barbaccia P, Gaglio R, Dazzi C, Miceli C, Bella P, Papa G Lo & Settanni L (2022). Plant Growth-Promoting Activities of Bacteria Isolated from Soil Located https://doi.org/10.3390/microorganisms10112167 in Agrigento Province. Microorganisms 10(11): 2167.
Bashan Y & de-Bashan L E (2010). How the plant growth-promoting bacterium Azospirillum promotes plant growth—a critical assessment. Advances in Agronomy 108: 77–136. https://doi.org/10.1016/s0065-2113(10)08002-8

Berendsen R L, Pieterse C M J & Bakker P A H M (2012). The rhizosphere microbiome and plant health. Trends in Plant Science 17(8): 478 486. https://doi.org/10.1016/j.tplants.2012.04.001
Bisht S, Singh S, Singh M & Sharma J G (2022). Augmentative role of Piriformospora indica fungus and plant growth promoting bacteria in mitigating salinity stress in Trigonella foenum-graecum. Journal of Applied Biology and Biotechnology 10(1): 85–94. https://doi.org/10.7324/jabb.2021.100111
Bruto M, Prigent-Combaret C, Muller D & Moënne-Loccoz Y (2014). Analysis of genes contributing to plant-beneficial functions in plant growth-promoting rhizobacteria and related Proteobacteria. Scientific Reports 4(1): 6261. https://doi.org/10.1038/srep06261
Busby P E, Soman C, Wagner M R, Friesen M L, Kremer J, Bennett A, Morsy M, Eisen J A, Leach J E & Dangl J L (2017). Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biology 15(3): e2001793. https://doi.org/10.1371/journal.pbio.2001793
Cherif-Silini H, Silini A, Yahiaoui B, Ouzari I & Boudabous A (2016). Phylogenetic and plant-growth-promoting characteristics of Bacillus isolated from the wheat rhizosphere. Annals of Microbiology 66(3): 1087–1097. https://doi.org/10.1007/s13213-016-1194-6
Chibani H R, Hamoum H & Chibani A (2022). Enhancement of phosphate solubilization by Bacillus subtilis induced by UV mutagenesis. International Journal of Biosciences (IJB) 21(5): 239–245. https://doi.org/10.12692/ijb/21.5.239-245
Contesto C, Milesi S, Mantelin S, Zancarini A, Desbrosses G, Varoquaux F, Bellini C, Kowalczyk M & Touraine B (2010). The auxin-signaling pathway is required for the lateral root response of Arabidopsis to the rhizobacterium Phyllobacterium brassicacearum. Planta 232(6): 1455–1470. https://doi.org/10.1007/s00425-010-1264-0
Costa P B Da, Granada C E, Ambrosini A, Moreira F, Souza R De, Passos J F M Dos, Arruda L & Passaglia L M P (2014). A Model to Explain Plant Growth Promotion Traits: A Multivariate Analysis of 2,211 Bacterial Isolates. PLOS ONE 9(12): e116020. https://doi.org/10.1371/journal.pone.0116020
Couillerot O, Prigent‐Combaret C, Caballero‐Mellado J & Moënne‐Loccoz Y (2009). Pseudomonas fluorescens and closely‐related fluorescent pseudomonads as biocontrol agents of soil‐borne phytopathogens. Letters in Applied Microbiology 48(5): 505–512. https://doi.org/10.1111/j.1472-765x.2009.02566.x
Courcelle J, Khodursky A, Peter B, Brown P O & Hanawalt P C (2001). Comparative gene expression profiles following UV exposure in wildtype and SOS-deficient Escherichia coli. Genetics 158(1): 41–64. https://doi.org/10.1093/genetics/158.1.41
Davies P J (1995). The Plant Hormones : Their Nature, Occurence, and Function. Plant Hormones: physiology, biochemistry and molecular biology: 1–12. https://doi.org/10.1007/978-94-011-0473-9_1
Ellis R J, Timms‐Wilson T M & Bailey M J (2000). Identification of conserved traits in fluorescent pseudomonads with antifungal activity. Environmental Microbiology 2(3): 274–284. https://doi.org/10.1046/j.1462-2920.2000.00102.x
Feklistova I N & Maksimova N P (2008). Obtaining Pseudomonas aurantiaca strains capable of overproduction of phenazine antibiotics. Microbiology 77(2): 176–180. https://doi.org/10.1134/s0026261708020094
Fitriani R, Putrie W, Widowati T & Sukiman H (2016). Strain improvement comparison of isolate H2 between nitric Acid mutation and UV rays mutation. The 6th International Symposium for Sustainable Humanosphere: 226–230
Gopinath K P, Murugesan S, Abraham J & Muthukumar K (2009). Bacillus sp. mutant for improved biodegradation of Congo red: random mutagenesis approach. Bioresource Technology 100(24): 6295–6300. https://doi.org/10.1016/j.biortech.2009.07.043
Gordon S A & Weber R P (1951). Colorimetric estimation of indoleacetic acid. Plant Physiology 26(1): 192–195. https://doi.org/10.1104/pp.26.1.192
Gupta V & Buch A (2019). Pseudomonas aeruginosa predominates as multifaceted rhizospheric bacteria with combined abilities of p solubilization and biocontrol. Journal of Pure and Applied Microbiology 13(1): 319–328. https://doi.org/10.22207/JPAM.13.1.35
Haas D & Défago G (2005). Biological control of soil-borne pathogens by fluorescent pseudomonads. Nature Reviews Microbiology 3(4): 307–319. https://doi.org/10.1038/nrmicro1129
Haas D & Keel C (2003). Regulation of antibiotic production in root-colonizing Pseudomonas spp. and relevance for biological control of plant disease. Annual Review of Phytopathology 41(1): 117–153. https://doi.org/10.1146/annurev.phyto.41.052002.095656
Hiltner L (1904). Über neuere Erfahrungen und Probleme auf dem Gebiet der Bodenbakteriologie und unter besonderer Berücksichtigung der Gründüngung und Brache. Arbeiten der deutschen landwirtschaftlichen gesellschaft 98: 59 Jackson M L (1958). Soil chemical analysis Englewood cliffs. NT Prentice Hall Inc 85(3): 251–252
Jakobsen I, Leggett M E & Richardson A E (2005). Rhizosphere microorganisms and plant phosphorus uptake. Phosphorus: agriculture and the environment 46: 437–494. https://doi.org/10.2134/agronmonogr46.c14
Khan A, Singh A V, Kumar R, Kukreti B, Bundela V & Upadhayay V K (2022). Relative impact of PGPR inoculation on biofortification and yield of wheat under field conditions and their performance assessment through statistical tools. The Pharma Innovation Journal 11(8): 490–495
Kim C H, Han S H, Kim K Y, Cho B H, Kim Y H, Koo B S & Kim Y C (2003). Cloning and expression of pyrroloquinoline quinone (PQQ) genes from a phosphate-solubilizing bacterium Enterobacter intermedium. Current Microbiology 47(6): 457–461. https://doi.org/10.1007/s00284-003-4068-7
Kim P-J & Price N D (2011). Genetic co-occurrence network across sequenced microbes. PLOS Computational Biology 7(12): e1002340. https://doi.org/10.1371/journal.pcbi.1002340
Kumari S, Vaishnav A, Jain S, Varma A & Choudhary D K (2015). Bacterial-mediated induction of systemic tolerance to salinity with expression of stress alleviating enzymes in soybean (Glycine max L. Merrill). Journal of Plant Growth Regulation 34(3): 558–573. https://doi.org/10.1007/s00344-015-9490-0
Liu S-T, Lee L Y, Tai C-Y, Hung C H, Chang Y S, Wolfram J H, Rogers R & Goldstein A H (1992). Cloning of an Erwinia herbicola gene necessary for gluconic acid production and enhanced mineral phosphate solubilization in Escherichia coli HB101: nucleotide sequence and probable involvement in biosynthesis of the coenzyme pyrroloquinoline quinone. Journal of Bacteriology 174(18): 5814–5819. https://doi.org/10.1128/jb.174.18.5814-5819.1992
Majumdar A (2023). Molecular techniques for the improvement of microbial biocontrol agents against plant pathogens. Egyptian Journal of Biological Pest Control 33(1): 103. https://doi.org/10.1186/s41938-023-00746-4
Mantelin S, Desbrosses G, Larcher M, Tranbarger T J, Cleyet-Marel J-C & Touraine B (2006). Nitrate-dependent control of root architecture and N nutrition are altered by a plant growth-promoting Phyllobacterium sp. Planta 223(3): 591–603. https://doi.org/10.1007/s00425-005 0106-y
Maqbool Z, Shahid M, Azeem F, Shahzad T, Mahmood F, Rehman M, Ahmed T, Imran M & Hussain S (2020). Application of a dyedecolorizing Pseudomonas aeruginosa strain ZM130 for remediation of textile wastewaters in aerobic/anaerobic sequential batch bioreactor and soil columns. Water, Air, & Soil Pollution 231(8): 386. https://doi.org/10.1007/s11270-020-04777-7
Martiny A C, Treseder K & Pusch G (2013). Phylogenetic conservatism of functional traits in microorganisms. The ISME Journal 7(4): 830 838. https://doi.org/10.1038/ismej.2012.160
Marzano M, Gallo A & Altomare C (2013). Improvement of biocontrol efficacy of Trichoderma harzianum vs. Fusarium oxysporum f. sp. lycopersici through UV-induced tolerance https://doi.org/10.1016/j.biocontrol.2013.09.008 to fusaric acid. Biological Control 67(3): 397–408.
Miller S H, Browne P, Prigent‐Combaret C, Combes‐Meynet E, Morrissey J P & O’Gara F (2010). Biochemical and genomic comparison of inorganic phosphate solubilization in Pseudomonas species. Environmental Microbiology Reports 2(3): 403–411. https://doi.org/10.1111/j.1758-2229.2009.00105.x
Misra H S, Rajpurohit Y S & Khairnar N P (2012). Pyrroloquinoline-quinone and its versatile roles in biological processes. Journal of Biosciences 37(2): 313–325. https://doi.org/10.1007/s12038-012-9195-5
Morales Sandoval P H, Ortega Urquieta M E, Valenzuela Ruíz V, Montañez Acosta K, Campos Castro K A, Parra Cota F I, Santoyo G & los Santos Villalobos S de (2024). Improving beneficial traits in Bacillus cabrialesii subsp. cabrialesii TE3T through UV-induced genomic changes. Plants 13(18): 2578. https://doi.org/10.3390/plants13182578
Nautiyal C S (1999). An efficient microbiological growth medium for screening phosphate solubilizing microorganisms. FEMS Microbiology Letters 170(1): 265–270. https://doi.org/10.1111/j.1574-6968.1999.tb13383.x
Nelofer R, Syed Q, Nadeem M, Bashir F, Mazhar S & Hassan A (2016). Isolation of Phosphorus-solubilizing fungus from soil to supplement biofertilizer. Arabian Journal for Science and Engineering 41(6): 2131–2138. https://doi.org/10.1007/s13369-015-1916-2
Olanrewaju O S, Ayangbenro A S, Glick B R & Babalola O O (2019). Plant health: feedback effect of root exudates-rhizobiome interactions. Applied Microbiology and Biotechnology 103(3): 1155–1166. https://doi.org/10.1007/s00253-018-9556-6
Philippot L, Raaijmakers J M, Lemanceau P & Putten W H Van Der (2013). Going back to the roots: the microbial ecology of the rhizosphere. Nature Reviews Microbiology 11(11): 789–799. https://doi.org/10.1038/nrmicro3109
Pullerits K, Ahlinder J, Holmer L, Salomonsson E, Öhrman C, Jacobsson K, Dryselius R, Forsman M, Paul C J & Rådström P (2020). Impact of UV irradiation at full scale on bacterial communities in drinking water. NPJ Clean Water 3(1): 11. https://doi.org/10.1038/s41545-020 0057-7
Rai A, Rai P K & Singh S (2018). Characterization of phosphate solubilizing fluorescent pseudomonads from the rhizosphere of Aloe vera (L.). Archives of Agronomy and Soil Science 64(7): 1032–1040. https://doi.org/10.1080/03650340.2017.1407869
Raymond N S, Gómez-Muñoz B, Bom F J T van der, Nybroe O, Jensen L S, Müller-Stöver D S, Oberson A & Richardson A E (2021). Phosphate-solubilising microorganisms for improved crop productivity: a critical assessment. New Phytologist 229(3): 1268–1277. https://doi.org/10.1111/nph.16924
Richardson A E (2001). Prospects for using soil microorganisms to improve the acquisition of phosphorus by plants. Functional Plant Biology 28(9): 897–906. https://doi.org/10.1071/pp01093
Shahid M, Usman M, Shahzad T, Ali I, Hassan M U, Mahmood F & Qari S H (2022). Enhancement of Wheat Growth by UV-Mutagenesis of Potential Chromium Tolerant https://doi.org/10.3390/su142215341 Bacillus sp. Strain SR-2-1/1. Sustainability (Switzerland) 14(22): 15341.
Sivasakthi S, Saranraj P & Sujitha D (2015). Mutation based strain improvement of PGPR Isolates (Pseudomonas fluorescens & Bacillus subtilis) for the Improvement of growth and yield of Paddy (Oryza sativa L.). J. Agric. & Environ. Sci 15(8): 1591–1601. https://doi.org/10.5829/idosi.aejaes.2015.15.8.94149
Spaepen S, Versées W, Gocke D, Pohl M, Steyaert J & Vanderleyden J (2007). Characterization of phenylpyruvate decarboxylase, involved in auxin production of Azospirillum brasilense. Journal of Bacteriology 189(21): 7626–7633. https://doi.org/10.1128/jb.00830-07
Voronina E, Sokolova E, Tromenschleger I, Mishukova O, Hlistun I, Miroshnik M, Savenkov O, Buyanova M, Ivanov I, Galyamova M & Smirnova N (2024). Properties of potential Plant-Growth-Promoting Bacteria and their effect on wheat growth promotion (Triticum aestivum) and soil characteristics. Microbiology Research 15(1): 20–32. https://doi.org/10.3390/microbiolres15010002
Walker V, Bruto M, Bellvert F, Bally R, Muller D, Prigent-Combaret C, Moënne-Loccoz Y & Comte G (2013). Unexpected phytostimulatory behavior for Escherichia coli and Agrobacterium tumefaciens model strains. Molecular plant-microbe interactions 26(5): 495–502. https://doi.org/10.1094/mpmi-12-12-0298-r
Wang Z, Zhang H, Liu L, Li S, Xie J, Xue X & Jiang Y (2022). Screening of phosphate-solubilizing bacteria and their abilities of phosphorus solubilization and wheat growth promotion. BMC Microbiology 22(1): 296. https://doi.org/10.1186/s12866-022-02715-7

Details

Primary Language

English

Subjects

Soil Biology, Soil Microbiology, Soil Sciences and Plant Nutrition (Other)

Journal Section

Research Article

Authors

Hakim Hamoum ^*
0009-0002-7824-5422
Algeria

Hiba Rahman Chibani This is me
0009-0000-2444-0949
Algeria

Ahcen Bouznad This is me
0009-0002-6236-358X
Algeria

Mehdi Naimi
0000-0001-8405-2251
Algeria

Abdelouaheb Chibani This is me
0000-0002-7407-5799
Algeria

Publication Date

October 12, 2026

Submission Date

October 29, 2025

Acceptance Date

June 9, 2026

Published in Issue

Year 2026 Volume: 32 Number: 4

DOI

https://doi.org/10.15832/ankutbd.1812966

IZ

https://izlik.org/JA96GE72UD

Cite

RIS / Bibtex

APA

Hamoum, H., Chibani, H. R., Bouznad, A., Naimi, M., & Chibani, A. (2026). Evaluating PGPR traits coupling under mutagenesis: A phenotypic and statistical framework for targeted improvement. Journal of Agricultural Sciences, 32(4), 1118-1131. https://doi.org/10.15832/ankutbd.1812966

AMA

1.Hamoum H, Chibani HR, Bouznad A, Naimi M, Chibani A. Evaluating PGPR traits coupling under mutagenesis: A phenotypic and statistical framework for targeted improvement. J Agr Sci-Tarim Bili. 2026;32(4):1118-1131. doi:10.15832/ankutbd.1812966

Chicago

Hamoum, Hakim, Hiba Rahman Chibani, Ahcen Bouznad, Mehdi Naimi, and Abdelouaheb Chibani. 2026. “Evaluating PGPR Traits Coupling under Mutagenesis: A Phenotypic and Statistical Framework for Targeted Improvement”. Journal of Agricultural Sciences 32 (4): 1118-31. https://doi.org/10.15832/ankutbd.1812966.

EndNote

Hamoum H, Chibani HR, Bouznad A, Naimi M, Chibani A (October 1, 2026) Evaluating PGPR traits coupling under mutagenesis: A phenotypic and statistical framework for targeted improvement. Journal of Agricultural Sciences 32 4 1118–1131.

IEEE

[1]H. Hamoum, H. R. Chibani, A. Bouznad, M. Naimi, and A. Chibani, “Evaluating PGPR traits coupling under mutagenesis: A phenotypic and statistical framework for targeted improvement”, J Agr Sci-Tarim Bili, vol. 32, no. 4, pp. 1118–1131, Oct. 2026, doi: 10.15832/ankutbd.1812966.

ISNAD

Hamoum, Hakim - Chibani, Hiba Rahman - Bouznad, Ahcen - Naimi, Mehdi - Chibani, Abdelouaheb. “Evaluating PGPR Traits Coupling under Mutagenesis: A Phenotypic and Statistical Framework for Targeted Improvement”. Journal of Agricultural Sciences 32/4 (October 1, 2026): 1118-1131. https://doi.org/10.15832/ankutbd.1812966.

JAMA

1.Hamoum H, Chibani HR, Bouznad A, Naimi M, Chibani A. Evaluating PGPR traits coupling under mutagenesis: A phenotypic and statistical framework for targeted improvement. J Agr Sci-Tarim Bili. 2026;32:1118–1131.

MLA

Hamoum, Hakim, et al. “Evaluating PGPR Traits Coupling under Mutagenesis: A Phenotypic and Statistical Framework for Targeted Improvement”. Journal of Agricultural Sciences, vol. 32, no. 4, Oct. 2026, pp. 1118-31, doi:10.15832/ankutbd.1812966.

Vancouver

1.Hakim Hamoum, Hiba Rahman Chibani, Ahcen Bouznad, Mehdi Naimi, Abdelouaheb Chibani. Evaluating PGPR traits coupling under mutagenesis: A phenotypic and statistical framework for targeted improvement. J Agr Sci-Tarim Bili. 2026 Oct. 1;32(4):1118-31. doi:10.15832/ankutbd.1812966