Skip to main content

Metabolomics and Proteomics Behind Plant Growth-Promoting Potential of Rhizobacteria

  • Chapter
  • First Online:
Metabolomics, Proteomes and Gene Editing Approaches in Biofertilizer Industry
  • 195 Accesses

Abstract

Plant growth-promoting rhizobacteria (PGPRs) are nature’s blessing for the host plant because their natural endowment allows the host plant to survive and grow in any biotic or abiotic stressed conditions. May it be availability of nutrients, harsh climatic conditions, or defense against pathogens, rhizobacteria have exclusive mechanisms to confront such stresses and defend the host plant. Hence researchers worldwide are exclusively interested to decode such incredible relationship shared between the host and rhizobacteria. Innumerous standard and advanced methods have been procured for the same, but the most reliable data procurement is offered by omic techniques, metabolomics, and proteomics. Metabolomic profiles exhibit the details of various complex biochemical pathways in living organisms and the effect of external conditions on them, whereas proteomics explicates all the proteins expressed in an organism, at a particular time, in specific conditions. The metabolome and proteome profiles, hence, are exclusively exploited to understand the mechanisms of growth-promoting potentials and variations in protein expressions at several stress conditions. In this chapter we are explaining various mechanisms by which rhizobacteria is capable of promoting host plant’s growth and the use of metabolomic and proteomic techniques to explore the pathways and expression of proteins in different stress conditions.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Adaway JE, Keevil BG, Owen LJ (2015) Liquid chromatography tandem mass spectrometry in the clinical laboratory. Ann Clin Biochem 52:18–38

    Article  PubMed  Google Scholar 

  • Adeleke BS, Babalola OO, Glick BR (2021) Plant growth-promoting root-colonizing bacterial endophytes. Rhizosphere 20:100433

    Article  Google Scholar 

  • Afridi MS, Fakhar A, Kumar A et al (2022) Harnessing microbial multitrophic interactions for rhizosphere microbiome engineering. Microbiol Res 265:127199

    Article  PubMed  Google Scholar 

  • Afroz A, Zahur M, Zeeshan N, Komatsu S (2013) Plant-bacterium interactions analyzed by proteomics. Front Plant Sci 4:21

    Article  PubMed  PubMed Central  Google Scholar 

  • Agtuca BJ, Stopka SA, Tuleski TR et al (2020) In-situ metabolomic analysis of Setaria viridis roots colonized by beneficial endophytic bacteria. Mol Plant-Microbe Interact 33:272–283

    Article  PubMed  Google Scholar 

  • Ahemad M, Kibret M (2014) Mechanisms and applications of plant growth promoting rhizobacteria: current perspective. J King Saud Univ 26:1–20

    Article  Google Scholar 

  • Aioub AAA, Elesawy AE, Ammar EE (2022) Plant growth promoting rhizobacteria (PGPR) and their role in plant-parasitic nematodes control: a fresh look at an old issue. J Plant Dis Prot 129:1–17

    Article  Google Scholar 

  • Alaux M, Rogers J, Letellier T et al (2018) Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data. Genome Biol 19:1–10

    Article  Google Scholar 

  • Alberton D, Müller-Santos M, Brusamarello-Santos LCC, Valdameri G, Cordeiro FA, Yates MG et al (2013) Comparative proteomics analysis of the rice roots colonized by Herbaspirillum seropedicae strain SmR1 reveals induction of the methionine recycling in the plant host. J Proteome Res 12:4757–4768. https://doi.org/10.1021/pr400425f

    Article  PubMed  Google Scholar 

  • Alberton D, Valdameri G, Moure VR et al (2020) What did we learn from plant growth-promoting rhizobacteria (PGPR)-grass associations studies through proteomic and metabolomic approaches? Front Sustain Food Syst 4:607343

    Article  Google Scholar 

  • Alexandridou A, Mouskeftara T, Raikos N, Gika HG (2020) GC-MS analysis of underivatised new psychoactive substances in whole blood and urine. J Chromatogr B 1156:122308

    Article  Google Scholar 

  • Ali GS, Norman D, El-Sayed AS (2015) Soluble and volatile metabolites of plant growth-promoting rhizobacteria (PGPRs): role and practical applications in inhibiting pathogens and activating induced systemic resistance (ISR). In: Advances in botanical research. Elsevier, Amsterdam, pp 241–284

    Google Scholar 

  • Alori ET, Glick BR, Babalola OO (2017) Microbial phosphorus solubilization and its potential for use in sustainable agriculture. Front Microbiol 8:971

    Article  PubMed  PubMed Central  Google Scholar 

  • Alves TO, D’Almeida CTS, Scherf KA, Ferreira MSL (2019) Modern approaches in the identification and quantification of immunogenic peptides in cereals by LC-MS/MS. Front Plant Sci 10:1470

    Article  PubMed  PubMed Central  Google Scholar 

  • Appels R, Eversole K, Feuille C et al (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361:10–1126

    Google Scholar 

  • Ayaz M, Ali Q, Farzand A et al (2021) Nematicidal volatiles from Bacillus atrophaeus GBSC56 promote growth and stimulate induced systemic resistance in tomato against Meloidogyne incognita. Int J Mol Sci 22:5049

    Article  PubMed  PubMed Central  Google Scholar 

  • Baber M, Fatima M, Abbas R et al (2018) Weed rhizosphere: a source of novel plant growth promoting rhizobacteria (PGPR). Int J Biosci 13:224–234

    Article  Google Scholar 

  • Bakker PAHM, Berendsen RL, Van Pelt JA et al (2020) The soil-borne identity and microbiome-assisted agriculture: looking back to the future. Mol Plant 13:1394–1401

    Article  PubMed  Google Scholar 

  • Banerjee S, Mazumdar S (2012) Electrospray ionization mass spectrometry: a technique to access the information beyond the molecular weight of the analyte. Int J Anal Chem

    Google Scholar 

  • Berg H, Martin MAW, Niesteruk A, et al (2021) NMR-based fragment screening in a minimum sample but maximum automation mode. J Vis Exp e62262

    Google Scholar 

  • Bertrand C, Gonzalez-Coloma A, Prigent-Combaret C (2021) Plant metabolomics to the benefit of crop protection and growth stimulation. In: Advances in botanical research. Elsevier, Amsterdam, pp 107–132

    Google Scholar 

  • Bhadrecha P, Bala M, Kumar M, Panwar JS, Sharma NR (2018) Seabuckthorn rhizobacteria produce ACC deaminase and exhibit PGPR traits. Ecol Environ Conserv 24(1):240–245

    Google Scholar 

  • Bhadrecha P, Bala M, Khasa YP, Arshi A, Singh J, Kumar M (2020) Hippophae rhamnoides L. rhizobacteria exhibit diversified cellulase and pectinase activities. Physio Mol Biol Plants 26(5):1075–1085. https://doi.org/10.1007/s12299020-00778-2

    Article  Google Scholar 

  • Bhadrecha P, Bala M, Kaushik V, Gaur NA, Singh S, Singh J, Kumar M (2021) Folate producing rhizobacteria of Hippophae rhamnoides L. from Indian trans-Himalaya low atmospheric zone. Biocell 45(2):387–394. https://doi.org/10.32604/biocell.2021.013824

    Article  Google Scholar 

  • Bhattacharyya PN, Jha DK (2012) Plant growth-promoting rhizobacteria (PGPR): emergence in agriculture. World J Microbiol Biotechnol 28:1327–1350

    Article  PubMed  Google Scholar 

  • Biswas R, Sarkar A (2018) ‘Omics’ tools in soil microbiology: the state of the art. In: Advances in soil microbiology: recent trends and future prospects. Springer, Singapore, pp 35–64

    Chapter  Google Scholar 

  • Boegelsack N, Sandau C, McMartin DW et al (2021) Development of retention time indices for comprehensive multidimensional gas chromatography and application to ignitable liquid residue mapping in wildfire investigations. J Chromatogr A 1635:461717

    Article  PubMed  Google Scholar 

  • Brader G, Compant S, Vescio K et al (2017) Ecology and genomic insights into plant-pathogenic and plant-nonpathogenic endophytes. Annu Rev Phytopathol 55:61

    Article  PubMed  Google Scholar 

  • Brunetti AE, Neto FC, Vera MC et al (2018) An integrative omics perspective for the analysis of chemical signals in ecological interactions. Chem Soc Rev 47:1574–1591

    Article  PubMed  Google Scholar 

  • Brusamarello-Santos LCC, Alberton D, Valdameri G et al (2019) Modulation of defence and iron homeostasis genes in rice roots by the diazotrophic endophyte Herbaspirillum seropedicae. Sci Rep 9:1–15

    Article  Google Scholar 

  • Cangahuala-Inocente GC, Plucani do Amaral F, Faleiro AC, Huergo LF, Maisonnave Arisi AC (2013) Identification of six differentially accumulated proteins of Zea mays seedlings (DKB240 variety) inoculated with Azospirillum brasilense strain FP2. Eur J Soil Biol 58:45–50. https://doi.org/10.1016/j.ejsobi.2013.06.002

    Article  Google Scholar 

  • Chamam A, Sanguin H, Bellvert F et al (2013) Plant secondary metabolite profiling evidences strain-dependent effect in the Azospirillum--Oryza sativa association. Phytochemistry 87:65–77

    Article  PubMed  Google Scholar 

  • Chamberlain J (2018) The analysis of drugs in biological fluids. CRC Press, Boca Raton

    Google Scholar 

  • Chandra S, Askari K, Kumari M (2018) Optimization of indole acetic acid production by isolated bacteria from Stevia rebaudiana rhizosphere and its effects on plant growth. J Genet Eng Biotechnol 16:581–586

    Article  PubMed  PubMed Central  Google Scholar 

  • Chauhan A, Saini R, Sharma JC (2021) Plant growth promoting rhizobacteria and their biological properties for soil enrichment and growth promotion. J Plant Nutr 45:273–299

    Article  Google Scholar 

  • Cheng Z, McConkey BJ, Glick BR (2010) Proteomic studies of plant--bacterial interactions. Soil Biol Biochem 42:1673–1684

    Article  Google Scholar 

  • Chung I-M, Park S-K, Thiruvengadam M et al (2018) Review of the biotechnological applications of rice allelopathy in agricultural production. Weed Biol Manag 18:63–74

    Article  Google Scholar 

  • Clavero VO (2014) A low-cost photonic method for monitoring different production processes involving contaminating materials using Fourier-transform Raman spectroscopy. Université de Strasbourg, Strasbourg

    Google Scholar 

  • da Cunha B, Fonseca LP, Calado CRC (2020) Metabolic fingerprinting with Fourier-transform infrared (FTIR) spectroscopy: towards a high-throughput screening assay for antibiotic discovery and mechanism-of-action elucidation. Metabolites 10:145

    Article  Google Scholar 

  • Datta A, Singh RK, Kumar S, Kumar S (2015) An effective and beneficial plant growth promoting soil bacterium “rhizobium”: a review. Ann Plant Sci 4:933–942

    Google Scholar 

  • del Cappellari LR, Chiappero J, Palermo TB et al (2020) Volatile organic compounds from rhizobacteria increase the biosynthesis of secondary metabolites and improve the antioxidant status in Mentha piperita L. grown under salt stress. Agronomy 10:1094

    Article  Google Scholar 

  • del Carmen Orozco-Mosqueda M, Fadiji AE, Babalola OO et al (2022) Rhizobiome engineering: unveiling complex rhizosphere interactions to enhance plant growth and health. Microbiol Res 236:127137

    Article  Google Scholar 

  • Demarque DP, Dusi RG, de Sousa FDM et al (2020) Mass spectrometry-based metabolomics approach in the isolation of bioactive natural products. Sci Rep 10:1–9

    Article  Google Scholar 

  • Dhawi F, Datta R, Ramakrishna W (2015) Mycorrhiza and PGPB modulate maize biomass, nutrient uptake and metabolic pathways in maize grown in mining-impacted soil. Plant Physiol Biochem 97:390–399

    Article  PubMed  Google Scholar 

  • Dhawi F, Datta R, Ramakrishna W (2017) Proteomics provides insights into biological pathways altered by plant growth promoting bacteria and arbuscular mycorrhiza in sorghum grown in marginal soil. Biochim Biophys Acta Proteins Proteomics 1865:243–251. https://doi.org/10.1016/j.bbapap.2016.11.015

    Article  PubMed  Google Scholar 

  • Dhawi F, Datta R, Ramakrishna W (2018) Metabolomics, biomass and lignocellulosic total sugars analysis in foxtail millet (Setaria italica) inoculated with different combinations of plant growth promoting bacteria and mycorrhiza. Commun Plant Sci 8:8

    Article  Google Scholar 

  • Dill AL, Ifa DR, Manicke NE, Ouyang Z, Cooks RG (2009) Mass spectrometric imaging of lipids using desorption electrospray ionization. J Chromatogr B 877(26):2883–2889

    Article  Google Scholar 

  • Dirks NF, Ackermans MT, Lips P et al (2018) The when, what & how of measuring vitamin D metabolism in clinical medicine. Nutrients 10:482

    Article  PubMed  PubMed Central  Google Scholar 

  • Dutta A (2017) Fourier transform infrared spectroscopy. In: Spectroscopic methods for nanomaterials characterization. Elsevier, Amsterdam, pp 73–93

    Chapter  Google Scholar 

  • Elliani R, Andò S, Tagarelli A (2019) Development and optimization of analytical protocols based on microextraction techniques for clinical screening and environmental control

    Google Scholar 

  • Emwas A-H, Roy R, McKay RT et al (2019) NMR spectroscopy for metabolomics research. Metabolites 9:123

    Article  PubMed  PubMed Central  Google Scholar 

  • Faleiro AC, Neto PAV, de Souza TV, Santos M, Arisi ACM (2015) Microscopic and proteomic analysis of Zea mays roots (P30F53 variety) inoculated with Azospirillum brasilense strain FP2. J Crop Sci Biotech 18:63–71. https://doi.org/10.1007/s12892-014-0061-x

    Article  Google Scholar 

  • Gaby JC, Buckley DH (2012) A comprehensive evaluation of PCR primers to amplify the nifH gene of nitrogenase. PLoS One 7(7):e42149

    Article  PubMed  PubMed Central  Google Scholar 

  • Gade RM, Koche MD (2022) Enhancing the growth and disease suppression ability of Pseudomonas fluorescens. In: New and future developments in microbial biotechnology and bioengineering. Elsevier, Amsterdam, pp 351–368

    Chapter  Google Scholar 

  • Garcia-Perez I, Posma JM, Serrano-Contreras JI, Boulangé CL, Chan Q, Frost G, Stamler J, Elliott P, Lindon JC, Holmes E, Nicholson JK (2020) Identifying unknown metabolites using NMR-based metabolic profiling techniques. Nat Protoc:1–30

    Google Scholar 

  • Genre A, Lanfranco L, Perotto S, Bonfante P (2020) Unique and common traits in mycorrhizal symbioses. Nat Rev Microbiol 18:649–660

    Article  PubMed  Google Scholar 

  • Ghosh D, Gupta A, Mohapatra S (2019) Dynamics of endogenous hormone regulation in plants by phytohormone secreting rhizobacteria under water-stress. Symbiosis 77:265–278

    Article  Google Scholar 

  • Glickstein J, Mandal S (2022) A cryogenically-cooled high-sensitivity nuclear quadrupole resonance spectrometer. arXiv Prepr arXiv220801552

    Google Scholar 

  • González A, Fillat MF, Bes M-T et al (2018) The challenge of iron stress in cyanobacteria. IntechOpen, London, pp 109–138

    Google Scholar 

  • Grainger R, Whibley S (2021) A perspective on the analytical challenges encountered in high-throughput experimentation. Org Process Res Dev 25:354–364

    Article  Google Scholar 

  • Gupta G, Parihar SS, Ahirwar NK et al (2015) Plant growth promoting rhizobacteria (PGPR): current and future prospects for development of sustainable agriculture. J Microb Biochem Technol 7:96–102

    Google Scholar 

  • Gupta S, Chaturvedi P, Kulkarni MG, Van Staden J (2020) A critical review on exploiting the pharmaceutical potential of plant endophytic fungi. Biotechnol Adv 39:107462

    Article  PubMed  Google Scholar 

  • Gupta P, Verma A, Rai N et al (2021) Mass spectrometry-based technology and workflows for studying the chemistry of fungal endophyte derived bioactive compounds. ACS Chem Biol 16:2068–2086

    Article  PubMed  Google Scholar 

  • Hajieghrari B, Farrokhi N (2022) Plant RNA-mediated gene regulatory network. Genomics 114:409–442

    Article  PubMed  Google Scholar 

  • Han C, Liu R, Luo H et al (2019) Pollution profiles of volatile organic compounds from different urban functional areas in Guangzhou China based on GC/MS and PTR-TOF-MS: atmospheric environmental implications. Atmos Environ 214:116843

    Article  Google Scholar 

  • Haroon U, Khizar M, Liaquat F et al (2022) Halotolerant plant growth-promoting rhizobacteria induce salinity tolerance in wheat by enhancing the expression of SOS genes. J Plant Growth Regul 41:2435–2448

    Article  Google Scholar 

  • Harris GA, Galhena AS, Fernandez FM (2011) Ambient sampling/ionization mass spectrometry: applications and current trends. Anal Chem 83(12):4508–4538

    Article  PubMed  Google Scholar 

  • He Y, Pantigoso HA, Wu Z, Vivanco JM (2019) Co-inoculation of Bacillus sp. and Pseudomonas putida at different development stages acts as a biostimulant to promote growth, yield and nutrient uptake of tomato. J Appl Microbiol 127:196–207

    Article  PubMed  Google Scholar 

  • Holčapek M, Jirásko R, Lísa M (2012) Recent developments in liquid chromatography--mass spectrometry and related techniques. J Chromatogr A 1259:3–15

    Article  PubMed  Google Scholar 

  • Hou X, Lv S, Chen Z, Xiao F (2018) Applications of Fourier transform infrared spectroscopy technologies on asphalt materials. Measurement 121:304–316

    Article  Google Scholar 

  • Jääskeläinen T, Kärkkäinen O, Jokkala J et al (2018) A non-targeted LC-MS profiling reveals elevated levels of carnitine precursors and trimethylated compounds in the cord plasma of pre-eclamptic infants. Sci Rep 8:1–12

    Article  Google Scholar 

  • Jadhav MR, Pudale A, Raut P et al (2019) A unified approach for high-throughput quantitative analysis of the residues of multi-class veterinary drugs and pesticides in bovine milk using LC-MS/MS and GC--MS/MS. Food Chem 272:292–305

    Article  PubMed  Google Scholar 

  • Jiménez-Mejía R, Medina-Estrada RI, Carballar-Hernández S et al (2022) Teamwork to survive in hostile soils: use of plant growth-promoting bacteria to ameliorate soil salinity stress in crops. Microorganisms 10:150

    Article  PubMed  PubMed Central  Google Scholar 

  • Kamran S, Shahid I, Baig DN et al (2017) Contribution of zinc solubilizing bacteria in growth promotion and zinc content of wheat. Front Microbiol 8:2593

    Article  PubMed  PubMed Central  Google Scholar 

  • Ke J, Wang B, Yoshikuni Y (2021) Microbiome engineering: synthetic biology of plant-associated microbiomes in sustainable agriculture. Trends Biotechnol 39:244–261

    Article  PubMed  Google Scholar 

  • Khanna K, Kohli SK, Ohri P, Bhardwaj R (2021a) Plants-nematodes-microbes crosstalk within soil: a trade-off among friends or foes. Microbiol Res 248:126755

    Article  PubMed  Google Scholar 

  • Khanna K, Kohli SK, Sharma P et al (2021b) Antioxidant potential of plant growth-promoting rhizobacteria (PGPR) in agricultural crops infected with root-knot nematodes. In: Antioxidants in plant-microbe interaction. Springer, Berlin, pp 339–379

    Chapter  Google Scholar 

  • Khatabi B, Gharechahi J, Ghaffari MR et al (2019) Plant--microbe symbiosis: what has proteomics taught us? Proteomics 19:1800105

    Article  Google Scholar 

  • Khatoon Z, Huang S, Rafique M et al (2020) Unlocking the potential of plant growth-promoting rhizobacteria on soil health and the sustainability of agricultural systems. J Environ Manag 273:111118

    Article  Google Scholar 

  • Kim ST, Kim SG, Agrawal GK et al (2014) Rice proteomics: a model system for crop improvement and food security. Proteomics 14:593–610

    Article  PubMed  Google Scholar 

  • Köhl J, Kolnaar R, Ravensberg WJ (2019) Mode of action of microbial biological control agents against plant diseases: relevance beyond efficacy. Front Plant Sci 10:845

    Article  PubMed  PubMed Central  Google Scholar 

  • Kruve A, Rebane R, Kipper K et al (2015) Tutorial review on validation of liquid chromatography--mass spectrometry methods: part I. Anal Chim Acta 870:29–44

    Article  PubMed  Google Scholar 

  • Kumar A, Patel JS, Meena VS (2018) Rhizospheric microbes for sustainable agriculture: an overview. In: Role of rhizospheric microbes in soil. Springer, Berlin, pp 1–31

    Google Scholar 

  • Kumar A, Dewangan S, Lawate P et al (2019) Zinc-solubilizing bacteria: a boon for sustainable agriculture. In: Plant growth promoting rhizobacteria for sustainable stress management. Springer, Berlin, pp 139–155

    Chapter  Google Scholar 

  • Lade SB, Román C, Cueto-Ginzo AI, Serrano L, Sin E, Achón MA et al (2018) Host-specific proteomic and growth analysis of maize and tomato seedlings inoculated with Azospirillum brasilense Sp7. Plant Physiol Biochem 129:381–393. https://doi.org/10.1016/j.plaphy.2018.06.024

    Article  PubMed  Google Scholar 

  • Lade SB, Román C, del Cueto-Ginzo AI, Serrano L, Sin E, Achón MA et al (2019) Differential proteomics analysis reveals that Azospirillium brasilense (Sp7) promotes virus tolerance in maize and tomato seedlings. Eur J Plant Pathol 155:1241–1263. https://doi.org/10.1007/s10658-019-01852-6

    Article  Google Scholar 

  • Lakshmanan V, Ray P, Craven KD (2017) Toward a resilient, functional microbiome: drought tolerance-alleviating microbes for sustainable agriculture. In: Plant stress tolerance. Springer, Berlin, pp 69–84

    Chapter  Google Scholar 

  • Lee YS, Anees M, Park YS et al (2014) Purification and properties of a Meloidogyne-antagonistic chitinase from Lysobacter capsici YS1215. Nematology 16:63–72

    Article  Google Scholar 

  • Lery LMS, Hemerly AS, Nogueira EM et al (2011) Quantitative proteomic analysis of the interaction between the endophytic plant-growth-promoting bacterium Gluconacetobacter diazotrophicus and sugarcane. Mol Plant-Microbe Interact 24:562–576

    Article  PubMed  Google Scholar 

  • Li D (2019) MicroRNAs and immunomodulation by vitamin D. University of Birmingham, Birmingham

    Google Scholar 

  • Llorens E, González-Hernández AI, Scalschi L et al (2020) Priming mediated stress and cross-stress tolerance in plants: concepts and opportunities. In: Priming-mediated stress and cross-stress tolerance in crop plants. Elsevier, Amsterdam, pp 1–20

    Google Scholar 

  • Lykogianni M, Papadopoulou E-A, Sapalidis A et al (2020) Metabolomics reveals differential mechanisms of toxicity of hyperbranched poly (ethyleneimine)-derived nanoparticles to the soil-borne fungus Verticillium dahliae Kleb. Pestic Biochem Physiol 165:104535

    Article  PubMed  Google Scholar 

  • Lynch KL (2017) Toxicology: liquid chromatography mass spectrometry. In: Mass spectrometry for the clinical laboratory. Elsevier, Amsterdam, pp 109–130

    Chapter  Google Scholar 

  • Makaza W, Kamutando CN (2022) Harnessing beneficial plant-microbe interactions for enhanced plant adaptation to abiotic stresses. In: Plant defense mechanisms, vol 143. IntechOpen, London

    Google Scholar 

  • Maldonado S, Rodríguez A, Ávila B et al (2020) Enhanced crop productivity and sustainability by using native phosphate solubilizing rhizobacteria in the agriculture of arid zones. Front Sustain Food Syst 4:607355

    Article  Google Scholar 

  • Mapodzeke JM, Adil MF, Sehar S et al (2021) Myriad of physio-genetic factors determining the fate of plant under zinc nutrient management. Environ Exp Bot 189:104559

    Article  Google Scholar 

  • Mareya CR, Tugizimana F, Piater LA et al (2019) Untargeted metabolomics reveal defensome-related metabolic reprogramming in Sorghum bicolor against infection by Burkholderia andropogonis. Metabolites 9:8

    Article  PubMed  PubMed Central  Google Scholar 

  • Mashabela M, Tugizimana F, Steenkamp P et al (2022) Untargeted metabolite profiling to elucidate rhizosphere and leaf metabolome changes of wheat cultivars (Triticum aestivum L.) treated with the plant growth-promoting rhizobacteria Paenibacillus alvei (T22) and Bacillus subtilis. Front Microbiol 13:971836

    Article  PubMed  PubMed Central  Google Scholar 

  • Meena KK, Sorty AM, Bitla UM et al (2017) Abiotic stress responses and microbe-mediated mitigation in plants: the omics strategies. Front Plant Sci 8:172

    Article  PubMed  PubMed Central  Google Scholar 

  • Mirsaleh-Kohan N, Robertson WD, Compton RN (2008) Electron ionization time‐of‐flight mass spectrometry: historical review and current applications. Mass Spectrom Rev 27(3):237–285

    Article  PubMed  Google Scholar 

  • Miura D, Fujimura Y, Wariishi H (2012) In situ metabolomic mass spectrometry imaging: recent advances and difficulties. J Proteome 75(16):5052–5060

    Article  Google Scholar 

  • Mohanty P, Singh PK, Chakraborty D et al (2021) Insight into the role of PGPR in sustainable agriculture and environment. Front Sustain Food Syst 5:667150

    Article  Google Scholar 

  • Mukherjee PK (2019) Chapter 11-LC--MS: a rapid technique for understanding the plant metabolite analysis. In: Quality control and evaluation of herbal drugs. Elsevier, Amsterdam, pp 459–479

    Chapter  Google Scholar 

  • Mushtaq Z, Asghar HN, Zahir ZA (2021) Comparative growth analysis of okra (Abelmoschus esculentus) in the presence of PGPR and press mud in chromium contaminated soil. Chemosphere 262:127865

    Article  PubMed  Google Scholar 

  • Mushtaq Z, Liaquat M, Nazir A et al (2022) Potential of plant growth promoting rhizobacteria to mitigate chromium contamination. Environ Technol Innov 22:102826

    Article  Google Scholar 

  • Nardi S, Schiavon M, Francioso O (2021) Chemical structure and biological activity of humic substances define their role as plant growth promoters. Molecules 26:2256

    Article  PubMed  PubMed Central  Google Scholar 

  • Nitu R, Rajinder K, Sukhminderjit K (2020) Zinc solubilizing bacteria to augment soil fertility--a comprehensive review. Int J Agric Sci Vet Med 8:38–44

    Google Scholar 

  • Niu L, Zhang H, Wu Z et al (2018) Modified TCA/acetone precipitation of plant proteins for proteomic analysis. PLoS One 13:e0202238

    Article  PubMed  PubMed Central  Google Scholar 

  • Niu L, Zhang H, Wu Z et al (2019) Correction: modified TCA/acetone precipitation of plant proteins for proteomic analysis. PLoS One 14:e0211612

    Article  PubMed  PubMed Central  Google Scholar 

  • Nyadong L, Hohenstein EG, Galhena A, Lane AL, Kubanek J, Sherrill CD, Fernández FM (2009) Reactive desorption electrospray ionization mass spectrometry (DESI-MS) of natural products of a marine alga. Anal Bioanal Chem 394:245–254.ort

    Article  Google Scholar 

  • Olanrewaju OS, Ayangbenro AS, Glick BR, Babalola OO (2019) Plant health: feedback effect of root exudates-rhizobiome interactions. Appl Microbiol Biotechnol 103:1155–1166

    Article  PubMed  Google Scholar 

  • Passarelli MK, Winograd N (2011) Lipid imaging with time-of-flight secondary ion mass spectrometry (ToFSIMS). Biochimica et Biophysica Acta (BBA)-Mol Cell Biol Lipids 1811(11):976–990

    Article  Google Scholar 

  • Philippot L, Raaijmakers JM, Lemanceau P, Van Der Putten WH (2013) Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol 11:789–799

    Article  PubMed  Google Scholar 

  • Piasecka A, Kachlicki P, Stobiecki M (2019) Analytical methods for detection of plant metabolomes changes in response to biotic and abiotic stresses. Int J Mol Sci 20(2):379

    Article  PubMed  PubMed Central  Google Scholar 

  • Porcari AM, Fernandes GD, Barrera-Arellano D, Eberlin MN, Alberici RM (2016) Food quality and authenticity screening via easy ambient sonic-spray ionization mass spectrometry. Analyst 141(4):1172–1184

    Article  PubMed  Google Scholar 

  • Portolés T, Sancho JV, Hernandez F, Newton A, Hancock P (2010) Potential of atmospheric pressure chemical ionization source in GC‐QTOF MS for pesticide residue analysis. J Mass Spectrom 45(8):926–936

    Article  PubMed  Google Scholar 

  • Portwood JL, Woodhouse MR, Cannon EK et al (2019) MaizeGDB 2018: the maize multi-genome genetics and genomics database. Nucleic Acids Res 47:D1146–D1154

    Article  PubMed  Google Scholar 

  • Prabha R, Singh DP, Gupta VK (2019) Insights into the unidentified microbiome: current approaches and implications. In: Microbial interventions in agriculture and environment. Springer, Singapore, pp 93–130

    Chapter  Google Scholar 

  • Prinsi B, Negri AS, Failla O et al (2018) Root proteomic and metabolic analyses reveal specific responses to drought stress in differently tolerant grapevine rootstocks. BMC Plant Biol 18:1–28

    Article  Google Scholar 

  • Raina R, Hall P (2008) Comparison of gas chromatography-mass spectrometry and gas chromatography-tandem mass spectrometry with electron ionization and negative-ion chemical ionization for analyses of pesticides at trace levels in atmospheric samples. Anal Chem Insights 3:ACI-S1005

    Article  Google Scholar 

  • Rout ME, Southworth D (2013) The root microbiome influences scales from molecules to ecosystems: the unseen majority. Am J Bot 100:1689–1691

    Article  PubMed  Google Scholar 

  • Routray S, Kumari S, Borah B et al (2021) A review on rhizobia and PGPRs interactions in legumes. J Pharm Innov 10:1448–1457

    Google Scholar 

  • Roy T, Bandopadhyay A, Sonawane PJ et al (2018) Bio-effective disease control and plant growth promotion in lentil by two pesticide degrading strains of Bacillus sp. Biol Control 127:55–63

    Article  Google Scholar 

  • Santoro MV, Zygadlo J, Giordano W, Banchio E (2011) Volatile organic compounds from rhizobacteria increase biosynthesis of essential oils and growth parameters in peppermint (Mentha piperita). Plant Physiol Biochem 49:1177–1182

    Article  PubMed  Google Scholar 

  • Segers K, Declerck S, Mangelings D et al (2019) Analytical techniques for metabolomic studies: a review. Bioanalysis 11:2297–2318

    Article  PubMed  Google Scholar 

  • Setiawati TC, Erwin D, Mandala M, Hidayatulah A (2022) Use of bacillus as a plant growth-promoting rhizobacteria to improve phosphate and potassium availability in acidic and saline soils. In: KnE life sciences, pp 541–558

    Google Scholar 

  • Shen M-R, He Y, Shi S-M (2021) Development of chromatographic technologies for the quality control of traditional Chinese medicine in the Chinese pharmacopoeia. J Pharm Anal 11:155–162

    Article  PubMed  Google Scholar 

  • Singh P, Dwivedi P (2019) Micronutrients zinc and boron enhance stevioside content in Stevia rebaudiana plants while maintaining genetic fidelity. Ind Crop Prod 140:111646

    Article  Google Scholar 

  • Singh J, Mehta A (2020) Rapid and sensitive detection of mycotoxins by advanced and emerging analytical methods: a review. Food Sci Nutr 8:2183–2204

    Article  PubMed  PubMed Central  Google Scholar 

  • Singh N, Singh G (2018) Plant growth promoting rhizobacteria and rhizobium combinations are the key to reduce dependence on phosphorus fertilizers in lentil—a review. Agric Rev 39

    Google Scholar 

  • Singh P, Singh RK, Zhou Y et al (2022) Unlocking the strength of plant growth promoting pseudomonas in improving crop productivity in normal and challenging environments: a review. J Plant Interact 17:220–238

    Article  Google Scholar 

  • Sivasakthi S, Usharani G, Saranraj P et al (2014) Biocontrol potentiality of plant growth promoting bacteria (PGPR)-Pseudomonas fluorescens and Bacillus subtilis: a review. Afr J Agric Res 9:1265–1277

    Google Scholar 

  • Sorty AM, Meena KK, Choudhary K et al (2016) Effect of plant growth promoting bacteria associated with halophytic weed (Psoralea corylifolia L) on germination and seedling growth of wheat under saline conditions. Appl Biochem Biotechnol 180:872–882

    Article  PubMed  Google Scholar 

  • Stettin D, Poulin RX, Pohnert G (2020) Metabolomics benefits from orbitrap GC--MS—comparison of low-and high-resolution GC--MS. Metabolites 10:143

    Article  PubMed  PubMed Central  Google Scholar 

  • Straub D, Yang H, Liu Y, Tsap T, Ludewig U (2013) Root ethylene signalling is involved in Miscanthus sinensis growth promotion by the bacterial endophyte Herbaspirillum frisingense GSF30 T. J Exp Bot 64:4603–4615. https://doi.org/10.1093/jxb/ert276

    Article  PubMed  PubMed Central  Google Scholar 

  • Sujatha N, Ammani K (2013) Siderophore production by the isolates of fluorescent Pseudomonads. Int J Curr Res Rev 5:1

    Google Scholar 

  • Sundaram L, Rajendran S, Subramanian N (2021) Metal stress impacting plant growth in contaminated soil is alleviated by microbial siderophores. In: Role of microbial communities sustain. Springer, Berlin, pp 317–332

    Chapter  Google Scholar 

  • Swarnalatha GV, Goudar V, Reddy ECRGS et al (2022) Siderophores and their applications in sustainable management of plant diseases. In: Secondary metabolites and volatiles of PGPR in plant-growth promotion. Springer Nature, Berlin, pp 289–302

    Chapter  Google Scholar 

  • Tabatabaei Anaraki M (2021) Development of solution-state in vivo NMR: towards an understanding of aquatic toxicity

    Google Scholar 

  • Tallapragada P, Matthew T (2021) Potassium solubilizing microorganisms (KSM) A very promising biofertilizers. In: Agriculturally important microorganisms. CRC Press, Boca Raton, pp 153–174

    Chapter  Google Scholar 

  • Tan C-Y, Dodd IC, Chen JE et al (2021) Regulation of algal and cyanobacterial auxin production, physiology, and application in agriculture: an overview. J Appl Phycol 33:2995–3023

    Article  Google Scholar 

  • Tariq M, Noman M, Ahmed T et al (2017) Antagonistic features displayed by plant growth promoting rhizobacteria (PGPR): a review. J Plant Sci Phytopathol 1:38–43

    Article  Google Scholar 

  • Tavakoli MT, Chenari AI, Rezaie M et al (2014) The importance of micronutrients in agricultural production. Adv Environ Biol:31–36

    Google Scholar 

  • Thomas S, Thomas R, Zachariah AK, Mishra RK (2017) Spectroscopic methods for nanomaterials characterization. Elsevier, Amsterdam

    Google Scholar 

  • Timofeeva AM, Galyamova MR, Sedykh SE (2022) Bacterial siderophores: classification, biosynthesis, perspectives of use in agriculture. Plants 11:3065

    Article  PubMed  PubMed Central  Google Scholar 

  • Toju H, Peay KG, Yamamichi M et al (2018) Core microbiomes for sustainable agroecosystems. Nat Plants 4:247–257

    Article  PubMed  Google Scholar 

  • Tugizimana F, Mhlongo MI, Piater LA, Dubery IA (2018) Metabolomics in plant priming research: the way forward? Int J Mol Sci 19:1759

    Article  PubMed  PubMed Central  Google Scholar 

  • Ullah MA, Abdullah-Zawawi M-R, Zainal-Abidin R-A et al (2022) A review of integrative omic approaches for understanding rice salt response mechanisms. Plants 11:1430

    Article  PubMed  PubMed Central  Google Scholar 

  • Valdameri G, Alberton D, Moure VR, Kokot TB, Kukolj C, Brusamarello-Santos LCC et al (2017) Herbaspirillum rubrisubalbicans, a mild pathogen impairs growth of rice by augmenting ethylene levels. Plant Mol Biol 94:625–640. https://doi.org/10.1007/s11103-017-0629-1

    Article  PubMed  Google Scholar 

  • Vervoort N, Goossens K, Baeten M, Chen Q (2021) Recent advances in analytical techniques for high throughput experimentation. Anal Sci Adv 2:109–127

    Article  Google Scholar 

  • Vincenti M (2001) The renaissance of desorption chemical ionization mass spectrometry: characterization of large involatile molecules and nonpolar polymers. Int J Mass Spectrom 212(1–3):505–518

    Article  Google Scholar 

  • von Aulock FW, Kennedy BM, Schipper CI et al (2014) Advances in Fourier transform infrared spectroscopy of natural glasses: from sample preparation to data analysis. Lithos 206:52–64

    Article  Google Scholar 

  • Wahab A, Abdi G, Saleem MH et al (2022) Plants’ physio-biochemical and phyto-hormonal responses to alleviate the adverse effects of drought stress: a comprehensive review. Plants 11:1620

    Article  PubMed  PubMed Central  Google Scholar 

  • Walker V, Bertrand C, Bellvert F et al (2011) Host plant secondary metabolite profiling shows a complex, strain-dependent response of maize to plant growth-promoting rhizobacteria of the genus Azospirillum. New Phytol 189:494–506

    Article  PubMed  Google Scholar 

  • Walker V, Couillerot O, Von Felten A et al (2012) Variation of secondary metabolite levels in maize seedling roots induced by inoculation with Azospirillum, Pseudomonas and Glomus consortium under field conditions. Plant Soil 356:151–163

    Article  Google Scholar 

  • Wang W, Chen LN, Wu H, Zang H, Gao S, Yang Y et al (2013) Comparative proteomic analysis of rice seedlings in response to inoculation with Bacillus cereus. Lett Appl Microbiol 56:208–215. https://doi.org/10.1111/lam.12035

    Article  PubMed  Google Scholar 

  • Wang Y, et al (2019) Advances in liquid chromatography and liquid chromatography mass spectrometry for the analysis of biologically important pharmaceuticals, glycosaminoglycans and amino acids

    Google Scholar 

  • Wang S, Chen H, Sun B (2020) Recent progress in food flavor analysis using gas chromatography--ion mobility spectrometry (GC--IMS). Food Chem 315:126158

    Article  PubMed  Google Scholar 

  • Wang J-Q, Yin J-Y, Nie S-P et al (2021) A review of NMR analysis in polysaccharide structure and conformation: PROGRESS, challenge and perspective. Food Res Int 143:110290

    Article  PubMed  Google Scholar 

  • Wishart DS, Cheng LL, Copié V et al (2022) NMR and metabolomics—a roadmap for the future. Metabolites 12:678

    Article  PubMed  PubMed Central  Google Scholar 

  • York LM, Carminati A, Mooney SJ et al (2016) The holistic rhizosphere: integrating zones, processes, and semantics in the soil influenced by roots. J Exp Bot 67:3629–3643

    Article  PubMed  Google Scholar 

  • Zambonin C, Aresta A (2021) Recent applications of solid phase microextraction coupled to liquid chromatography. Separations 8:34

    Article  Google Scholar 

  • Zeki ÖC, Eylem CC, Reçber T et al (2020) Integration of GC--MS and LC--MS for untargeted metabolomics profiling. J Pharm Biomed Anal 190:11350

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Pooja Bhadrecha .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Bhadrecha, P., Bhawana (2023). Metabolomics and Proteomics Behind Plant Growth-Promoting Potential of Rhizobacteria. In: Kaur, S., Dwibedi, V., Sahu, P.K., Kocher, G.S. (eds) Metabolomics, Proteomes and Gene Editing Approaches in Biofertilizer Industry . Springer, Singapore. https://doi.org/10.1007/978-981-99-3561-1_16

Download citation

Publish with us

Policies and ethics