Plant growth promoting bacteria (PGPB)-induced plant adaptations to stresses: an updated review

Search methodology

The main purpose of this review is to emphasize the significance of plant growth-promoting organisms, especially bacteria in the mitigation of various biotic and abiotic factor-induced stress on plants, and their mechanisms employed to improve the quality and quantity of plant products to achieve sustainable agriculture. To ensure the comprehensive and unbiased coverage of the literature, we focus on the latest publications in each of their particular area, between 2000 to 2024 including research articles, review articles, and case studies using Google as a search engine. To elucidate some points, terms like bioinoculants, bioformulants, and bioactive compounds were searched. Some properties of PGPB including bioremediating potential, Pharmaceutical potential, and genetics involved in the plant growth-promoting ability are excluded in this review which may be diverted from this review’s goals and confuse the readers.

Rationale and intended audience

Agricultural system using beneficial bacteria as bioinoculants is a promising way of achieving a sustainable future. It is a good alternative to chemical fertilizer as an efficient, eco-friendly, productive fertilizer that may aid provide the food demand of the growing global population. They not only enhanced the plant growth but also maintained the soil fertility and enhanced the soil microbiome.

Abiotic stress factor

Climate change induces several abiotic stresses such as drought, salinity, temperature, and heat. These along with nutrient limitations and the presence of heavy metals are crucial players behind compromised yield by crop plants (Naing, Maung & Kim, 2021). In the following points, we will discuss the abiotic stress tolerance mechanisms offered by PGPB.

Biotic stresses

PGPM can potentially inhibit biotic stress in plants, induced by pathogenic fungi, bacteria, nematodes, insects, and weeds (Gupta et al., 2021), this type of resistance is known as Systemic acquired resistance (SAM), also when the plant growth-promoting bacteria elicit the biotic stress by producing elicitors like volatile organic compounds, microbe associated molecular patterns (MAMPs) in, and bioactive secondary metabolites, it is called induced systemic resistance (ISR) (Romera et al., 2019; Dubey et al., 2020).

According to Migunova & Sasanelli (2021), the PGPB inhibits pathogenic nematodes directly by releasing different lytic enzymes, antibiotics, and volatile organic compounds indirectly through nitrogen fixation, siderophores, and solubilizing phosphate phytohormones production. Bacterial strains such as Pasteuria penetrans (Mohan et al., 2020) and Brevibacillus laterosporus produce proteases that inhibit the nematode Heteroderaglycines (Abd-Elgawad & Askary, 2018). Bacillus megaterium also produces proteases against M. graminocula (Liang et al., 2019). Also, P. aeruginosa, P. cepacia, and P. fluorescens have anthelmintic, antimicrobial, antiviral, cytotoxic, and antitumor properties that can fight against phytopathogens (Bhavya & Geetha, 2021) Moreover, bacteria like B. subtilis, and B. pumilus produce chitinase that combats nematodes like M. hapla and Meloidogyne sp. (Kohli et al., 2018) by causing hydrolysis, disrupting chitin synthesis, producing volatile compounds acting as antifungal (Xie et al., 2020). B. amyloliquefaciens FZB42 produces bacteriocins inhibiting M. incognita (Liang et al., 2019). According to Aeron et al. (2019), Anthrobacter nicotianae and Bacillus sp. release volatile compounds that exhibit activity against M. graminicola and M. incognita. Lyseni bacillus, Staphyococcus, Pseudomonas, and Enterobacter also have antibacterial, and antifungal properties (Mamonokane, Eunice & Mahloro, 2018).

According to Oleńska et al. (2020), the interactions between plants and various bacteria have an array of effects on plant productivity and soil fertility by producing various chemicals like siderophores, phytohormones, and antibiotics, which inhibit the efficacy of various pathogenic fungi, dissolve phosphate in the soil, and produce indole acetic acid, which promotes plant growth. Moreover, the PGPB must possess inherent rhizospheric competency which enables it to colonize the rhizosphere in addition to the previously stated properties.

PGPB also reduces or stops the effect of specific pathogens that compete for nutrients and interact with certain beneficial microorganisms and indirectly encourages plant productivity (Benizri et al., 2021). PGPB synthesizes antimicrobials like bacteriocins, antibacterial proteins, and enzymes that induce both narrow- and broad-spectrum inhibition of bacteria by altering the structural membrane and damaging the cell wall (Nazari & Smith, 2020; Mak, 2018) The antagonistic effect of PGPR can occur by producing cell wall hydrolases such as chitinase, glucanase, proteases, and ligases that can destroy the pathogenic cell (Pérez-Montaño et al., 2014). Other than directly acting as an anti-pathogenic activity, the antibiotic also triggers the induced systematic resistance (ISR) in plants, suppressing the disease and acting as a biocontrolling agent. The pathogenic bacteria mainly belong to bacterial genera like Erwinia, Pectobacterium, Pantoea, Agrobacterium, Pseudomonas, Ralstonia, Burkholderia, Acidovorax, Xanthomonas, Clavibacter, Streptomyces, Xylella, Spiroplasma, and Phytoplasma. They cause various diseases, including wilting of leaves, spots, galls, blights, and root rot (Nabila & Kasiamdari, 2021). Some examples of the most common disease-causing plant pathogens and the PGP strain that suppresses them are listed in Table 2.

Based on their interactions with plants

Based on interactions, PGPB can be categorized into two types, namely free-living rhizobacteria and symbiotic bacteria. The free-living rhizobacteria are present outside the plant cells, while the symbiotic bacteria, also called endophytes, reside in the intercellular spaces of the plant allowing them direct access to the exchange of metabolites (Turan et al., 2016).

Following Djaya et al. (2019), endophytic bacteria are the organisms that colonize the internal tissues of plants at least once in any part of their lifetime. Various endophytic bacteria colonize different plant parts such as leaves, stems, roots, and flowers (Santoyo et al., 2016). The density of culturable bacterial cells per gram retrieved from the root is higher than that of stem and leaves, then flowers and fruits (Amend et al., 2019). According to Afzal et al. (2019), the diversity of bacteria depends upon the conducive conditions, genetic composition, and physiology of the plant parts they colonize. The relationship between plants and endophytes is considered to be symbiotic and interacts with the root more efficiently. Still, recent studies reveal that the microorganism’s mutualism or pathogenicity depends on the genetic composition, environmental factors, and co-colonization of bacteria. Therefore, the term endophytes also includes the pathogen colonizing the plant tissue (Compant et al., 2021). The endophytic bacteria can be pre-inoculated in the seeds, enhancing the seed quality, increasing the shelf life, and boosting the plant’s endurance to specific stresses (Zapata-Sarmiento et al., 2020). Besides, the rhizospheric bacteria can penetrate the plant tissues through the cracks in the roots and cause various tissue injuries to the plant due to the continuous growth of the plant (Sørensen & Sessitsch, 2007). Endophytic bacteria can also be used as bio-controlling agents; they help in plant growth directly and indirectly (Hernández-León et al., 2014), such as the production of antibiotics, cell wall degrading enzymes, and pathogen-resistant volatile compounds. They induce systemic resistance and reduce ethylene production (Santoyo et al., 2016). Furthermore, endophytic actinobacteria also generate secondary metabolites, improving the growth and resilience to various environmental stresses (Girão et al., 2019).

The study performed by Pitiwittayakul, Wongsorn & Tanasupawat (2021) shows the endophytes isolated such as Nguyenibacter vanlangensis, Acidomonas methanolica, Asaia bogorensis, Tanticharoeniaaidae, Burkholderia gladioli, and Bacillus altitudinis from the stem of sugarcane from the Nakhon Ratchasima Province in Thailand effectively inhibit the mycelial growth of F.moniliforme AITO1. These isolates also exhibit plant growth promotion properties through ammonia production, zinc, phosphate solubilization, and biosynthesis of auxin and siderophores. This result highlights that endophytes can be potentially used as PGP and antifungal.

Plant growth-promoting rhizobacteria (PGPR) refers to the bacteria that colonize the rhizospheric region, and aid in plant growth and development by producing beneficial metabolites (Santoyo et al., 2021). The bacteria must have the ability to induce plant growth, suppress or stop the pathogen, and should be invasive (More et al., 2022). PGPR affects the plant by producing and releasing secondary metabolites, which can be employed for crop nutrition and protection, increasing the availability and uptake of different micronutrients from the soil and replacing chemical pesticides (Ramakrishna, Yadav & Li, 2019; Zhao et al., 2021). The rhizospheric microbial diversity is determined by the exudates and metabolites secreted by the roots that provide the optimum environment for microbial growth regarding nutrient availability (Zhao et al., 2021; Vives-Peris et al., 2020).

A study by Dörr, Moynihan & Mayer (2019) and Lee et al. (2022) reported that the tomato seeds inoculated with a PGPR Rhodopseudomonas palustris enhance the overall plant post-harvest quality and increase the nutrient availability in the fruits.

Based on their cell wall composition

According to Dörr, Moynihan & Mayer (2019), the PGPB can also be classified based on the composition of their cell wall; the bacteria that consist of a thick peptidoglycan wall can retain a Gram dye are called Gram-positive, while the ones that have a thin peptidoglycan wall and cannot keep the Gram’s dye are known as Gram-negative.

The Gram-positive PGPB includes B. alveli, B. thuringeansis, Clostridium novyi, C.limosum, Symbiobacterium thermophillum, etc., Gram-negative PGPB includes Citrobacter sp., C. freundii, C. intermedius, C. koseri, E. coli, Enterobacterderogenes, Flavobacterium sp. (Rodrigues et al., 2016), Azotobacter chroococcum, A. insignis, A. nigricans, A. brasilense, Az. salinestris, and Az. vinelandii (Shelat, Vyas & Jhala, 2017).

Antagonistic activity (indirect mechanism)

Production of lytic enzymes

Plant growth-promoting bacteria serve as defendants of other bacterial pathogens by producing several enzymes, they are elaborated in the following.

Hydrogen cyanide production

Hydrogen cyanide is a highly toxic volatile compound capable of cellular respiration disruption (Alemu, 2016). They inhibit pathogenic fungi, nematodes, insects, and termites (Sehrawat, Sindhu & Glick, 2022). The HCN produced by rhizospheric bacteria also acts as a controlling agent for weeds by colonizing the plant roots and hindering their growth. It has no adverse effect on the plant host.

Hydrogen cyanide production can be screened according to a method described by Lorck (1948). According to him, bacteria were streaked in an agar media containing 4.4 g L⁻¹ of glycine. The Whatman filter paper was soaked in an alkaline prate solution and put on the lid of the culture plate and then inoculated at 28 °C for 3 days. The color change was observed and considered hydrogen cyanide production.

The HCN-producing bacteria mainly belong to Pseudomonas and Bacillus species (Voisard et al., 1989; Lieberei, Fock & Biehl, 1996; Damodaran et al., 2013), Bacillus pumilus, and Bacillus subtilis (Damodaran et al., 2013).

Phytohormone production

Plant hormones are indispensable chemical messengers that direct the plant’s ability to react to the environment (Gutiérrez-Mañero et al., 2001; Vejan et al., 2016). Both plants and microorganisms can carry out the biosynthesis of plant hormones like cytokinins and auxin. The study carried out by Daud et al. (2019), Swarnalakshmi et al. (2020) and Mekureyaw et al. (2022). Certain bacteria like Paenibacillus polymyxa, Rhizobium leguminosarum and Pseudomonas fluorescens are known to be cytokine producers. However, the production of cytokinins is not well studied and investigated due to their diverse compound groups, usually present in minute amounts, making them difficult to identify and quantify.

Moreover, studies regarding the gibberellic acid’s production as a plant growth promoter are limited; only a few studies were conducted during the last 20 years; from the latest study performed by Gutiérrez-Mañero et al. (2001), bacterial strains B. pumilus and Bacillus licheniformis produced four forms of gibberellic acid. Among all the plant hormones, IAA is most commonly investigated and regarded as one of the critical PGB traits for plant growth promotion. It is a heterocyclic compound with a carboxymethyl group that induces leaf formation, embryo development, root initiation and growth, phototropism, geotropism, and fruit development (Chandra et al., 2019). A carboxymethyl group, acetic acid, is responsible for all the functions performed by IAA (Mike-Anosike, Braide & Adeleye, 2018). Certain studies indicated that some rhizospheric bacteria can produce physiologically active IAA, which inspires root elongation, cell division, and plant growth (Rehman et al., 2020). The bacteria that produced phytohormone include Azospirillum (Pedraza et al., 2020; Raffi & Charyulu, 2020), Arthrobacter spp. Bradyrhizobium, Bacillus, Pantoea, Rhanella, Burkholderia, Arthrobacter, Herbaspirillum, Pseudomonas, Enterobacter, Mesorhizobium, and Brevundimonas (Prasad et al., 2019). Plants and microbes synthesized IAA through several interrelated pathways. One of them is the dependent pathway. Microbes’ IAA varies by physiological parameters like pH, temperature, carbon, and nitrogen sources (Chandra, Askari & Kumari, 2018). The bacterial strains like Bacillus paenibacillus polymyxa, Bacillus subtilis, Camamonas acidovorans, Bacillus megatarium, B. simplex, and Enterobacter cancerogenus, produce IAA, which enable the plant to absorb more nutrients from the soil, resulting in the overall enhancement of growth and development in plants (Goswami et al., 2013).

IAA production by rhizobacteria can be analyzed as per the method described by Ahmed & Hasnain (2010). Here, the bacterial isolates were grown in nutrient broth supplemented with 0.5% of L-tryptophan at 27 °C for 3 days. The suspension was then centrifuged at 11,000 rpm for 10 min, and collect the supernatant. Further, 1 ml of the supernatant was added to 2 ml of Salkwoski reagent (1 ml of 0.5 M FeCl₃ + +50 ml of 35% perchloric acid) and incubated at room temperature in the dark for 30 min. The formation of a pink color indicated that the bacteria produced IAA. Production of IAA is quantitatively determined by taking OD at 530 nm, and the concentration was expressed in μg/ml. This is an efficient protocol commonly used for qualitative and quantitative estimation of IAA production.

Phosphate solubilization

According to Satyaprakash et al. (2017), phosphorus is considered the second most essential nutrient for the plant; inadequate phosphorus eventually hinders the growth of the plant. Studies have reported the ability of bacteria to solubilizes the inorganic phosphate compounds like tricalcium phosphate, dicalcium phosphate, hydroxyapatite, as well as rock phosphate into a soluble organic phosphate by releasing organic acids (Verma et al., 2017) like citric acid and gluconic acid which chelate the cations of phosphate using the hydroxyl and carboxyl groups present in them (Youssef, 2014).

Several studies involving phosphorus-solubilizing bacteria for plant growth improvement report the treatment of maize, wheat, and lettuce seeds with phosphate-solubilizing bacteria (PSB) such as Pseudomonas putida, Azospirillum lipoferum, Bacillus firmus and Bacillus polymyxa, enhance the solubility of phosphorus in the soil (Mohamed et al., 2019). Other species like P. chlororaphis, Serratia marcescens, B.subtilis, B. megaterium, Arthrobacter aureofaciens, Phyllobacterium myrsinacearum, Rhodococcus erythropolis (Kaymak, 2011), Burkholderia, flavobacterium, Rhizobium, Erwinia, Acetobacter, Micrococcus, Agrobacterium and Achromobacterium (Youssef, 2014) were identified as phosphate solubilizing bacteria.

According to studies conducted by Lin et al. (2023) in the potato plant, the phosphate-solubilizing bacteria strain Bacillus megaterium activated the gene expression responsible for salinity, drought, and heat stress. Furthermore, the bacteria also trigger different metabolic processes in the plant.

Moreover, the application of B. subtilis, A. brasilense, and P. fluorescens as a single and combined or coupled with different application rates of phosphorous pentoxide increases the overall sugarcane yields (Rosa et al., 2022, 2023).

Screening for phosphate solubilization by bacteria can be done by following the method described by Kesaulya, Zakaria & Syaiful (2015).

Ammonia production

Ammonia production is a remarkable trait of PGPR for plant growth promotion. When ammonia produced by bacteria is accumulated in the soil, it resulted in alkalinity conditions that repress many phytopathogen. Moreover, ammonia supplies nitrogen to the plant, resulting in root and shoot elongation and biomass growth with increased plant biomass, eventually enhanced the plant growth indirectly (Bhattacharyya et al., 2020; Gohil et al., 2022). The bacterial isolates can be screened for ammonia production by a method described by Bhattacharyya et al. (2020). The bacteria incubated for 5 days at 30 °C in a broth containing peptone, NaCl, and yeast extract were centrifuged at 10,000 rpm for 15 min, and subsequently, 0.5 ml Nessler reagent was added. The development of a brown and yellow color indicated ammonia production, and the light absorbance was determined using a Spectrophotometer at 450 nm. The ammonia-producing microbe includes Pseudomonas putida (Ahemad & Khan, 2012), Klebsiella sp. (Ahemad & Khan, 2010), Enterobacter asburiae (Wickramasinghe et al., 2021).

Nitrogen fixation

Nitrogen is considered the most essential nutrient for plant development since it is required for the overall growth and the production of fruits and seeds (Mahmud et al., 2020). Plants cannot directly utilize atmospheric nitrogen; therefore, bacteria assist in nutrient uptake by a symbiotic relationship with plant roots or by non-symbiotic bacteria (Batista et al., 2018).

Bacterial genera that form a symbiotic relationship with the plant roots include Bradyrhizobium, Mesorhizobium, Sinorhizobium, Azhorhizobium, Pararhizobium, Neorhizobium, and Pseudomonas (Nascimento et al., 2019). A non-symbiotic bacteria includes Achromobacter, Herbespirillum, Azoarcus (Turan et al., 2016) Glucanoacetobacter, Azoarcus, Azotobacter, Azospirillum, Acetobacter, Enterobacter, Burkholderia, Pseudomonas, Cyanobacteria and Diazotrophicus (Basile & Lepek, 2021).

A study by Galindo et al. (2024) shows that the application of microbial consortia such as A. subtilis and A. brasilense combined with different nitrogen application rates upregulate the root and shoot development, carbon dioxide uptake, transpiration and leaf chlorophyll index. Also, these microbial consortia inoculated in the seed improved the grain yield and nitrogen accumulation of wheat (Gaspareto et al., 2023). Moreover, Bradyrhizobium sp. and Bacillus sp. co-inoculation improve nodule formation thereby enhancing the nitrogen fixation resulting in the overall plant yield of Vigna unguiculata (Galindo et al., 2022).

Zinc solubilization

Zinc serves as an essential co-factor for enzyme activity that is involved in plant growth promotion by the microbes; the siderophore production and zinc ion production are also correlated (Eshaghi et al., 2019). The optimum zinc concentration in plants is about 30 to 100 mg/kg; below this level results in deficiency (Fasim et al., 2002). According to Singh et al. (2005), zinc deficiency resulted in the slow growth and arising of necrotic marks in the plants. Zinc solubilizing bacteria play an essential role in overcoming inadequate zinc availability. The rhizobacteria mostly solubilizes zinc by producing organic acid metabolites, which lowers the pH of the soil where it is produced and iron chelating enzymes (Fasim et al., 2002). The plant enzymes like carbonic anhydrase and superoxide dismutase are bound structurally by the zinc.

The microbes like P.aeruginosa, Gluconacetobacter diazotrophicus, P. striata, P.fluorescense, Burkholderia cenocepacia, S. liquifaciens, S. marcescens, B. thurigeansis, B.aryabhattai (Kamran et al., 2017), B. subtilis, Thiobacillus thioxidans, and cyanobacteria (Hussain et al., 2015) are reported to solubilize zinc. Also, genera like Rhizobium, Pseudomonas, and Bacillus promote the zinc translocation towards plants from soil, thereby improving the grain yield and zinc biofortification (Jalal et al., 2022) These zinc-solubilizing microbes improve the overall quality and productivity of wheat by producing exopolysaccharides and siderophores (Jalal, Júnior & Teixeira Filho, 2024). Moreover, co-inoculation of B.subtilis and foliar zinc oxide, P. fluorescence and foliar zinc oxide improved the the chlorophyll content, an amino acids, grains glutelin and prolamin in maize (Jalal et al., 2023b).

The zinc solubilization potential of bacteria can be screened using a modified Pikovskaya Agar containing insoluble zinc oxide. On the medium, 5 µL of bacterial culture was inoculated, then incubated at 28 ± 2 °C; the result can be observed after the 2, 4, and 7 days. The potential for zinc solubilization of the isolate was indicated by developing a distinct halo zone around the bacterial growth spot (Sharma et al., 2012). The zinc solubilizing index can be calculated by the ratio of Halo zone formed + colony/colony diameters (Saravanan, Madhaiyan & Thangaraju, 2007).

According to a study by Wu et al. (2013), zinc inhibited biofilm production by A.pleuropneumoniae, Salmonella typhymurium, E.coli, S.aureus, and Streptococcus suis efficiently. The zinc nanoparticles obtained from the bacteria can also be used to enhance the antimicrobial and biocidal activity of the human oral microbiome (Lallo da Silva et al., 2019).

Potassium solubilization

Potassium is naturally present in the soil but they are not readily absorbed by it since it exists in an insoluble form, therefore plant growth-promoting bacteria solubilize potassium by proffering a variety of organic acids including citric acid, oxalic acid, and tartaric acid (Olaniyan et al., 2022). Potassium has several critical functions, as it can alter enzymes physical structures and expose the active site for the reactions. Furthermore, it activates at least 60 enzymes involved in plant growth (Prajapati & Modi, 2012). According to Rawat, Pandey & Saxena (2022), plants depend on potassium to open and close stomata. The high level of potassium content in plants resulted in improved disease resistance, fiber quality in cotton, and durability of fruit and vegetables and their physical quality (Prajapati & Modi, 2012).

Potassium concentration in the plants regulates water retained in the plant, and low potassium content results in sensitivity to water stress. Bacteria including Acidithiobacillus, Burkholderia and Pseudomonas (Sharma, Shankhdhar & Shankhdhar, 2016), Bacillus megaterium, Arthrobacter (Keshavarz Zarjani et al., 2013), Pantoea ananatis,Rahnella aquatilis, Enterobacter sp. (Bakhshandeh, Pirdashti & Lendeh, 2017), Bacillus mucilaginosus, Paenibacillus mucilaginosus (Hu, Chen & Guo, 2006), Bacillus licheniformis, Pseudomonas azotoformans (Maurya et al., 2016), Bacillus edaphicus (Sheng, Huang & YongXian, 2000), and Pseudomonas putida (Bagyalakshmi, Ponmurugan & Marimuthu, 2012) have been identified as a potent K solubilizer.

The bacteria’s ability to saturate the potassium can be studied by spot inoculation in Aleksandrow agar medium, the halo zone formed around the bacteria after seven days suggests the potential to solubilize potassium (Sood et al., 2023). This protocol is time-friendly, and commonly used for quality testing.