The VMD, spanning 39,000 km², is Vietnam’s primary rice production region, which has contributed over 50% of national rice yield and 90% of rice exports (Thach et al., 2023; Tuan et al., 2024). However, saline intrusion, driven by complex interactions of climatic, geological, and anthropogenic factors, poses significant threat to this agricultural region. Coastal provinces, such as Ben Tre, Tra Vinh, Soc Trang, and Ca Mau, confront heightened vulnerability due to their inherently low elevation and proximity to the East Sea. Since the 1990s, salinity intrusion has increased its magnitude, penetrating deeper inland and lasting longer, particularly during the dry season. This phenomenon disrupts irrigation systems which are critical for rice cultivation. Salinity intrusion jeopardizes farmer livelihoods and necessitate innovative solutions like salt-tolerant rice varieties and plant growth promoting rhizobacteria (PGPR). The primary causes and effects of saline intrusion are summarized in Table 1 .

Sea-level rise, which is propelled by climate change, accelerates saline intrusion by penetrating seawater into the irrigation canal network in the VMD. Previous data indicate that salinity intrusion has worsened since the 1990s, and projections suggest a one-meter sea-level rise could submerge approximately 90% of the VMD by 2100, detrimentally affecting provinces like Bac Lieu (39% land at risk) and Tra Vinh (Danh and Khai, 2014; Ngo et al., 2016). During the dry season, low river discharge and tidal amplification enable seawater to penetrate 50–130 km inland, which salinizes irrigation systems in Ben Tre and Soc Trang, where rice fields heavily rely on freshwater (Nguyen et al., 2024).

Upstream hydropower dams in the Mekong River Basin significantly alters downstream hydrology by reducing freshwater flow, intensifying salinity intrusion during the dry season. By 2016, 56 dams, including mega-dams Xiaowan and Nuozhadu, disrupt flow patterns, decrease frequency and intensity of seasonal floods, contributing to severe droughts in 2015–2016 and 2019–2020 (Phuong et al., 2018). These upstream dams also trap nutrient-rich sediments, reducing soil fertility and exacerbating salinity destructive impacts (Loc et al., 2021). The limited coordination and collaboration restrict Vietnam to secure sufficient amount of freshwater for irrigation and household consumption, especially during dry season. Furthermore, riverbed sand mining with approximately 8,5–45,7 Mm³ annually causes riverbed incision, pushing seawater intrusion and destabilizing riverbanks (Hackney et al., 2020). Illegal sand mining, a long lasting and unsolvable environmental issue, which is linked to construction demand, magnifies ecological damage, including loss of fish habitats that support rice-based agroecosystems (Park et al., 2020; Yuen et al., 2024) (Park et al., 2020; Yuen et al., 2024). Additionally, land subsidence, which fundamentally caused by excessive extraction of groundwater for domestic, agricultural, and industrial activities, aggravates this fragility. Subsidence rates average around 2,5 cm year⁻¹ and reach 4 cm year⁻¹ in Ca Mau, outpacing global sea-level rise (2,8–3,6 mm year ⁻¹). This crucial threat lowers the VMD’s elevation and increases flooding risks in rice field (Minderhoud et al., 2017; Qin et al., 2013). Moreover, over-extraction of groundwater has depleted aquifers, leading to the infiltration of saline water through capillary rise, degrading arable land (Erban et al., 2014).

Saline intrusion significantly damages rice production. During severe events such as the El Nino-driven droughts and reduced river flow in 2015–2016 and 2019–2020, the impacts were extensive ( Figure 1 ). In 2016, approximately 224,000 ha of paddy field, 13,000 ha of cash crops, 25,500 ha of fruit trees, and 14,400 ha of aquaculture were damage (CGIAR Research Centers in Southeast Asia, 2016). In the 2020 event, salt concentrations reached 4 g L⁻¹, with seawater penetrating 50–130 km into major rivers, affecting an estimated 215,445 ha of rice and causing economic losses of 337 million USD (Park et al., 2022; Baca et al., 2017). Household affected by salinity intrusion experience lower total production with approximately 761,47 kg ha⁻¹ less for rice, resulting in reduced total and net revenues compared to unaffected farmers (Thanh et al., 2023). In Lich Hoi Thuong area, Soc Trang province, salinity reduced rice yields by 2,54 tons ha⁻¹ annually (Khai et al., 2018). Besides agriculture, these climatic events also disrupted water supplies for millions of residents in the VMD (Tran and Yong, 2025).

Salinity has driven significant shifts in agricultural practices, moving farmers from traditional triple- or double-rice cropping to aquaculture, or even pushing farmer displacement and migration to urban sectors (Binh et al., 2025; Le et al., 2022; Tran et al., 2021). Adaptation strategies including sluice gates and dikes cost money but also face challenges due to funding restraints and rising salinity levels (Duy et al., 2025; Tran et al., 2021). In the near future, Vietnam faces economic challenges including reduced global rice export competitiveness and increased food security risks (Vietnam Chamber of Commerce and Industry (VCCI), 2025). Therefore, enhanced transboundary water management and an intensified investment in salinity-tolerant rice and PGPR technologies are strongly required to address these pressing issues (Mills et al., 2025; Pdr and Nam, 2017).

Traditionally, the VMD relied on seasonal flooding to enrich soils and wash out toxic residuals from rice fields, supporting agricultural production. The floodwaters supplied alluvial sediment, rejuvenating the fields with essential macronutrients such as N, phosphorous (P), potassium (K), calcium (Ca), magnesium (Mg), and sulfur (S) and micronutrients such as boron (B), iron (Fe), copper (Cu), manganese (Mn), molybdenum (Mo), and zinc (Zn). The amount of sediment largely varied from few to ten tons per hectare. Interestingly, natural fish in the floodwaters serve as biocontrol agents in rice ecosystems (Tong, 2017). However, in recent decades, many contributors, such as climate change, upstream dam operation, sea-level rise, and reduced freshwater discharge, intensify salinity intrusion. This threat jeopardizes rice cultivation and risks livelihood of million people in the region (Hoang et al., 2018). On a global scale, soil salinization has emerged as a critical constraint on crop production. In some provisions, by 2050, nearly half of the global arable land could be affected by salinity, dramatically reducing food security worldwide (Hasanuzzaman et al., 2014). Salinization can be classified into two types: primary salinization originated from natural processes such as mineral weathering and salt accumulation via capillary rise from saline groundwater, and secondary salinization caused by anthropogenic factors, for example improper irrigation practices and poor drainage (Butcher et al., 2016; Mohanavelu et al., 2021).

Salinity alters soil chemistry by increasing concentrations of primary cations (Na⁺, K⁺, Ca²⁺, and Mg²⁺), and anions (Cl⁻, SO₄ ²⁻, NO₃ ²⁻, and HCO₃ ⁻). Among them, Na⁺ and Cl⁻ are considered the most harmful contributors to rice metabolism (Corwin, 2021). Excess Na⁺ disrupts soil structure and enzyme activity, while Cl⁻ interfere with photosynthesis. Ion toxicity disrupts intracellular signaling and displaces essential nutrients, particularly K⁺, leading to nutrient deficiency (Assaha et al., 2017). The accessibility of other important nutrients like Ca²⁺, Mg²⁺, Mn²⁺, and Fe²⁺ are also reduced by the abundance of Na⁺ and Cl⁻ in soils (Tavakkoli et al., 2010).

An obvious effect of salinity stress is osmotic stress, which is caused by a rise of soil’s osmotic potential, restricting plant water uptake. This results in dehydration-like symptoms, stomatal closure, and suppressed photosynthesis (Katori et al., 2010). In general, plant responses to salinity stress occur in two phases: (i) an initial, rapid osmotic stress phase, or so-called ion-independent, happening within minutes to days, primarily affecting water uptake and cell turgor. The ion-independent phase involves rapid signaling cascades and hormonal adjustment in response to Na⁺ influx; (ii) a slower, long-term ion toxicity phase, so called ion-dependent response, lasting days to weeks and is characterized by toxic ion accumulation in shoots (Balasubramaniam et al., 2023; Munns and Tester, 2008).

The metabolic disruptions lead to an overproduction of reactive oxygen species (ROS) such as superoxide radicals, hydrogen peroxide, and hydroxyl radicals (Khan et al., 2016). Oxidative stress triggers significant cellular damages, including lipid peroxidation in membranes, which indicated by increased malondialdehyde (MDA), and MDA content, and increases electrolyte leakage (Degon et al., 2023; Jaemsaeng et al., 2018). Hormones like abscisic acid and ethylene rise dramatically in response to salt, regulating stomatal behavior and stress signaling. Ethylene biosynthesis, driven by 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase, also leads to the emission of volatile organic compounds (VOCs). These VOCs (e.g., benzenoids, terpenes, and aldehydes) play dual roles as antioxidants and interplant messengers (Chatterjee et al., 2018). An excess amount of ethylene is often associated with senescence (Dubois et al., 2018).

Growth and development of rice plants are obviously impacted under salinity conditions. Salinity reduces plant height and leaf expansion, shoot and root biomass, and survival rates. It negatively impacts yield components such as panicle length, thousand-grain weight, percentage of filled grains, and the number of effective tillers (Debapriya Choudhury et al., 2024; Li et al., 2024). Early exposure to salinity during the grain-filling stage has been shown to reduce grain quality and yield in fragrant rice cultivars, with average yield reductions of 33,8% across four consecutive seasons in Thailand (Dangthaisong et al., 2023). Rice variety Huanghuazhan, after exposure to 50 mM sodium chloride (NaCl) for two weeks, showed severe chlorophyll degradation, root inhibition, and reduced biomass (Xue et al., 2024).

Rice plants have evolved a complex, multi-layered defense system to cope with the detrimental effects of salt stress. This adaptation involves a tightly coordinated interplay of molecular, physiological, and even biotic mechanisms, from maintaining cellular ion balance to recruiting beneficial microbes in the root environment. Recent studies, which utilized high-throughput omics platforms, has illuminated these integrated pathways, allowing for a comprehensive understanding of how tolerant genotypes thrive under saline conditions. A primary challenge under salt stress is the toxic accumulation of Na⁺ ions. Rice plants manage this through a combination of ion transport and osmotic adjustment (Kumar et al., 2013). The Salt Overly Sensitive (SOS) pathway represents a fundamental line of defense. When high salt levels induce cytosolic Ca²⁺ spikes, the Ca²⁺-binding protein SOS3 senses this signal, activating the kinase SOS2. This, in turn, phosphorylates the plasma membrane Na⁺/H⁺ antiporter SOS1, which actively extrudes Na⁺ from the roots, thus preventing its upward movement to the shoots (Qiu et al., 2002; Xiao and Zhou, 2023). In addition to this extrusion mechanism, rice employs intracellular strategies. The vacuolar Na⁺/H⁺ antiporter OsNHX1 sequesters excess Na⁺ into the vacuole, effectively isolating it from the cytoplasm to maintain cellular ion homeostasis and protect metabolic processes (Fukuda et al., 2004). Similarly, the high-affinity K ⁺ transporter OsHKT1;5, located on the Saltol QTL, plays a crucial role in maintaining the essential K⁺ balance (Platten et al., 2013). It facilitates the unloading of Na⁺ from the xylem into root cells, thereby reducing its harmful accumulation in the shoots (Ren et al., 2005). The expression of OsHKT1;5 is itself meticulously regulated by a complex centered on the transcription factor OsMYB106 and its cofactors OsDNAJ15, OsSUVH7, and OsBAG4 (Liu et al., 2023), highlighting a key intersection between ion transport and transcriptional control. Beyond managing ion toxicity, rice plants also counter the osmotic stress. This is achieved by accumulating compatible solutes like proline and various sugars, which act as osmolytes to maintain turgor pressure. This process is often complemented by robust antioxidant defense mechanisms involving enzymes such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), which detoxify the reactive oxygen species (ROS) produced under stress conditions.

These physiological responses are orchestrated at the genetic level by various transcription factors (TFs), acting as central hubs in stress-responsive signaling cascades. These regulatory networks are often influenced by hormonal signals, particularly abscisic acid (ABA), which can activate both ABA-dependent and ABA-independent pathways. Many studies elucidated critical roles of transcription factor families in regulating expression of stress-related genes in response to salinity. AP2/ERF family is central to regulating stomatal closure, antioxidant defenses, and osmotic adjustment. DREB TFs, for example, enhance salt tolerance by regulating osmoprotection, with some like OsDREB1F participating in ABA-dependent pathways while others function independently (Ito et al., 2006). A related TF, OsEREBP1, enhances salt tolerance through the jasmonic acid (JA) and ethylene pathways, further demonstrating the interconnectedness of hormone signaling (Wang et al., 2020). bZIP family is characterized by a conserved basic leucine zipper domain, these TFs are primarily involved in the ABA-dependent pathway. OsABF2, a key member, acts as a positive regulator of salt stress by binding to ABRE to activate downstream genes (Hossain et al., 2010), while OsHBP1b enhances antioxidant defenses (Das et al., 2019). The NAC family modulates other TFs like DREB, MYB, and bZIP to enhance salt tolerance by upregulating genes for osmoprotection, ion homeostasis, and antioxidant defense. Key members like ONAC022 and OsNAC10 positively regulate salt tolerance through ABA-mediated pathways (Hong et al., 2016; Jeong et al., 2010). In addition, MYB and Zinc Finger (ZF) TFs also play critical roles in salt stress tolerance. OsMYBc enhances salt tolerance by regulating the expression of the ion transporter OsHKT1;1 (Xiao et al., 2022). Meanwhile, C2H2-type ZF TFs like ZFP179 and ZFP252 positively regulate the synthesis of compatible solutes like proline (Sun et al., 2010), while the DST gene, another C2H2-type ZF TF, acts as a negative regulator of salt tolerance by modulating stomatal closure (Huang et al., 2009).

Beyond these internal cellular and genetic mechanisms, the plant’s response is further shaped by its interaction with the soil environment. Recent research has revealed that the rhizosphere microbiome plays a significant role in mediating salt tolerance. A key discovery was the SST (Seedling Salt Tolerant) gene, whose mutation in rice leads to enhanced growth under salt stress by reducing Na⁺ uptake and increasing K⁺ accumulation (Lian et al., 2020). This improved ion homeostasis is coupled with a significant shift in the rhizosphere microbiome, suggesting a link between the plant’s internal genetics and its ability to recruit beneficial microbes. Specifically, salt-tolerant rice varieties maintain greater bacterial diversity in the rhizosphere compared to salt-sensitive ones, and they actively recruit distinct bacterial consortia. For example, tolerant rice plants enrich bacteria with functional genes related to saline-alkali tolerance, such as those for ABC transporters and biofilm formation (Lei et al., 2025). This biotic interaction underscores the need for a consortium approach using multiple beneficial microbes rather than a single strain to effectively enhance salt tolerance in agriculture. The combined evidence from molecular, physiological, and microbial studies presents a more holistic view of rice remarkable resilience to salt stress.

The plant’s response to environmental stress is not limited to internal cellular and genetic mechanisms. It is further shaped by its interaction with the soil environment. Rice plant is not a passive recipient, instead, it actively influences the associated PGPR communities and their activities. This sophisticated, mutualistic relationship is driven by several factors, including the release of root exudates that act as chemical signals influencing PGPR activity and colonization. Recent research has revealed that the rhizosphere microbiome plays a significant role in mediating salt tolerance, a process strongly influenced by root exudates, soil metabolites, and the plant’s genotype (Yusuf et al., 2025; Fan et al., 2025). These factors collectively drive a sophisticated feedback loop that enhances plant growth and resilience. The rhizosphere is a dynamic interface where plants, microbes, and soil continuously interact, with root exudates serving as a crucial communication factor (Bacilio-Jiménez et al., 2003). These exudates, composed of small, low-molecular-weight organic compounds known as soil metabolites—including sugars, amino acids, and organic acids—serve as a primary source of carbon and nutrients for microorganisms (Song et al., 2024; Bolan et al., 2011). They also enable plants to selectively recruit beneficial microbes, such as PGPR (Parasar, Sharma, and Agarwala 2024). Rice root exudates induce a higher chemotactic response for endophytic bacteria, facilitating their colonization (Zhang et al., 2022). In addition to providing nutrients, these exudates contain secondary metabolites like phenolic compounds, flavonoids, and volatile organic compounds that act as signaling molecules, antimicrobial agents, or chemoattractants, directly influencing the structure and function of microbial communities (Bais et al., 2006; Hu et al., 2018; Zhalnina et al., 2018). Beyond plant-derived exudates, the soil metabolite pool is also shaped by microbial byproducts and specific signaling compounds like quorum-sensing molecules, which regulate microbial communication and impact plant-microbe interactions (Venturi and Fuqua, 2013). Quorum-sensing molecules, like N-acyl-homoserine lactones, regulate microbial communication, impacting plant-microbe interactions (Venturi and Fuqua, 2013). Precise identification and quantification of these metabolites are critical for understanding rhizosphere dynamics under environmental stresses. Gas Chromatography-Mass Spectrometry (GC-MS) and Liquid Chromatography-Mass Spectrometry (LC-MS) are standard for metabolite profiling. GC-MS detects volatile and semi-volatile compounds, such as VOCs, while LC-MS analyzes polar and non-volatile metabolites, including organic acids and amino acids (Lisec et al., 2006). These complementary platforms enable comprehensive analysis of the rhizosphere metabolome. Emerging techniques, such as Matrix-Assisted Laser Desorption/Ionization Imaging Mass Spectrometry (MALDI-IMS), provide spatial resolution of metabolite distribution around rice roots, revealing localized interactions between roots and microbes (Yang et al., 2012). This is particularly valuable for studying metabolite gradients in rice paddies. Complex datasets from untargeted metabolomics are analyzed using bioinformatics and statistical tools, such as principal component analysis (PCA) or partial least squares-discriminant analysis (PLS-DA), to identify key metabolites differentiating rice genotypes or stress conditions (Li et al., 2023).

Plant genotypes substantially impact the composition of its root-associated microbial communities, and this effect is the most pronounced in the rhizosphere (Edwards et al., 2015). Different rice genotypes possess varying root exudate profiles, which influence the recruitment of specific bacteria. For example, the abundance of Bacillus and Candidatus_Koribacter differed significantly between rice genotypes under drought conditions (Li et al., 2023). A recent study by Zhong et al. (2025) analyzed rhizosphere microbial communities in rice varieties Jida177 and Tongxi933 under saline-alkaline stress. Proteobacteria dominated high-stress soils, with Jida177 showing higher microbial diversity and better stress tolerance, reducing soil salinity by 73%. Microbial functions varied, with pH as the primary driver of community structure (Zhong et al., 2025). An important finding was related to the SST (Seedling Salt Tolerant) gene, whose mutation in rice led to enhanced growth and improved ion homeostasis under salt stress by reducing Na⁺ uptake and increasing K⁺ accumulation (Lian et al., 2020). Importantly, this genetic alteration was coupled with a significant shift in the rhizosphere microbiome, suggesting a direct link between the plant’s internal genetics and its ability to recruit beneficial microbes. Salt-tolerant rice varieties, in general, are found to maintain greater bacterial diversity in the rhizosphere and actively recruit distinct bacterial consortia. For instance, these tolerant plants enrich bacteria with functional genes related to saline-alkali tolerance, such as those for ABC transporters and biofilm formation (Lei et al., 2025). The mutual interaction between PGPR and rice is a sophisticated and cooperative relationship. PGPR enhances rice growth and stress resilience through various modulations, while the rice plant, in turn, influences the survival, activity, and community structure of these beneficial bacteria. This understanding underscores the need for a consortium approach using multiple beneficial microbes rather than a single strain to overcome the inherent limitations of using a single microbial strain in complex agricultural systems, especially under challenging environmental conditions.

Implementations of PGPR significantly improve rice plants physiologically and morphologically ( Figure 2 ; Table 2 ). Inoculation with Azospirillum brasilense significantly improves total and root plant mass in rice plants grown under high salt concentrations (100 mM and 200 mM NaCl), with improvements observed seven and fourteen days after treatment (Degon et al., 2023). Bacillus siamensis BW-treated seeds exhibit rapid germination compared to untreated controls and show minimal reduction in shoot and root growth at the early seedling stage under saline conditions (75 mM to 150 mM NaCl) (Oubaha et al., 2024). Similarly, rice plants inoculated with Glutamicibacter sp. YD01 show less reduction in root and shoot length under NaCl stress, as this bacterium promotes root growth in seedlings. Glutamicibacter sp. YD01 also significantly enhances K⁺, reduces Na⁺ content in both leaves and roots, and increases relative water content (RWC) in rice seedlings (Ji et al., 2020). A study by Qin et al. (2018) found that Glutamicibacter halophytocola strain KLBMP 5180, isolated from the root tissue of Limonium sinense, significantly promoted host growth under NaCl stress by increasing concentrations of total chlorophyll, proline, antioxidative enzymes, flavonoids, K⁺, and Ca²⁺ in L. sinense leaves (Qin et al., 2018). Enterobacter asburiae D2 inoculation specifically promotes rice growth, including root length and dry weight, under both neutral (NaCl) and alkaline (Na₂CO₃) salt conditions (Ning et al., 2024). Additionally, Pseudomonas promysalinigenes RL-WG26 significantly increases plant biomass, root surface area, and root length in rice seedlings under both normal and saline conditions (Ren et al., 2024).

PGPR improve rice growth under salt stress by regulating the expression of key genes involved in defense and stress response (Giannelli et al., 2023). Transcriptomic studies have shown differentially expressed genes (DEGs) in A. brasilense-treated, salt-stressed rice roots, including those involved in defense and stress response (Degon et al., 2023). Other Bacillus strains, like NMTD17 and GBSW22, highly stimulated the expression of various DEGs related to salt stress, including OsSAMDC2, OsDREB1F, OsEREBP2, OsLEA3-1, OsERF104, and OsCYP89G1 (Ali et al., 2022). OsSAMDC2 is involved in polyamine biosynthesis, which helps mitigate oxidative damage under salinity (Sackey et al., 2025). Its expression is regulated by OsNAC45, a transcription factor involved in the salt stress response (Zhang et al., 2020). OsEREBP2 functions downstream of OsNAC45, and its expression is upregulated in response to salt treatment, suggesting its involvement in salt stress signaling (Zhang et al., 2020). OsLEA3 is a late embryogenesis abundant group 3 protein and its accumulation in the vegetative tissues of transgenic rice helped improve tolerance to salt stress and water deficit (Hu, 2008). While OsERF106 acts as a negative regulator of shoot growth and salinity tolerance in rice, the functions of its relative, OsERF104, in response to salinity remain unknown (Chen et al., 2021). OsCYP89G1, a CYP450 family member, encodes for cytochrome P450 monooxygenase. Its expression is upregulated by NaCl and repressed by ABA (Zhang et al., 2020). Although its specific role in rice salinity response is unclear, the overexpression of another family member, OsCYP75B4, improved salt tolerance in transgenic rice plants (Ruan et al., 2025). OsDREB1F belongs to the DREB transcription factor family, which plays a key role in plant stress signaling. Its expression is induced by salt, drought, cold stresses, and ABA, and its overexpression has been shown to enhance tolerance to these stresses in rice and Arabidopsis (Wang et al., 2008).

Salinity stress typically leads to oxidative stress and the accumulation of reactive oxygen species (ROS), which plants counteract using antioxidant enzymes like catalases (CAT), glutathione-S-transferases (GST), and superoxide dismutases (SOD) (Asif et al., 2023). Accordingly, genes encoding these enzymes are often upregulated in salt-stressed plants. However, PGPR treatment can have varied effects on these genes. A. brasilense treatment suppressed most of these antioxidant genes in salt-stressed rice roots, suggesting that A. brasilense inoculation relieves stress and reduces the need for the plant’s own antioxidant response (Degon et al., 2023). Similarly, Brevibacterium linens RS16 reduced plant antioxidant enzyme activity and lipid peroxidation (Chatterjee et al., 2018). Conversely, other PGPR strains, such as Glutamicibacter sp. YD01, Bacillus siamensis BW, Pseudomonas promysalinigenes RL-WG26, and Microbacterium ginsengiterrae S4, significantly increased the activity of antioxidant enzymes (SOD, Peroxidase, CAT, Ascorbate Peroxidase, and Glutathione Reducer) in rice seedlings under salinity stress (Oubaha et al., 2024; Sarkar et al., 2018; Ren et al., 2024; Chinachanta et al., 2023; Khan et al., 2021; Ji et al., 2024). This response is often accompanied by the upregulation of genes encoding these enzymes, including OsPOX1, OsFeSOD, OsGR2, OsCATA, and OsAPX1 (Asif et al., 2023; Sarkar et al., 2018; Khan et al., 2021). PGPR treatment also alters the expression of salt-induced ABA and JA signaling genes in rice roots (Degon et al., 2023). Other studies using Bacillus spp., Lysinibacillus fusiformis, Lysinibacillus sphaericus, and Brevibacterium pityocampae also reported decreased ABA content in PGPR-inoculated rice plants under salt stress (Khan et al., 2021; Asif et al., 2023), implying that these PGPRs alleviate stress to the extent that these hormone pathways are not strongly activated. ACC deaminase-producing PGPRs, such as Glutamicibacter sp. YD01 and P. promysalinigenes RL-WG26, reduce ACC content and ethylene production. This, in turn, downregulates ethylene-responsive genes (e.g., OsERF1) and alleviates growth inhibition caused by excessive ethylene under stress (Ganie et al., 2022; Ji et al., 2020; Ren et al., 2024). PGPRs also modulate genes involved in Na⁺ and P transport and Ca²⁺ signaling. Key genes like OsNHX1 (Na⁺/H⁺ antiporter), SOS1 (Salt Overly Sensitive 1), and OsHKT1 (high-affinity K⁺ transporter) are strongly regulated (Degon et al., 2023; Ganie et al., 2022). Glutamicibacter sp. YD01 upregulates OsHKT1 expression (Ganie et al., 2022), while Brevibacterium linens RS16 induces vacuolar H⁺ ATPase activity (Chatterjee et al., 2018), which helps to remove Na⁺ from the cytosol or maintaining a low Na⁺ concentration in plant cells. Bacillus spp. upregulates OsPIN1A expression (Khan et al., 2021), which is involved in auxin efflux and root development, thereby improving nutrient acquisition under salt stress (Xu et al., 2005).

Regarding TFs and other stress-related proteins, PGPRs influence the expression of various TF families, including WRKY, DREB, ERF, MYB, and bZIP, which are crucial regulators of plant stress responses (Ali et al., 2022). Glutamicibacter sp. YD01 upregulates OsWRKY11 and OsDREB2A (Ji et al., 2020), and Microbacterium ginsengiterrae S4 induces the upregulation of OsWRKY76 (Ji et al., 2024). Genes associated with abiotic stress tolerance, such as OsLEA3 and OsRab16A, also show markedly higher expression levels in Streptomyces albidoflavus OsiLf-2-inoculated rice under salt conditions (Niu et al., 2022; Ganguly et al., 2012; Ganguly et al., 2020). PGPR inoculation also leads to the upregulation of chaperone proteins, like the 60 kDa chaperonin, HSP20, GroEL, and calreticulin, which are crucial for refolding denatured proteins and maintaining protein homeostasis under stress (Meng et al., 2024). Some defense-related genes like chitinases also show altered expression patterns with A. brasilense inoculation (Degon et al., 2023).

EPS produced by halotolerant PGPR (e.g., Bacillus cereus DB2, Bacillus tequilensis, Bacillus siamensis BW, Enterobacter sp. JIV1) can bind Na⁺ ions in the rhizosphere, making them less available for plant uptake (Debapriya Choudhury et al., 2024; Oubaha et al., 2024; Shultana et al., 2020b; Wang et al., 2022; Ning et al., 2024; Ji et al., 2024). This physical barrier reduces the ionic stress on plant roots, thereby influencing the plant’s gene expression response to salinity.

Studies on PGPR on rice have shown promising results in Vietnam ( Table 3 ). For example, a significant field study across 20 farms over four consecutive growing seasons evaluated BioGro 2, a commercial biofertilizer containing Pseudomonas fluorescens, Bacillus subtilis, Bacillus amyloliquefaciens, and Candida tropicalis (Nguyen et al., 2017). While the product successfully replaced 23–52% of N requirements, maintaining grain yields comparable to conventional chemical fertilizers, its inability to substitute for P and K demands represents a significant limitation. Furthermore, the wide range of effectiveness (23–52%) and the notable influence of timing and dosage on its performance highlight a critical need for optimized, context-specific application strategies to ensure consistent results and minimize risks for farmers. In response to increasing saline intrusion in Vietnam’s coastal regions, such as Soc Trang and Ben Tre, researchers have focused on isolating salt-tolerant PGPR. A study in 2018 obtained 48 salt-tolerant isolates, of which 22 produced indole-3-acetic acid (IAA) and 17 showed potential for N fixation and PO₄ ³⁻ solubilization (Cuong et al., 2020). Six of these isolates, from the genera Bacillus, Halobacillus, Aeromonas, and Klebsiella, exhibited all three traits, indicating their potential as multifunctional biofertilizers for saline-affected soils.

Purple nonsulfur bacteria (PNSB), like Rhodopseudomonas palustris and Rhodopseudomonas harwoodiae, have also been explored as biofertilizers and bioremediators. Studies have shown they can enhance rice growth and grain yield while improving soil fertility and reducing toxic Mn accumulation (Khuong et al., 2017; 2022). Field trials combining mixed PNSB with 75% of the recommended NP fertilizer achieved yields comparable to those obtained with 100% NP fertilizer. While these results are promising, the reproducibility of these findings across Vietnam’s diverse acid sulfate soils has not been comprehensively evaluated. The effectiveness of these formulations may vary significantly with regional soil chemistry and climatic conditions. Similarly, other studies have investigated the growth-promoting effects of silicate-solubilizing bacteria (SSB) and N-fixing strains like Sinorhizobium fredii and Azospirillum spp (Điệp, 2005; Chiêu and Hiệp, 2010; Đường et al., 2018). These studies have provided evidence that such microbes can improve nutrient uptake, reduce fertilizer dependency, and increase stress tolerance. The commercial microbial formulation NPISi was shown to significantly increase grain yield and soil health in a rice-shrimp farming model (Nguyễn et al., 2021). However, a notable observation that the formulation elevated K levels in rice despite the absence of K-solubilizing bacteria highlights a critical knowledge gap regarding the full range of microbial functions and their complex interactions in the soil.

In summary, previous studies had some limitations as many field experiment were conducted for only one cropping season (Minh et al., 2020; Nguyễn et al., 2021). This drawback raises concerns reproducibility across seasons and long-term impacts of soil improvement products in salt-affected areas. Although the focus of these studies on specific soil conditions, e.g., salt-affected soil in a rice-shrimp farming system, salt-affected clay loam soil, and acid sulfate soil, is understandable due to limitations of time and budgets, their specificity may limit the generalizability of these findings (Đường and Nghĩa, 2020; Huy and Hiệp, 2019; Xuân et al., 2019). Therefore, future research should be systematically conducted across multiple-season field trials and on a wider range of soil types to thoroughly evaluate long-term effectiveness, consistency and applicability of these PGPR-based approaches. All studies provided initial characterization of the bacterial strains (Đường et al., 2018; Đường and Nghĩa, 2020; Giang et al., 2024; Huy and Hiệp, 2019; Minh et al., 2020; Nguyễn et al., 2021; Xuân et al., 2019). However, these studies did not provide data regarding the long-term consistency of these bacteria over generations. Moreover, potential genetic drift and phenotypic changes over time and in large-scale production were not mentioned. Therefore, comprehensive studies on the genetics and beneficial traits’ stability over successive generations and production cycles are critical to ensure their consistent performance and reliability as biofertilizers for widespread applications. Additionally, studies on the shelf-life and long-term storage stability of these biofertilizer formulations under various conditions and extended periods should be extensively carried out.