Exploring the Roles of Plant Growth-Promoting Rhizobacteria (PGPR) and Alternate Wetting and Drying (AWD) in Sustainable Rice Cultivation

Abstract

Rice sustains a large global population, making its sustainable production vital for food security. Alternate wetting-and-drying (AWD) irrigation offers a promising approach to reducing water use in rice paddies but can impact grain yields. Plant growth-promoting rhizobacteria (PGPR) can enhance rice productivity under AWD cultivation conditions. This review explores integrating PGPR into AWD systems, focusing on their mechanisms for promoting growth and water stress resilience. It examines diverse microbial communities, particularly bacteria, and their contributions to nutrient acquisition, root development, and other beneficial processes in rice under fluctuating moisture, as well as the influence of AWD on rice’s structural and physiological development. The challenges and opportunities of AWD are also addressed, along with the importance of bacterial selection and interactions with the native soil microbiome. This synthesizes current research to provide an overview of PGPR’s potential to improve sustainable and productive rice cultivation under AWD. Future studies can leverage powerful tools such as e-DNA and NGS for a deeper understanding of these complex interactions.

1. Introduction

Rice (Oryza sativa) is a staple food for over half of the world’s population and a cornerstone of global food security, alongside maize (Zea mays) and wheat (Triticum spp.). To sustain the current global population of 7.8 billion, more than 500 million metric tons of rice are required annually [1,2]. However, the World Economic Forum warns that rice yields are increasingly at risk due to climatic stresses [3]. By 2050, the global population is projected to exceed 10 billion, further intensifying the demand for rice [4]. Despite these challenges, increasing rice production is insufficient, therefore, modern agriculture must address the environmental and social consequences of conventional farming practices to ensure sustainability.

Conventional rice farming relies heavily on freshwater, synthetic fertilizers, herbicides, and pesticides to maximize yields. The widespread adoption of the continuous flooding method, a hallmark of traditional rice cultivation, exemplifies this resource-intensive approach. Producing 1 kg of rice requires approximately 3000 to 5000 L of water [3], making rice cultivation one of the most water-intensive agricultural practices. Prolonged droughts and water scarcity, exacerbated by climate change, threaten the viability of this method, rendering it increasingly unsustainable.

In addition to water usage, the excessive application of chemical inputs has far-reaching environmental consequences. For instance, plants absorb nutrients in ionic forms such as phosphate (HPO₄²⁻ and H₂PO₄⁻), nitrate (NO₃⁻), and ammonium (NH₄⁺). However, over 70% of nitrogen-based fertilizers are lost through leaching, volatilization, and runoff, influenced by soil type, climate, and farming practices [5]. These losses degrade soil health, pollute water systems, and contribute significantly to greenhouse gas (GHG) emissions, particularly carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O) [6,7]. Alarmingly, research indicates that rice fields account for approximately 11% of global GHG emissions [8], while the production of ammonium-based fertilizers alone is responsible for roughly 0.8% of global GHG emissions [9,10]. These environmental costs have made rice cultivation a notable contributor to climate change.

Due to these challenges, transitioning to more sustainable rice cultivation methods is imperative. Beneficial microorganisms, particularly Plant Growth-Promoting Rhizobacteria (PGPR), are critical components of this ecosystem. These bacteria colonize plant roots, forming intricate interactions that stimulate growth, enhance nutrient acquisition, and increase resilience to abiotic and biotic stresses [11,12,13]. Recent research underlines the potential of these microbes to improve crop performance and mitigate the environmental impacts of intensive agriculture.

The synergy between PGPR and Alternate Wetting and Drying (AWD) offers a sustainable approach to rice cultivation. This can be achieved by enhancing nutrient uptake, encouraging structural and physiological development, and yielding improvements while reducing synthetic inputs and environmental impact. However, the effectiveness of PGPR in AWD systems depends on understanding microbial dynamics under fluctuating soil moisture. This review examines the synergy between PGPR and AWD, their effects on growth and grain production, and their impact on soil health. The review also aims to identify key research gaps that must be addressed to optimize this approach for sustainable agriculture.

2. Alternate Wetting and Drying

2.1. History

AWD is a proven irrigation practice that significantly enhances water conservation and promotes sustainable rice production. Derived from traditional farming practices, AWD provides a modern, scientifically backed approach to field water management [14]. In many regions, farmers have long relied on intermittent drying periods during rice cultivation as a response to water scarcity and the need to manage soil moisture effectively. In the 1980s and 1990s, researchers in China and India refined these practices, transforming them into a more structured and efficient system. The International Rice Research Institute (IRRI) has played a pivotal role in advancing AWD technology, continuously improving it through rigorous, ongoing research. AWD is now recognized as a key innovation for sustainable rice farming, reducing water use while maintaining or even boosting productivity. [15].

2.2. Principles

The key principles of AWD involve a shift from continuous flooding to controlled cycles of flooding and drying. This practice offers significant advantages, primarily in reducing water consumption while maintaining or even enhancing rice yields. Ishfaq et al. [16] demonstrated the substantial water savings associated with AWD, noting that conventional rice production typically requires three to five times more water than other cereal crops. Their findings further revealed that implementing AWD can reduce water usage by a significant range of 25% to 70% compared to traditional continuous flooding, all without compromising rice yields.

2.3. Research Achievements and Basis

The conventional method involves continuous flooding, which is effective in the dispersal of nutrients, suppression of weeds, and yield improvement. However, paddy field conditions are a large source of methane emissions. Extensive field trials in the 1990s have shown that rice plants do not need to be grown under continuously flooded field conditions. It was observed that periodic drying of fields promotes soil reoxygenation without compromising plant health. Hence, researchers have proven that controlled water management could reduce water by 25% to 50% and methane emissions by 30% to 50%, making the AWD an environmentally friendly approach [17,18,19,20,21].

Research on intermittent irrigation commenced in the 1980s as scientists sought alternative approaches to continuous flooding methods. By the 1990s, studies demonstrated the feasibility of AWD, with pilot projects showcasing reductions in water usage and methane emissions. There was widespread promotion of AWD in the 2000s by the IRRI and various agricultural institutions and agencies throughout Asia. By the 2010s, AWD became a key component of global strategies for sustainable agriculture, including climate-smart farming initiatives. Moving into the 2020s, there has been a heightened emphasis on integrating AWD with digital farming technologies to enable precise water management [22,23,24].

3. The Role of Alternate Wetting and Drying

3.1. Physiological and Structural Changes in Roots Under AWD

3.1.1. Structural Changes

Several irrigation approaches are employed to deviate from continuous flooding in rice cultivation, such as intermittent irrigation, saturated soil cultivation, and AWD [25,26,27]. These practices are integrally related to the System of Rice Intensification (SRI) practice as they are crucial for effective water management. Each application periodically allows the soil to dry out between irrigation cycles, rather than maintaining continuous flooding, demonstrating a key aspect of SRI (Figure 1). Various studies have found less water use from 40% to 70% [25,26,27]. These conditions encourage longer root length growth and denser root development [28]. The morphological changes are observed in the root diameter, cell size, and tissue organization. They influence the root strength, which aids in carrying water and nutrients [29]. These enable better root plasticity and better resistance against biotic and abiotic stress.

The scarcity of nutrients and soil moisture triggers the plant’s mechanism to grow more lateral roots and root hairs, allowing rice plants to thrive under upland conditions. The extended root system also helps to maintain the soil integrity and prevent soil erosion and degradation [30]. When rice plants are cultivated under paddy or waterlogged conditions, the root cortical aerenchyma increases, thus facilitating internal oxygen transport while reducing hypoxia-induced stress [28]. The approach by AWD fosters a robust root system that is denser, deeper, and healthier, enabling rice plants to thrive even in harsh environmental conditions.

3.1.2. Physiological Changes

The architectural enhancement of the root system under the AWD practice offers numerous advantages to the internal processes and biochemical reactions within the root cells that influence growth and function. The morphological alterations have led to a wider root surface area, enhancing water and nutrient absorption efficiency under drought conditions. Plants also synthesize phytohormones such as auxins (IAA), gibberellins (GA₃), and cytokinins to influence root growth and development when exposed to stress. It also alters the plants’ metabolic pathways, such as respiration and photosynthesis, impacting energy production and nutrient utilization. The extensive root system provides an important link between the plants and the soil organisms. Through biochemical processes, plants release exudates that stimulate microbial activities within their rhizospheric zone [31].

3.2. Microbial Interactions in the Rhizosphere Under AWD

3.2.1. Microbial Interactions

The soil is abundant with various microorganisms, such as fungi, nematodes, protozoa, microarthropods, algae, viruses, and bacteria [32]. These microorganisms play a crucial role in agroecosystems. They contribute to nutrient cycling and fixation, water and nutrient uptake, soil structure improvement, and plant growth promotion. In addition, they can enhance plant tolerance to biotic and abiotic stresses and facilitate bioremediation processes. Fungi are eukaryotic microorganisms that occur naturally in soil and play an important role in soil health. They are an important component of the soil ecosystem and play a critical role in nutrient cycling and soil structure formation [29,33,34,35]. Among the commonly studied beneficial fungi are arbuscular mycorrhizal fungi (AMF), endophytic fungi, and Trichoderma spp. AMF forms a reciprocal relationship with plant roots and provides plants access to nutrients, especially P, in exchange for photosynthetically produced carbohydrates [36,37]. Endophytic fungi reside within plant tissues without causing apparent disease and can confer various benefits to their host, including enhanced tolerance to biotic and abiotic stresses, improved nutrient uptake, and even direct promotion of plant growth [38,39]. Trichoderma spp. are known for their biocontrol activities against various plant pathogens. They can also perform plant growth-promoting activities, such as the production of phytohormones and enzymes that facilitate nutrient and water uptake by plants [40,41].

Nematodes, protozoa, and microarthropods, like fungi, are eukaryotic organisms. Nematodes can be both beneficial and harmful in agricultural soils. They recycle nutrients by feeding on bacteria and fungi and prey on other nematodes, contributing to the decomposition of organic matter, which releases nutrients for plant uptake. The diversity and abundance of nematode communities indicate the status of soil health [42]. However, they can be problematic as they can feed on plant roots, damaging and reducing the plant’s growth [43]. Protozoa are also eukaryotic microorganisms. Protozoans maintain control of the population of bacteria. Feeding on excess bacteria prevents overpopulation and resource depletion. They then release NO₃⁻ and NH₄⁺ into the soil in the process of mineralization [44]. Protozoa are natural decomposers of organic matter. Their activities release nutrients that aid in the formation of soil aggregates, water retention, and aeration. Protozoa function as a biological control against some parasitic nematodes and other harmful microorganisms, suppressing plant diseases [45]. Microarthropods are tiny critters such as mites, springtails, and other organisms that contribute to the soil food web. They function as decomposers, breaking down plant residuals and dead animals into simpler substances. These substances are further broken down and cycled to plant-absorbable nutrients by other microorganisms [46,47]. These microarthropods also control the population of harmful nematodes and insects by feeding on their larvae. These activities contribute to the improvement of the soil structure, forming soil aggregation, aeration, and soil water-holding capacity [48].

Algae are eukaryotic organisms, although some are prokaryotic (cyanobacteria, often referred to as blue-green algae). They are photosynthetic, autotrophic organisms that can be either unicellular or multicellular and are primarily found in moist soil surfaces or waterlogged environments [49]. They are a source of a wide range of macro and micro nutrients. Nutrients such as N, P, potassium (K), sulfur (S), iron (Fe), copper Cu), bromine (Br), zinc (Zn), iodine (I), calcium (Ca), magnesium (Mg), and manganese (Mn) in their assimilable forms [50]. They can improve soil structure through the secretion of extracellular polysaccharides that bind soil particles, as observed in fine sandy soils [51]. Their presence enhances soil aeration and water retention, which can benefit crop growth, especially in degraded soils [52,53]. The presence and type of algal communities can indicate the ecological status of a soil or water body. They play a role in the promotion of CO₂ sequestration [54]. However, under certain conditions, excessive algal growth in aquatic systems can lead to eutrophication, depleting oxygen levels, and harming other aquatic life. Planting seeds in such low gas exchange conditions can hinder seed emergence.

Viruses are distinct from fungi, nematodes, protozoa, microarthropods, and algae as they are not considered cellular organisms. They are acellular entities that require a living host to replicate [55]. Viruses in agricultural systems can be both influential and detrimental. In soil ecosystems, they primarily infect bacteria (bacteriophages), fungi, and protozoa, thus playing a crucial role in regulating microbial populations and contributing to nutrient cycling through microbial turnover [56]. By lysing their microbial hosts, viruses release cellular contents into the soil, which can be mineralized and made available for plant uptake. It is often referred to as the “viral shunt,” as it influences the structure and function of microbial communities and soil biogeochemical processes [57,58]. However, viruses are also significant plant pathogens, capable of infecting a wide range of crops, causing diseases that can severely reduce plant growth and yield.

Bacteria are prokaryotic microorganisms naturally occurring in soil, water, and air. Like fungi, they are essential for decomposing organic matter and nutrient cycling in soil [59]. Besides known cultured bacteria species, it is important to acknowledge that there is a large group of unculturable microbes, often referred to as “dark matter microbiology.” This substantial portion of the bacterial community, which remains poorly understood due to limitations in current cultivation techniques, likely plays critical but yet-to-be-defined roles in soil ecosystems [60]. The most commonly researched beneficial bacteria include Rhizobia spp., Azospirillum spp., Bacillus spp., and Pseudomonas spp. [59,61]. Rhizobia form a symbiotic relationship with legumes in which they fix atmospheric N in the form of nitrite (NO₂⁻) and convert it into NO₃⁻ and NH₄⁺, which are forms available to the plants. Rice plants may benefit from the presence of rhizobia through the growth of leguminous plants like Sesbania spp. in paddy fields during fallowing. Azospirillum spp. also fix atmospheric N and promote plant growth through phytohormone synthesis [33]. They are also known for enhancing root development, soil aeration, and improving plants’ water retention [62]. Bacillus spp. are well documented for their role in a wide range of biological processes, such as synthesizing phytohormones, like IAA and GA₃. They also trigger metabolic processes such as N fixation and P solubilization. These stimulate root development and overall plant vigor, which improves nutrient and water uptake [62,63]. According to Lee et al. [62], Bacillus spp. can positively influence the composition of the rhizosphere microbiome, promoting beneficial microbial interactions that further enhance plant growth and health. Pseudomonas spp. are known for their biocontrol activities against plant pathogens and also have plant growth-promoting activities, such as the production of phytohormones, siderophores, and enzymes that facilitate nutrient uptake by plants [33,34,62]. Furthermore, some Pseudomonas spp. can help mobilize nutrients and improve plant stress tolerance, including drought conditions. Regardless of the genus and species, each group of bacteria is unique as it influences its host differently and to various degrees. The interactions among diverse bacterial communities complement their effects on the crops’ growth, triggering specific mechanisms that ensure plant growth and survival (Figure 2). Poor soil structure will have an insignificant relative abundance of bacterial communities.

These microorganisms play a critical role in the soil food web. They contribute to soil fertility by transforming nutrients, decomposing organic matter, and suppressing plant pathogens [64,65]. Notably, PGPRs within this diverse community engage in complex interactions mediated by a variety of antimicrobial compounds and other signaling molecules. These compounds influence the survival, competition, and growth of both the PGPRs themselves and the host plant. For instance, signaling molecules facilitate the establishment of beneficial symbiotic relationships, while antimicrobial compounds can suppress harmful pathogens, creating a more favorable environment for plant growth. Beyond direct effects, these microorganisms also promote plant growth, improving plant health and productivity [34]. They are essential components of soil health, influencing soil fertility, plant health, and crop productivity [12,66]. Their presence in the soil ecosystem can significantly impact crop growth and development, making them an important factor in sustainable agriculture. The AWD cultivation method creates a conducive condition for diverse communities of microbes to proliferate and form complex interactions in the rhizosphere. However, maintaining stable microbial populations remains a challenge under AWD. The dynamic shifts in oxygen and moisture regimes under AWD can cause physiological stress to some microbial communities, particularly those of the anaerobes or highly oxygen-sensitive PGPR strains that require consistent microhabitats for colonization and performance [67]. These abrupt transitions may impair microbial functions or reduce their population densities during re-flooding events, potentially limiting their full benefit to plant performance [68].

3.2.2. Microbial Density and Contributions

Chemical inputs disrupt microbial life. Although these inputs benefit the crop, continuous application disrupts microbial activities over time, eliminating most of the local soil’s microbiome [69]. A lack of soil microbial diversity results in soil degradation, poor soil fertility and water-holding capacity, and other adverse environmental issues [70]. Crops grown under such soil conditions rely heavily on fertilizer inputs to produce the desired yield. Additionally, these crops are highly susceptible to pests and to pathogenic attacks by fungi, bacteria, and viruses [69]. The AWD practice promotes the breakdown of organic matter, releasing nutrients for assimilation while reducing dependency on chemical inputs [30,71]. As such, synthetic fertilizer inputs are substituted with organic materials such as mulch, compost, and livestock residues like chicken manure. These organic materials improve soil structure, increase water retention, and attract and support a diverse and robust microbial community that engages in complex activities essential for sustainable rice production [72,73]. They may serve as reservoirs of nutrients that gradually release to plants, providing a more sustainable and long-term source of fertility compared to the quick-release nature of chemical fertilizers [74,75]. In addition, organic matter application is cost-effective for farmers, especially in regions where chemical fertilizers are expensive or less accessible.

The interactions between the diverse microbe community provide synergistic benefits to its host plants’ growth and productivity. Beneficial bacteria and mycelium occupy the crop rhizosphere, while some can enter the plant’s root tissues [76]. In exchange for root exudates, these microorganisms fix nutrients for the plant. Nitrogen is the primary element for plant growth. Diazotrophs, such as Azotobacter, Azospirillum, and Rhizobium, can convert atmospheric nitrogen into plant-usable forms, such as NH₄⁺, reducing the need for N fertilizers [59]. The second most demanded plant nutrient is P. It is a fundamental component in adenosine 5’-triphosphate (ATP), phosphorylated sugars (intermediates in glucose metabolism), nucleic acids, and other vital biological processes [76]. However, it is accessible to plants in the form of PO₄³⁻. Soil pH levels can easily manipulate their availability. It binds with iron (Fe⁺) and aluminum (Al⁺) in acidic soil (pH < 7) to form insoluble compounds. Whereas, in alkaline soil (pH > 7) conditions, it binds with calcium (Ca⁺). Paddy fields with clay soils have a high surface area and are negatively charged, reducing availability. Some microorganisms act as decomposers and recyclers, breaking down organic matter into essential macronutrients (N, P, K, Ca, Mg, and S) and micronutrients (Fe, Mn, Zn, and Cu) in the soil, making them available for plant uptake [33,62,64,66].

Microbes can mitigate stress on crops through several pathways. For instance, Trichoderma spp. (primarily fungi) and Bacillus spp. suppress plant pathogens by producing antimicrobial compounds [42,62]. Certain beneficial microbes can also infiltrate plant tissues, stimulating the deposition of lignin and other cell wall components [77], thereby enhancing the crop’s structural integrity to withstand pest attacks and strong winds, preventing lodging and grain loss. Furthermore, specific bacterial species are well-documented for their positive effects on plant physiology. Studies by Morgenstern et al. [78] and Spaepen et al. [79] showed that the bacterial strain Azospirillum brasilense produces auxins and other growth-promoting substances that enhance root development and nutrient uptake. Similarly, certain Bacillus strains, such as Bacillus subtilis, have been shown to produce cytokinins, further contributing to plant growth and development [80,81]. Regarding water stress, the AWD practice encourages limited water use, and this can be complemented by the action of exopolysaccharide (EPS)-producing bacteria. An example of such a bacterial strain is the Bacillus amyloliquefaciens. According to Han et al. [82], the strain has been reported to produce significant amounts of EPS, which can improve soil water retention and enhance water availability to plant roots during dry periods. In saline soils, halotolerant bacteria play a crucial role. Pseudomonas putida, for example, can produce osmoprotectants like proline and glycine betaine, which help rice plants maintain osmotic balance and tolerate ionic stress [83,84].

4. The Role of Plant Growth-Promoting Rhizobacteria

4.1. Plant Growth-Promoting Rhizobacteria

PGPR is a group of beneficial bacteria that colonize the roots and the surrounding soils, establishing a mutually beneficial relationship with the plant. According to Kloepper and Schroth [85], PGPR triggers the synthesis of plant growth regulators, phytohormones, and many biologically active substances in the host plant. PGPR usage in crop production has gained attention as a sustainable and environmentally friendly alternative to chemical fertilizers and pesticides. Besides growth promotion and increased yield, its application improved soil fertility and enhanced resilience to environmental stresses such as drought and salinity while reducing the crops’ reliance on chemical inputs [64,86,87]. It can also reduce GHG emissions, maintain soil health, and protect biodiversity [88]. Several families of bacteria are commonly used as PGPR, including Rhizobium, Azospirillum, Azotobacter, Bacillus, Pseudomonas, and Streptomyces. While these bacteria have been extensively studied and shown effectiveness in promoting plant growth across various crops [61,76], it is crucial to acknowledge the potential influence of survivorship bias in reported research. Studies demonstrating positive effects may be preferentially published over those showing no significant impact.

4.2. Mechanism of PGPR

PGPR exerts its beneficial effects on plants through both direct and indirect mechanisms. The direct mechanisms include the production of phytohormones such as IAA, abscisic acid (ABA), GA₃, cytokinins (zeatin), and ethylene, which are critical in influencing healthy plant growth and development. Additionally, PGPR can function as a biofertilizer, as shown in Figure 3. This includes the fixation of N, the production of siderophores, and the solubilization of mineral nutrients such as P, K, and Fe, making them more accessible to the plant [89,90]. For instance, Lee et al. [91] reported that Bacillus megaterium was reported to promote various mechanisms during rice development, such as P solubilization, N fixation, IAA production, improved siderophore secretion, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, and exopolysaccharide production.

Indirect mechanisms involve the tolerance or suppression of abiotic stresses, such as drought and salinity, through the synthesis of antioxidants, compatible solutes (osmoprotectants), and stress-related enzymes. Moreover, PGPR also functions as a biological control against biotic stresses such as pests and diseases. PGPR enhances a plant’s defense by triggering its innate immune system, which leads to the increased production of pathogenesis-related (PR) proteins [93,94]. Simultaneously, it influences the production of volatile organic compounds (VOCs) and enzymes that enhance the plant’s ability to tolerate various stresses [81,95,96]. This interconnection of functions is a key feature of PGPR strains and their host plant defenses, enabling them to thrive under challenging environmental conditions. [89,90,97,98].

4.3. Benefits of PGPR in Rice Cultivation

PGPR has demonstrated considerable potential in enhancing rice growth and yield across various environmental conditions. Azospirillum-based biofertilizers have increased seasonal rice yields by 5–18%. At the same time, strains like A. brasilense, A. lipoferum, and Pseudomonas sp. have shown significant grain weight and biomass increases in laboratory and field trials [99,100]. P. putida nearly doubled rice grain iron content, while Bacillus pumilus improved plant height, root length, and dry weight by up to 30.89% [101,102]. Dual inoculations of Azospirillum brasilense and Pseudomonas fluorescens also improved water and N use efficiency, extending leaf area duration by 35–110 days [103]. PGPR strains enhance stress tolerance and nutrient uptake, particularly under salinity and drought conditions [104,105]. For instance, priming biochar with PGPR, Pseudomonas koreensis, and Bacillus coagulans effectively mitigated salt stress, boosting grain yields [105]. Strains like Sphingobium yanoikuyae and B. megaterium improved drought tolerance by promoting IAA synthesis, P solubilization, and upregulating antioxidant and drought-responsive genes [91,106]. Azotobacter and P. fluorescens significantly increased organic carbon content and nutrient uptake, with N and P availability rising to levels that promote healthy rice growth under challenging conditions [107].

In addition to reducing chemical inputs by 25% to 50% when integrated with inorganic fertilizers, PGPR offers a sustainable alternative for improving soil fertility and crop performance [108,109]. Strains such as Bacillus aryabhattai, B. subtilis, and Rhizobium larrymoorei show multifunctional capabilities, including N fixation, P solubilization, and IAA production, which collectively increase yields by up to 30.89% [110,111]. These findings highlight the potential of PGPR as an eco-friendly biofertilizer for sustainable rice cultivation. Further research should focus on large-scale field trials, optimization of inoculation methods, and evaluation of long-term effects on soil health and crop productivity.

4.4. Limitations of PGPR

Although PGPR offers numerous benefits in the field of agriculture and perhaps other industries, its application may have certain limitations and challenges that must not be overlooked. A major concern is the specificity of interaction between PGPR and host plants. As seen in leguminous crops, whereby they interact with only certain bacterial species, different crops often require specific strains of PGPR. Notably, a strain that works well for one plant may not be effective for another. Furthermore, the performance of PGPR can be heavily influenced by environmental factors such as soil type, temperature, and moisture levels [61,112,113]. There is also a risk that some PGPR, especially when applied excessively or inappropriately, could cause harm. Certain strains may produce toxic compounds or lead to plant infections if they penetrate plant tissues [112]. Beyond plant health, PGPR use can also raise ecological concerns. Introducing non-native bacterial strains into a new environment may disrupt existing microbial communities or interfere with natural soil nutrient cycling [114]. It is important to recognize that while PGPR can enhance nutrient bioavailability and support plant growth, they do not represent a complete substitution for conventional practices such as chemical fertilization. Synthetic fertilizers offer a more rapid and often more consistent supply of macronutrients and micronutrients, which the nutrient mobilization and cycling activities of PGPR may not always fully and immediately replicate [109]. Hence, options for integration practices are introduced, potentially leading to an economically and environmentally sustainable farming approach.

5. Challenges of PGPR and AWD Synergy

Despite limited direct studies on PGPR inoculation under AWD, the existing literature suggests promising interactive effects. However, it is critical to acknowledge key implementation challenges. The strain compatibility with fluctuating soil environments remains a major barrier. Many commercial PGPR strains perform well under controlled environments but show inconsistent efficacy in open field conditions due to variations in soil physicochemical parameters, native microbial competition, or periodic soil drying and rewetting [115]. Additionally, microbial washout during re-flooding events can displace rhizobacteria from the root zone, particularly in soils with low organic matter content or poor structure [68]. This instability may reduce the long-term persistence and effectiveness of introduced beneficial strains.

Furthermore, maintaining stable microbial populations remains a challenge under AWD. The frequent changes under the AWD condition can cause physiological stress to some microbial communities, particularly the anaerobic strains [67]. Oxygen fluctuation during AWD cycles can alter microbial redox environments, disrupting enzymatic activity or metabolic pathways in sensitive microbial taxa [116,117]. Certain nitrogen-fixing bacteria, such as those of the Azospirillum spp., may experience inhibited function during aerobic drying phases [118], while obligate aerobes may decline rapidly during re-flooding [68]. These contradictory effects emphasize the need for carefully selecting robust, field-compatible strains capable of enduring fluctuating water regimes during rice cultivation.

6. Alignment with United Nations Sustainable Development Goals

AWD has emerged as an integral component of sustainable rice production strategies globally. It is now endorsed as a best practice of rice cultivation practices such as the System of SRI [25,119,120]. PGPR has played a transformative role in agriculture, significantly benefiting both human livelihoods and environmental sustainability. These methods are promoted by various initiatives focused on achieving the United Nations Sustainable Development Goals (SDGs). The AWD concerns water use efficiency (SDG 6) and climate action (SDG 13). Recent advancements have incorporated AWD with smart technologies, such as soil moisture sensors and automated irrigation systems, enhancing its precision and efficiency [23,24,121]. PGPR, on the other hand, emphasizes food security (SDG 2) as well as ensuring sustainable consumption and production patterns (SDG 12), climate mitigation (SDG 13), and conservation and sustainability of terrestrial ecosystems (SDG 15).

7. Future Directions

7.1. Information Gaps

Despite the growing interest in integrating PGPR into AWD rice systems, significant information gaps remain regarding their impact on soil health and bacterial ecology. Specifically, research is needed to elucidate how the shift between aerobic and anaerobic conditions impacts PGPR survival, colonization, and interactions with the native soil microbiome. Additionally, the influence of PGPR on nutrient cycling, particularly N and P availability, under the variable redox potentials of AWD soils, requires further investigation. Little is known about how repeated wetting and drying cycles impact soil structure and whether PGPR can contribute to maintaining soil aggregation and stability in these dynamic environments.

Another key area requiring further study concerns the bacterial ecology of PGPR adaptation to AWD. A fundamental question is whether the mechanisms by which PGPR promotes rice growth under AWD differ from those observed in traditional farming conditions and periodic drought stress. Furthermore, understanding how PGPR adapts to the periodic drought stress imposed by AWD may create conditions that facilitate horizontal gene transfer (HGT) between PGPR and native microbes, with potential implications for microbial function, stress adaptation, and antibiotic resistance. Next-generation sequencing (NGS) is a powerful approach to investigating these complex interactions. It enables a deeper understanding of PGPR adaptation to AWD, potential horizontal gene transfer, and its broader implications for microbial function and stress resilience [122,123,124].

NGS technologies are crucial for understanding PGPR in dynamic agricultural systems like AWD in rice farming. Amplicon sequencing identifies successful PGPR strains, while metagenomics reveals their genetic potential for direct and indirect mechanisms. Metatranscriptomics shows gene expression under varying conditions, and high-resolution NGS tracks strain fate and potential gene transfer [123,124]. Furthermore, the application of eDNA analysis, facilitated by NGS, offers a non-destructive and holistic perspective on these processes [125,126,127]. By analyzing e-DNA from soil and water samples across different AWD cycles, researchers can detect PGPR dynamics, species interactions, and functional gene presence without the need for direct bacterial isolation.

7.2. System of Probiotics in Rice Intensification

The synergistic benefits observed from combining PGPR with AWD irrigation practices in rice cultivation have paved the way for a novel conceptual framework aimed at transforming sustainable rice production. Building upon the foundational principles of the SRI, which emphasize reduced water use, improved root health, and soil microbial activity, we introduce the System of Probiotics in Rice Intensification (SPRI). The core aim of SPRI is to create a synergistic ecosystem within the rice paddy that enhances nutrient cycling, improves plant health and resilience, optimizes water use, and ultimately leads to increased and sustainable rice yields while minimizing negative environmental impacts.

This section introduces the SPRI concept, a comprehensive exploration of its theoretical underpinnings, operational framework, and potential applications, along with supporting justification and case studies. However, it is beyond the scope of the current manuscript. This forthcoming publication will provide a detailed definition, outline an operational framework, and present potential case studies to further explain and validate the SPRI concept.

8. Conclusions

The strategic application of PGPR within the context of AWD irrigation offers a promising avenue for enhancing rice production sustainably. Harnessing the beneficial activities of PGPR can contribute significantly to improved rice yields, enhanced soil health, and reduced dependence on synthetic inputs. This approach aligns with the growing global need for environmentally sound and sustainable agricultural practices. Realizing the full potential of PGPR within AWD systems requires continued research on understanding the complex interactions between the soil microbes, predominantly the beneficial bacteria, the rice plant, and the dynamic soil environment under fluctuating moisture conditions. However, several potential knowledge gaps remain to be investigated. NGS and e-DNA sequencing provide powerful tools for tracking microbial diversity, strain persistence, and gene activity in AWD soils. Leveraging these advanced technologies will be key to developing robust, PGPR-based solutions for sustainable rice production in the face of evolving environmental challenges.