1 Introduction

Rice (Oryza sativa L.) is a staple food for more than half of the world's population, playing a crucial role in global food security. Despite its importance, rice production has stagnated over the past two decades, necessitating innovative approaches to enhance yield and sustainability (Doni et al., 2022). Traditional rice cultivation methods often rely heavily on chemical fertilizers, which can have detrimental environmental impacts. Therefore, there is a growing interest in sustainable agricultural practices that can improve rice productivity while minimizing environmental harm.

Endophytic microbes, which live inside plant tissues without causing harm, have emerged as a promising tool in sustainable agriculture. These microbes can enhance plant growth, improve nutrient uptake, and increase resistance to biotic and abiotic stresses (Saha et al., 2016; Ding et al., 2019). In rice cultivation, endophytic microbes have been shown to significantly influence plant health and productivity. For instance, non-rhizobial endophytes from Typha angustifolia have been found to improve nitrogen metabolism in rice, leading to increased biomass and chlorophyll content. Similarly, the application of endophytic Azotobacter sp. has demonstrated potential in reducing the need for chemical nitrogen fertilizers while maintaining high yields (Banik et al., 2019; Xu et al., 2019).

This study aims to summarize current understanding of the interactions between rice plants and non-rhizobial endophytic microorganisms, providing deeper insights into the potential benefits of using these microorganisms to enhance rice growth, yield, and stress resistance. Furthermore, it explores the mechanisms through which non-rhizobial endophytes exert beneficial effects on rice plants, identifies gaps in the current research, and proposes future directions for the application of non-rhizobial endophytic microorganisms in sustainable rice cultivation. The goal is to highlight the potential of non-rhizobial endophytic microorganisms as a sustainable solution for improving rice yield and promoting global food security.

2 Overview of Non-Rhizobial Endophytic Microbes

2.1 Definition and classification

Non-rhizobial endophytic microbes are bacteria that reside within plant tissues without causing any apparent harm to their host. These microbes are distinct from rhizobial bacteria, which are typically associated with root nodules in legumes. Non-rhizobial endophytes can be found in various plant parts, including roots, stems, and leaves, and they often contribute to plant growth and health by promoting nutrient uptake, enhancing stress resistance, and protecting against pathogens (Saha et al., 2016; Lata et al., 2018).

2.2 Differences from rhizobial endophytes

While rhizobial endophytes are primarily known for their ability to fix nitrogen in symbiotic relationships with leguminous plants, non-rhizobial endophytes exhibit a broader range of plant growth-promoting traits. Non-rhizobial endophytes can solubilize phosphate, produce siderophores, and synthesize plant hormones such as indole-3-acetic acid (IAA). They also exhibit antifungal activities and can enhance the plant's defense mechanisms against pathogens (Verma et al., 2017; Hernández et al., 2021). Unlike rhizobial endophytes, which are often limited to leguminous plants, non-rhizobial endophytes can colonize a wide variety of plant species, including rice (Hardoim et al., 2012; Jha et al., 2019).

2.3 Common non-rhizobial endophytes in rice

Several non-rhizobial endophytes have been identified in rice plants. Pseudomonas is known for its plant growth-promoting properties, including nitrogen fixation and phosphate solubilization (Sahu et al., 2020). Bacillus is effective in promoting plant growth and inducing systemic resistance against pathogens such as Rhizoctonia solani. Azotobacter is renowned for its nitrogen-fixing ability and has been shown to increase rice yields under both greenhouse and field conditions. Sphingomonas is found in rice seeds and can promote root and shoot growth while protecting seedlings from soil pathogens. Enterobacter is known for producing IAA (Indole-3-acetic acid) and solubilizing phosphate, contributing to plant growth promotion (Zhang et al., 2022). These non-rhizobial endophytes play a crucial role in enhancing the growth and health of rice plants by improving nutrient uptake, promoting stress resistance, and protecting against diseases.

3 Mechanisms of Action

3.1 Nutrient uptake enhancement

3.1.1 Nitrogen fixation by non-rhizobial endophytes

Non-rhizobial endophytic microbes play a significant role in enhancing nitrogen uptake in rice plants. For instance, a consortium of endophytic microbes isolated from Typha angustifolia has been shown to improve nitrogen metabolism in rice. These endophytes, predominantly nitrogen-fixing, significantly increased biomass, shoot length, and chlorophyll content in rice plants under both nitrogen-sufficient and nitrogen-deficient conditions. The upregulation of nitrogen uptake and assimilation genes in treated plants suggests that horizontal gene transfer of the dinitrogen reductase gene within the consortium is a key mechanism for nitrogen fixation (Kakar et al., 2016). Additionally, strains such as Bacillus siamensis and Priestia megaterium have demonstrated biological nitrogen fixation capacity, contributing to increased agronomic parameters in rice (Rios-Ruiz et al., 2023). Furthermore, Azotobacter sp. strain Avi2 has been shown to enhance nitrogen fixation, leading to better vegetative and reproductive growth in rice.

3.1.2 Phosphorus solubilization

Phosphorus solubilization is another critical mechanism by which non-rhizobial endophytes enhance nutrient uptake in rice. For example, Bacillus siamensis TUR07-02b has been identified for its ability to solubilize phosphate-Ca, which is crucial for improving phosphorus availability to rice plants (Figure 1) (Rios-Ruiz et al., 2023). Endophytic bacteria isolated from rice roots have shown significant phosphate solubilizing capabilities, with higher diversity and population density in root tissues compared to leaf tissues (Shofiyah et al., 2023). The endophytic fungus Phomopsis liquidambari also plays a role in optimizing phosphorus activation in paddy soil, thereby enhancing nutrient turnover and availability (Tang et al., 2019).

Figure 1 Effect of inoculation of B. siamensis TUR07-02b and B. vietnamiensis TUR04-01a on Oryza sativa var. “Bellavista”, compared to the control without inoculation (Adopted from Rios-Ruiz et al., 2023)

The rice root development of TUR07-02b is significantly superior to the control group, particularly in terms of root length and branching numbers. This indicates that TUR07-02b not only aids in the dissolution of calcium phosphate, making phosphorus more accessible for absorption by the rice from the soil, but also enhances the nutrient uptake capacity of rice by promoting root growth. The phosphorus-solubilizing mechanism of this endophyte offers an important sustainable agricultural strategy that can significantly increase crop yields while reducing the use of chemical fertilizers. Studies show that TUR07-02b can significantly improve agronomic parameters of rice under greenhouse conditions, such as panicle length, number of grains per panicle, grain yield, and harvest index. These results highlight the potential of using endophytes as biological inoculants to replace part of the chemical fertilizers, especially in soils with low phosphorus availability.

3.1.3 Potassium mobilization

While specific studies on potassium mobilization by non-rhizobial endophytes in rice are limited, the overall enhancement of nutrient uptake by these microbes suggests a potential role in potassium mobilization. The increased nutrient uptake, including potassium, observed in rice plants inoculated with various endophytic bacteria supports this hypothesis (Etesami and Alikhani, 2016).

3.2 Disease suppression

Non-rhizobial endophytes also contribute to disease suppression in rice plants. Certain endophytic bacteria have been isolated for their fungicide tolerance and plant growth-promoting traits, which include potential nitrogen fixation and phosphorus solubilization. These bacteria, such as Bacillus aryabhattai MN1, have shown tolerance towards multiple fungicides and conferred growth-promoting abilities to rice, indicating their potential role in disease suppression (Shen et al., 2019). The modulation of rhizospheric microbial communities by non-rhizobial endophytes can enhance the plant's resistance to pathogens (Debnath et al., 2023).

3.3 Growth promotion

The growth-promoting effects of non-rhizobial endophytes in rice are well-documented. These microbes enhance various growth parameters, including plant height, root length, leaf area, and chlorophyll content. For instance, the co-inoculation of endophytic and rhizosphere bacteria has been shown to significantly increase root and stem height, root fresh weight, and shoot dry weight in rice plants (Etesami and Alikhani, 2016). The endophytic colonization by nitrogen-fixing bacteria, such as Azotobacter sp. strain Avi2, has also been associated with higher photosynthetic rates and improved yield. Moreover, the production of phytohormones like indole-3-acetic acid (IAA) by endophytic bacteria further promotes plant growth and development.

Non-rhizobial endophytic microbes enhance nutrient uptake, suppress diseases, and promote growth in rice plants through various mechanisms, including nitrogen fixation, phosphorus solubilization, and modulation of rhizospheric microbial communities. These beneficial effects highlight the potential of non-rhizobial endophytes as sustainable alternatives to chemical fertilizers and pesticides in rice cultivation.

4 Benefits in Rice Cultivation

4.1 Improved yield and quality

The application of non-rhizobial endophytic microbes in rice cultivation has shown significant improvements in yield and quality. For instance, a consortium of endophytic microbes isolated from Typha angustifolia was found to enhance nitrogen metabolism in rice, leading to increased biomass, shoot length, and chlorophyll content under both nitrogen-sufficient and nitrogen-deficient conditions (Saha et al., 2016; Jhuma et al., 2021). Microbial inoculants have been shown to improve photosynthetic efficiency and root architecture, which are critical for better nutrient uptake and overall plant health.

4.2 Enhanced stress tolerance

4.2.1 Abiotic stress resistance

Endophytic microbes play a crucial role in enhancing rice tolerance to abiotic stresses such as drought and salinity. Streptomyces albidoflavus OsiLf-2, for example, produces osmolytes like proline and soluble sugars, which help rice plants adjust osmotically under drought and salt stress conditions. This leads to improved physiological and biochemical responses, ultimately raising rice yields even under adverse conditions (Niu et al., 2021). Similarly, endophytic bacteria such as Bacillus haynesii and Bacillus safensis have been shown to alleviate salinity stress by modulating antioxidant enzyme activities and enhancing root architecture (Gupta et al., 2023).

4.2.2 Biotic stress resistance

Endophytic microbes also contribute to biotic stress resistance by suppressing pathogen virulence and deterring herbivores. For instance, endophytic bacteria have been shown to produce various enzymes and secondary metabolites that inhibit the growth of fungal pathogens and reduce disease incidence in rice (Shahid et al., 2022). These microbes can also induce systemic resistance in plants, making them more resilient to pest attacks.

4.2.3 Hormonal regulation under stress conditions

Endophytic microbes influence hormonal regulation in rice plants under stress conditions. For example, certain bacterial endophytes have been found to reduce the levels of abscisic acid (ABA) while increasing glutathione (GSH) and sugar content in rice under salt stress. This hormonal modulation helps in better stress management and promotes growth (Khan et al., 2020). These microbes can enhance the expression of stress-responsive genes, further aiding in the plant's ability to withstand adverse conditions (Gupta et al., 2023).

4.3 Reduced need for chemical inputs

The use of non-rhizobial endophytic microbes in rice cultivation can significantly reduce the need for chemical inputs such as fertilizers and pesticides. These microbes enhance nutrient uptake and assimilation, thereby reducing the dependency on chemical fertilizers (Saha et al., 2016). They also offer a natural means of pest and disease control, which can decrease the reliance on chemical pesticides (White et al., 2019). This not only makes rice cultivation more sustainable but also reduces the environmental impact associated with chemical inputs. The application of non-rhizobial endophytic microbes in rice cultivation offers multiple benefits, including improved yield and quality, enhanced stress tolerance, and reduced need for chemical inputs. These advantages make them a promising tool for sustainable and resilient rice farming.

5 Application Strategies in Rice Cultivation

5.1 Inoculation techniques

Inoculation techniques for non-rhizobial endophytic microbes in rice cultivation involve several methods to ensure effective colonization and growth promotion. One approach is the use of a consortium of endophytic microbes, such as those isolated from Typha angustifolia, which have shown significant benefits in rice growth by enhancing nitrogen metabolism and biomass production. Another method includes the co-inoculation of rhizosphere and endophytic bacteria, which has been demonstrated to reduce the need for chemical nitrogen fertilizers while maintaining or even improving rice growth indices. Additionally, large-scale field inoculation trials with endophytic strains, such as Rhizobium leguminosarum bv. trifolii, have proven effective in increasing grain yield and overall plant health (Yanni and Dazzo, 2010).

5.2 Integration with traditional farming practices

Integrating non-rhizobial endophytic microbes with traditional farming practices can enhance the sustainability and productivity of rice cultivation. For instance, the natural endophytic association between Rhizobium leguminosarum bv. trifolii and rice roots in fields rotated with clover has been shown to significantly improve rice growth and yield. This integration reduces the dependency on chemical fertilizers and leverages the benefits of crop rotation. Furthermore, the use of microbial inoculants as part of integrated nutrient management strategies can optimize fertilizer use and promote healthier plant growth (Etesami and Alikhani, 2016). The application of these microbes in conjunction with traditional practices can lead to more sustainable and eco-friendly rice production systems (Doni et al., 2022).

5.3 Monitoring and assessment

Monitoring and assessment of the application of non-rhizobial endophytic microbes in rice cultivation are crucial for understanding their impact and optimizing their use. Techniques such as 16S rDNA taxonomic profiling can be employed to study the diversity and colonization patterns of endophytic and rhizospheric bacteria in rice roots (Moronta-Barrios et al., 2018). Long-term field trials and greenhouse experiments are essential to evaluate the effectiveness of microbial inoculants under various environmental conditions (Hernández et al., 2021). Regular assessment of plant growth parameters, nitrogen uptake, and gene expression related to nitrogen metabolism can provide insights into the mechanisms of growth promotion and help refine inoculation strategies. By continuously monitoring and assessing these factors, farmers and researchers can ensure the successful implementation of non-rhizobial endophytic microbes in rice cultivation.

6 Case Studies and Field Trials

6.1 Successful applications in various regions

Several studies have demonstrated the successful application of non-rhizobial endophytic microbes in rice cultivation across different regions. Endophytic bacteria such as Bacillus haynesii and Bacillus safensis have been shown to alleviate salinity stress in rice, further demonstrating the versatility and effectiveness of these microbes in different environmental conditions (Figure 2) (Gupta et al., 2023). A consortium of endophytic microbes isolated from Typha angustifolia significantly improved nitrogen metabolism and overall growth in rice plants. This consortium increased biomass, shoot length, and chlorophyll content under both nitrogen-sufficient and nitrogen-deficient conditions, showcasing its potential as a plant probiotic (Saha et al., 2016). Another study highlighted the use of Azotobacter sp. strain Avi2, which enhanced rice yield and photosynthetic rates in both greenhouse and field conditions, indicating its effectiveness as a bio-formulation for sustainable rice production.

Figure 2 Effect of inoculation of halotolerant endophytes and rhizobacteria on two rice varieties (A) CO51, and (B) Pusa Basmati 1 (Adopted from Gupta et al., 2023) Image caption: T1=Negative control, T2=Positive control (200 mM NaCl), T3 = 200 mM NaCl + Trichoderma viride, T4 = 200 mM NaCl + Bacillus haynesii 2P2, T5 = 200 mM NaCl + Bacillus safensis BTL5, T6 = 200 mM NaCl + Brevibacterium frigoritolerans W19, and T7 = 200 mM NaCl + Pseudomonas fluorescens (Adopted from Gupta et al., 2023)

The image shows that rice inoculated with Bacillus haynesii and Bacillus safensis exhibits significantly better growth under salt stress compared to the control group (T2). For example, the treatment groups T4 (inoculated with Bacillus haynesii) and T5 (inoculated with Bacillus safensis) displayed better plant growth in both CO51 and PB1 varieties, particularly in terms of leaf greenness, plant height, and root development. These treatments significantly mitigated the negative effects of salinity on rice. The study results indicate that endophytic bacteria enhance salt tolerance in rice by promoting antioxidant enzyme activity, regulating the accumulation of osmoregulatory substances (such as proline), and modulating the expression of genes related to salt stress. These bacteria not only improve rice growth and biomass accumulation but also reduce ionic imbalance and oxidative stress caused by salinity, thus enhancing the overall health and yield of the plants.

6.2 Comparative studies with conventional practices

Comparative studies have shown that the use of non-rhizobial endophytic microbes can be as effective, if not more so, than conventional agricultural practices. For example, treatments with Azotobacter sp. strain Avi2 resulted in similar yield parameters when compared to the recommended dose of nitrogen fertilizer, suggesting that these endophytes can reduce the need for chemical fertilizers. Another study compared the effects of urea fertilizer and rhizobial biofertilizer on the root-associated microbiome of rice. The results indicated that biofertilizer treatments significantly restructured the endophyte-enriched communities, leading to positive synergistic impacts on rice growth (Jha et al., 2019). These findings suggest that endophytic microbes can offer a sustainable alternative to traditional agricultural inputs, potentially reducing the reliance on agrochemicals (White et al., 2019).

6.3 Long-term impact on soil health

The long-term impact of non-rhizobial endophytic microbes on soil health has also been a subject of investigation. Long-term manure application, for instance, was found to alter the microbial community structure in the rice rhizosphere, increasing the abundance of beneficial bacteria such as Rhizobium and Burkholderia (Tang et al., 2021). These changes in microbial communities can enhance nutrient cycling and soil fertility over time. Additionally, the use of endophytic microbes has been shown to improve the resilience of rice plants to environmental stresses, such as salinity and oxidative stress, which can have positive long-term effects on soil health by maintaining plant productivity and reducing soil degradation (Breidenbach et al., 2016). Overall, the integration of non-rhizobial endophytic microbes into rice cultivation practices holds promise for enhancing soil health and sustainability in the long term.

7 Challenges and Considerations

7.1 Environmental factors

The application of non-rhizobial endophytic microbes in rice cultivation is influenced by various environmental factors. Temperature, rainfall, seasonal variations, and UV radiation can impact the efficacy of these microbial communities. For instance, the study on Azotobacter sp. strain Avi2 highlighted that endophytic microbes are less affected by these physical factors compared to rhizospheric and phylloplane microbes, making them more stable in varying environmental conditions (Imchen et al., 2019; Tian et al., 2021). However, the specific environmental conditions of the rice-growing regions must be considered to ensure the optimal performance of these endophytes.

7.2 Microbial consortia compatibility

Compatibility among microbial consortia is crucial for the successful application of endophytic microbes. The interaction between different microbial strains and their ability to coexist and function synergistically can significantly affect plant growth promotion. For example, a consortium of non-rhizobial endophytic microbes from Typha angustifolia was shown to improve nitrogen metabolism in rice, indicating the importance of selecting compatible microbial strains (Sahu et al., 2020). The study on Rhizobium leguminosarum bv. trifolii demonstrated that multi-strain consortia could significantly increase grain yield, emphasizing the need for careful selection and compatibility testing of microbial consortia.

7.3 Economic and practical aspects

The economic and practical aspects of using non-rhizobial endophytic microbes in rice cultivation include the cost of microbial inoculants, application methods, and potential reduction in chemical fertilizer usage. The use of endophytic microbes can lead to a substantial reduction in nitrogen fertilizer requirements, as demonstrated by the application of Azotobacter sp. strain Avi2, which achieved similar yield parameters with only 50% of the recommended nitrogenous fertilizer dose. This reduction in fertilizer use can lower production costs and minimize environmental impact. However, the initial cost of developing and producing microbial inoculants, as well as the need for specialized application techniques, must be considered. Large-scale field trials, such as those conducted in the Nile delta with Rhizobium leguminosarum bv. trifolii, are essential to validate the economic viability and practical implementation of these microbial solutions (Yanni and Dazzo, 2010).

Acknowledgments

Thanks very much for the feedback from the reviewers on the manuscript, which has made this study more comprehensive.

Conflict of Interest Disclosure

The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

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