1 Introduction

Rice (Oryza sativa) is one of the most critical food crops globally, serving as a staple for over half of the world's population. It plays a vital role in food security, particularly in Asia, where more than 90% of the world's rice is produced and consumed. Beyond its significance in food production, rice cultivation is an essential economic activity that supports millions of livelihoods, especially in rural areas. The unique nature of rice paddies, which have evolved to maximize yield under flooded conditions, profoundly impacts both the environment and the microbiota within these ecosystems. However, the increasing demand for rice, driven by global population growth, presents challenges for sustainable production, making it imperative to adopt agricultural practices that sustain soil health, productivity, and environmental integrity (Edwards et al., 2015).

Soil microbiota, which include bacteria, fungi, archaea, and other microorganisms, are fundamental to soil health and agricultural productivity. These microorganisms are involved in various essential processes such as nutrient cycling, organic matter decomposition, and the suppression of soil-borne diseases. In the context of rice cultivation, soil microbiota play a crucial role in making nutrients available to plants, particularly through the transformation of nitrogen, phosphorus, and other essential elements (Das et al., 2019). The interaction between rice plants and their associated microbiota in the rhizosphere, rhizoplane, and endosphere is key to enhancing crop resilience against biotic and abiotic stresses. Thus, understanding and managing soil microbiota is essential for promoting sustainable agricultural practices that enhance crop productivity while maintaining environmental health (Liu et al., 2020).

This study aims to explore the role of soil microbiota in rice cultivation and its implications for agricultural sustainability. Specifically, it seeks to review the current understanding of how soil microbiota contribute to the productivity and sustainability of rice cropping systems, examine the interactions between rice plants and their associated soil microbiota across different soil compartments, discuss the potential of soil microbiota management in improving soil health, reducing greenhouse gas emissions, and enhancing crop yields, and highlight the challenges and opportunities in integrating soil microbiota research into sustainable rice farming practices.

2 Soil Microbiota in Rice Cultivation

Soil microbiota are integral to the sustainability and productivity of rice cultivation systems. These microorganisms, which include bacteria, fungi, archaea, and other microorganisms, are responsible for a range of ecological functions that support the growth and health of rice plants. The intricate relationships between these microorganisms and the rice plants they interact with are vital for nutrient cycling, plant growth promotion, and the maintenance of soil structure and fertility. Understanding the diversity and function of these microorganisms is essential for improving rice yield and sustainability, particularly in the context of global food security challenges. The unique flooded conditions of rice paddies create a specialized environment where these microorganisms thrive, contributing to both the positive and negative outcomes in rice agriculture. The study of soil microbiota in rice systems not only enhances our understanding of these ecosystems but also provides insights into how we can manipulate these microorganisms to achieve better agricultural outcomes, reduce greenhouse gas emissions, and promote long-term soil health.

2.1 Types of soil microorganisms relevant to rice (e.g., bacteria, fungi, archaea)

Rice paddies are home to a diverse range of soil microorganisms, each playing distinct roles within the ecosystem. Bacteria, including nitrogen-fixing species like Rhizobium and Azospirillum, are crucial for converting atmospheric nitrogen into ammonia, which rice plants can then utilize for growth. Phosphate-solubilizing bacteria such as Pseudomonas are also essential, transforming insoluble forms of phosphorus into bioavailable forms. These bacterial communities are complemented by fungi, particularly mycorrhizal fungi, which form symbiotic relationships with rice roots. These fungi enhance nutrient uptake, particularly phosphorus, and provide protection against soil-borne pathogens. Archaea, especially methanogenic archaea, are key players in the carbon cycle within flooded rice paddies, where they contribute to methane production—a significant greenhouse gas. The unique conditions of flooded paddies foster a distinct microbial community that is highly adapted to anaerobic conditions, allowing these microorganisms to thrive and perform essential ecological functions. This microbial diversity is not just critical for nutrient cycling but also for maintaining the balance of the ecosystem, influencing everything from soil structure to plant health (Edwards et al., 2015; Ding et al., 2019).

2.2 Roles and functions of soil microbiota in the rice ecosystem

2.2.1 Nutrient cycling (nitrogen fixation, phosphorus solubilization)

Soil microbiota in rice paddies are indispensable for maintaining the health and productivity of the rice ecosystem. These microorganisms are involved in several critical functions that contribute to the overall sustainability of rice cultivation. One of the primary roles of soil microbiota in rice ecosystems is nutrient cycling, particularly through processes such as nitrogen fixation and phosphorus solubilization.

Nitrogen-fixing bacteria, such as those in the genera Rhizobium and Azospirillum, play a crucial role by converting atmospheric nitrogen into ammonia, which is then used by rice plants to support growth and development. This process is vital for sustaining the nitrogen balance in paddy soils, where synthetic nitrogen fertilizers are often expensive or environmentally damaging. Similarly, phosphate-solubilizing bacteria like Pseudomonas convert insoluble phosphorus compounds into soluble forms that rice plants can absorb, thereby supporting robust plant growth. These nutrient cycling processes are essential not only for plant health but also for maintaining soil fertility over time, as they reduce the need for chemical fertilizers and enhance the natural fertility of the soil (Rao, 2018; Jiao et al., 2019).

2.2.2 Plant growth promotion (phytohormone production, disease resistance)

In addition to their role in nutrient cycling, soil microbiota are also crucial for promoting plant growth and enhancing disease resistance in rice plants. Certain rhizosphere bacteria produce phytohormones, such as auxins, gibberellins, and cytokinins, which stimulate root development and improve the plant’s ability to absorb nutrients. These phytohormones are key to optimizing root architecture, thereby enhancing the plant’s access to water and nutrients. Furthermore, soil microbiota can induce systemic resistance in rice plants, making them more resilient to a variety of pathogens.

For example, some beneficial bacteria can outcompete harmful microorganisms in the soil, reducing the incidence of diseases such as rice blast and sheath blight. This competitive exclusion, along with the activation of the plant’s immune responses, helps in safeguarding the plant against infections, thereby ensuring better crop health and higher yields. The synergistic effects of these microorganisms on plant growth and disease resistance make them an integral part of sustainable rice farming practices (Zhang et al., 2022).

2.2.3 Soil structure and fertility enhancement

Soil microbiota contribute significantly to the enhancement of soil structure and fertility, which are vital for the sustainability of rice cultivation. The decomposition of organic matter by soil microorganisms leads to the formation of soil aggregates, which are clusters of soil particles that improve soil texture, aeration, and water retention. These aggregates create a stable soil structure that is less prone to erosion and compaction, allowing for better root penetration and healthier plant growth.

Additionally, the metabolic activities of soil microbiota release organic acids that weather soil minerals, thereby increasing the availability of essential nutrients such as calcium, magnesium, and potassium. These processes not only enhance soil fertility but also promote the long-term resilience of the soil, ensuring that it can continue to support productive rice cultivation over successive planting cycles. The role of soil microbiota in maintaining soil health is thus a critical component of sustainable agricultural practices, particularly in the context of intensive rice farming (Rao, 2018; Liu et al., 2020).

3 Interactions Between Soil Microbiota and Rice Plants

The interactions between soil microbiota and rice plants are complex and multifaceted, involving a range of symbiotic, endophytic, and epiphytic relationships that collectively influence plant health and productivity. These interactions are crucial for the sustainability and efficiency of rice cultivation, as they can significantly enhance nutrient uptake, disease resistance, and overall crop yield.

3.1 Symbiotic relationships (e.g., mycorrhizae, rhizobia)

Symbiotic relationships between rice plants and soil microorganisms, particularly mycorrhizal fungi and rhizobia, play a pivotal role in enhancing nutrient availability and plant growth. Mycorrhizal fungi, such as arbuscular mycorrhizal fungi (AMF), form symbiotic associations with rice roots, facilitating the uptake of essential nutrients like phosphorus, which is often limited in flooded rice paddies. These fungi extend their hyphae into the soil, increasing the surface area for nutrient absorption and improving the plant's access to nutrients that are otherwise inaccessible.

Additionally, AMF can enhance the plant's tolerance to environmental stresses such as drought and salinity by improving water uptake and root growth. Rhizobia, although traditionally associated with legumes, have also been found to interact beneficially with rice plants, particularly in enhancing nitrogen fixation and uptake. These symbiotic relationships are critical in reducing the dependency on chemical fertilizers, thereby promoting sustainable agricultural practices (Bernaola et al., 2018; Okonji et al., 2018).

3.2 Endophytic and epiphytic microorganisms

Endophytic and epiphytic microorganisms inhabit the internal and external surfaces of rice plants, respectively, playing crucial roles in plant health and growth. Endophytes, which live within plant tissues without causing harm, can enhance plant growth by producing phytohormones, facilitating nutrient uptake, and inducing resistance against pathogens. For example, endophytic bacteria like Serratia nematodiphila have been shown to improve rice growth in acidic soils by enhancing root surface area and biomass, thereby aiding in the plant's adaptation to stress conditions.

Epiphytic microorganisms, which reside on the plant surface, contribute to plant health by forming a protective barrier against pathogens and aiding in nutrient absorption. These microorganisms can also modulate the plant’s immune responses, leading to increased resistance to diseases and pests. The dynamic interactions between rice plants and these microorganisms highlight the importance of understanding and managing the rice microbiome to optimize plant health and yield (Wang et al., 2016; Das et al., 2020).

3.3 Effects of microbiota on rice plant health and yield

Soil microbiota have profound effects on the health and yield of rice plants. These effects are mediated through various mechanisms, including nutrient cycling, disease suppression, and the enhancement of stress tolerance. For instance, the inoculation of rice plants with beneficial microbes such as Phomopsis liquidambari can significantly improve nitrogen and phosphorus uptake, leading to enhanced grain yield and quality.

This fungus not only helps in nutrient acquisition but also modifies the soil microbial community, promoting a more efficient nutrient cycling process. Additionally, the presence of beneficial microorganisms in the rhizosphere can suppress the growth of harmful pathogens through competitive exclusion and the production of antimicrobial compounds. The overall effect of a well-balanced microbial community is a healthier plant with increased resilience to environmental stresses and higher productivity. These insights underscore the potential of harnessing soil microbiota for sustainable rice cultivation, reducing the need for chemical inputs, and improving crop yields (Harman and Uphoff, 2019; Tang et al., 2021).

4 Impact of Agricultural Practices on Soil Microbiota

The impact of agricultural practices on soil microbiota is profound, as these practices determine the composition, diversity, and functionality of microbial communities in the soil. Understanding how different farming methods influence soil microbiota is crucial for developing strategies that support sustainable agriculture.

4.1 Conventional vs. sustainable agricultural practices

Conventional agricultural practices, which typically involve the extensive use of chemical fertilizers, pesticides, and intensive tillage, have been shown to negatively impact soil microbial diversity and health. These practices often lead to soil compaction, reduced organic matter, and a decline in beneficial microbial populations. In contrast, sustainable agricultural practices, such as organic farming, conservation tillage, and crop rotation, tend to promote microbial diversity and enhance soil health. Organic farming, for example, avoids synthetic inputs and instead relies on organic amendments, which support a diverse and active microbial community.

Studies have shown that soils managed under organic systems exhibit higher microbial biomass and enzyme activities, which are indicative of a healthy and resilient soil ecosystem. These sustainable practices help in maintaining the ecological balance, enhancing nutrient cycling, and improving the overall fertility of the soil, making them more conducive to long-term agricultural productivity (Chen et al., 2020; Tahat et al., 2020).

4.2 Influence of pesticides, fertilizers, and tillage on soil microbial communities

The application of pesticides and chemical fertilizers significantly alters the structure and function of soil microbial communities. Pesticides, while targeting specific pests, can also inadvertently harm non-target soil organisms, leading to a reduction in microbial diversity and disrupting soil ecological processes. Similarly, the overuse of chemical fertilizers can lead to nutrient imbalances in the soil, which may favor certain microbial populations over others, reducing overall diversity. Tillage practices also have a substantial impact on soil microbiota. Conventional tillage disrupts the soil structure, exposing microbial communities to environmental stresses such as oxygen fluctuations and moisture loss, which can decrease microbial diversity and activity.

In contrast, conservation tillage, which minimizes soil disturbance, has been found to preserve soil structure and enhance microbial diversity and functional stability. The integration of organic fertilizers and reduced tillage has been shown to support a more diverse and resilient microbial community, which is essential for maintaining soil health and productivity (Nivelle et al., 2016; Babin et al., 2019).

4.3 Case studies on organic farming and microbiota diversity

Numerous case studies have demonstrated the positive effects of organic farming on soil microbiota diversity. For instance, research conducted on farms transitioning from conventional to organic practices revealed a significant increase in microbial diversity over time. Organic farming practices, which typically involve the application of compost, manure, and other organic amendments, create a favorable environment for a wide range of microorganisms. These organic inputs provide a continuous source of nutrients for soil microbes, enhancing their activity and diversity (Barea, 2015; O’Callaghan et al., 2022).

In a study comparing organic and conventional farming systems, it was found that organic fields had a more complex and stable microbial network, with higher levels of beneficial microbes such as mycorrhizal fungi and nitrogen-fixing bacteria. This increased microbial diversity is associated with improved soil structure, enhanced nutrient availability, and greater resilience to environmental stresses, all of which contribute to the sustainability of agricultural systems. The findings from these studies underscore the importance of adopting organic farming practices to maintain and enhance soil health (Lupatini et al., 2017; Nam et al., 2023) (Figure 1).

5 Innovations in Microbiota Management for Sustainable Rice Cultivation

5.1 Biofertilizers and biopesticides: types, application methods, and benefits

Innovations in microbiota management are at the forefront of efforts to enhance the sustainability and productivity of rice cultivation. These innovations include the development and application of biofertilizers and biopesticides, the use of microbial consortia, and advances in microbial inoculant technologies. Biofertilizers and biopesticides represent a significant shift away from conventional chemical inputs in agriculture. These biological products harness the power of beneficial microorganisms to improve plant nutrition and protect crops from pests and diseases.

Biofertilizers, such as those based on nitrogen-fixing bacteria (Rhizobium, Azospirillum) and phosphate-solubilizing microbes, enhance soil fertility by increasing the availability of essential nutrients like nitrogen and phosphorus. These microorganisms are applied through various methods, including seed treatment, soil inoculation, and foliar sprays. Biopesticides, on the other hand, utilize microbial agents such as Bacillus thuringiensis and Trichoderma species to control pests and pathogens by producing toxins, competing for resources, or inducing plant resistance. The benefits of using biofertilizers and biopesticides are manifold, including reduced reliance on chemical fertilizers and pesticides, improved soil health, enhanced crop yields, and minimized environmental impact (Yadav, 2018; Seenivasagan and Babalola, 2021).

5.2 Microbial consortia for enhancing soil health and plant growth

The use of microbial consortia—combinations of different microbial species—has emerged as a promising strategy to improve soil health and plant growth. These consortia are designed to take advantage of the synergistic interactions between different microbes, leading to more efficient nutrient cycling, enhanced disease resistance, and better stress tolerance in plants. For instance, a consortium of nitrogen-fixing bacteria, mycorrhizal fungi, and phosphate-solubilizing bacteria can provide a more comprehensive nutrient profile for rice plants, leading to improved growth and yield.

The application of microbial consortia is typically done through soil inoculation, seed coating, or as a component of organic fertilizers. Research has shown that these consortia not only improve the immediate nutritional status of crops but also contribute to long-term soil fertility by increasing organic matter content and microbial diversity. This approach is particularly effective in organic and low-input farming systems where chemical inputs are minimized (Seenivasagan and Babalola, 2021; Mallano et al., 2022).

5.3 Advances in microbial inoculant technologies

Recent advances in microbial inoculant technologies have focused on improving the efficacy, stability, and application methods of these products. One key development is the formulation of microbial inoculants with protective carriers that enhance the survival and activity of beneficial microbes in the soil. These carriers can include materials like peat, clay, or biochar, which protect the microbes from environmental stresses and ensure their gradual release into the soil (Barea, 2015; Edwards et al., 2019).

Another innovation is the use of liquid biofertilizers, which offer better shelf life and ease of application compared to traditional solid formulations. Additionally, the development of microbial consortia that include specific strains tailored to the local soil and crop conditions has improved the consistency and effectiveness of inoculants in the field. Advances in genomic and synthetic biology have also enabled the engineering of microbes with enhanced traits, such as improved nitrogen fixation or phosphate solubilization, further boosting the potential of microbial inoculants in sustainable agriculture (Batista and Singh, 2021; O’Callaghan et al., 2022).

6 Case Studies

6.1 Successful integration of microbial management in rice cultivation

Case studies in the context of rice cultivation have provided significant insights into the successful application of microbial management strategies, comparative regional analyses of rice yield and sustainability, and long-term impacts of these practices on soil microbiota and productivity. A landmark case study from Nanchang, China, demonstrates the long-term benefits of integrating microbial management with conventional farming practices. Over a 32-year period, researchers observed the effects of combining manure with chemical fertilizers on rice yield, soil chemical properties, and microbial communities.

The study revealed that using 70% manure combined with 30% chemical fertilizer not only sustained high rice yields but also led to significant improvements in soil organic matter, microbial biomass, and bacterial diversity. This approach mitigated soil acidification, a common issue in intensive farming systems, and maintained a healthy and resilient microbial community. These changes in soil health were directly linked to sustained high crop productivity, illustrating the potential of integrating organic inputs to enhance the effectiveness of chemical fertilizers. The success of this method underscores the importance of a balanced approach that leverages both organic and inorganic inputs to support sustainable agriculture. This case highlights how the thoughtful integration of microbial management can lead to long-term improvements in both soil health and crop productivity, offering a model for sustainable rice cultivation (Chen et al., 2017).

6.2 Comparative analysis of rice yield and sustainability in different regions

Comparative studies across various regions have shed light on the effectiveness of different microbial management strategies in enhancing rice yield and sustainability. One extensive study across the Indo-Gangetic Plains of India evaluated the impacts of organic, inorganic, and integrated crop management practices on rice and wheat systems over 15 years. The findings revealed substantial regional differences in productivity and sustainability. In regions like Pantnagar, where organic and integrated management practices were implemented, soil microbial biomass and nutrient availability were significantly higher, leading to better crop yields and a higher sustainability yield index compared to regions relying solely on inorganic practices (Edwards et al., 2019; Jiao et al., 2022) (Figure 2).

The study highlighted the superiority of integrated crop management practices, which not only improved soil health but also enhanced overall farm productivity and economic returns. This regional analysis underscores the need for localized adaptation of microbial management strategies to optimize agricultural outcomes based on specific environmental and soil conditions. Such insights are crucial for guiding sustainable agricultural practices that can be tailored to different agro-ecological zones, thereby maximizing both yield and sustainability (Panwar et al., 2022).

6.3 Long-term field studies on soil microbiota and rice productivity

Long-term field studies have been pivotal in understanding the sustained impact of microbial management on soil health and rice productivity. In Uganda, a 20-year study focused on upland rice fields provided valuable data on how different fertilizer management practices influence soil biochemical properties and microbial biomass. The study employed integrated nutrient management (INM), which combined chemical fertilizers with organic inputs such as poultry manure. Results indicated that INM significantly increased soil organic carbon sequestration and microbial activity, leading to enhanced soil fertility and higher rice yields.

Moreover, the microbial communities under INM were more diverse and functionally robust, contributing to improved resilience against environmental stresses and reduced greenhouse gas emissions. These findings highlight the long-term benefits of integrating organic amendments with conventional fertilizers to maintain soil health and sustain agricultural productivity. The success of INM in this study suggests that similar approaches could be vital in other regions, particularly where sustainable intensification of agriculture is a priority (Inubushi et al., 2020).

7 Challenges and Future Perspectives

7.1 Limitations in current research and technological applications

The management of soil microbiota in rice cultivation offers tremendous potential for enhancing agricultural sustainability. However, there are significant challenges and barriers that need to be addressed to fully realize this potential. This section discusses the current limitations in research and technology, environmental and socio-economic barriers, and the future directions that could lead to breakthroughs in soil microbiota management (Das et al., 2019; O’Callaghan et al., 2022).

One of the primary limitations in current research on soil microbiota management is the incomplete understanding of the complex interactions between soil microorganisms and rice plants. While advances in genomic and metagenomic technologies have greatly expanded our knowledge of microbial diversity and function, many soil microorganisms remain uncultured and undescribed. This lack of comprehensive knowledge hinders the development of effective microbial inoculants and biofertilizers tailored to specific soil and crop conditions. Moreover, the scalability of lab-based research findings to field applications presents another significant challenge. Most studies on microbial management are conducted under controlled conditions, and translating these results to real-world agricultural systems with diverse and dynamic environments can be difficult. Additionally, the long-term stability and efficacy of microbial inoculants in the field remain uncertain, as soil and environmental conditions can significantly alter microbial community composition and function over time (Barea, 2015; Sergaki et al., 2018).

7.2 Environmental and socio-economic barriers to widespread adoption

Environmental and socio-economic factors also pose considerable barriers to the widespread adoption of microbial management practices in rice cultivation. One of the key environmental challenges is the variability in soil types, climate, and agricultural practices across different regions, which can affect the performance of microbial products. For example, microbial inoculants that are effective in one region may not perform well in another due to differences in soil pH, organic matter content, or moisture levels.

This variability necessitates the development of region-specific microbial solutions, which can be costly and time-consuming. On the socio-economic side, smallholder farmers, who constitute a large portion of rice producers globally, may lack the resources or knowledge to adopt new microbial technologies. The initial costs of microbial inoculants, coupled with the uncertainty of their benefits, can deter farmers from transitioning away from conventional chemical inputs. Furthermore, there is often a lack of extension services and training programs to educate farmers on the benefits and proper use of microbial products, further limiting their adoption (Rothenberg et al., 2016; Liu et al., 2020).

7.3 Future research directions and potential breakthroughs in soil microbiota management

Future research in soil microbiota management for rice cultivation should focus on several key areas to overcome current challenges and achieve potential breakthroughs. First, there is a need for more field-based studies that evaluate the long-term effects of microbial inoculants on soil health and crop productivity across different environments. Such studies should also explore the interactions between microbial inoculants and native soil microorganisms to understand how these interactions influence the efficacy of microbial products.

Advances in synthetic biology and microbial engineering could lead to the development of customized microbial consortia with enhanced functional traits, such as improved nitrogen fixation or phosphate solubilization, tailored to specific soil conditions. Additionally, integrating soil microbiota management with other sustainable agricultural practices, such as conservation tillage and organic farming, could create synergistic effects that enhance soil health and crop yields. The development of low-cost, easy-to-use microbial products and the establishment of robust extension services to educate farmers on their benefits and usage will be critical for increasing adoption rates among smallholder farmers. These efforts could pave the way for more sustainable and resilient rice production systems that rely on biological inputs rather than chemical ones (Barea, 2015; Chialva et al., 2020).

8 Implications for Agricultural Sustainability

8.1 Contribution of soil microbiota to sustainable rice farming

The role of soil microbiota in rice cultivation extends far beyond crop productivity, influencing broader aspects of agricultural sustainability, ecosystem services, and biodiversity. This section explores the contributions of soil microbiota to sustainable farming, their role in enhancing ecosystem functions, and policy recommendations for integrating microbiota management into agricultural practices.

Soil microbiota play a crucial role in sustainable rice farming by enhancing soil health, promoting nutrient cycling, and improving plant resilience to stresses. The diverse microbial communities in the soil are responsible for the decomposition of organic matter, nitrogen fixation, and phosphorus solubilization, which are vital for maintaining soil fertility without relying heavily on chemical inputs. For example, long-term studies have demonstrated that the application of organic amendments such as manure and compost, which enrich microbial diversity, leads to sustained improvements in soil structure and nutrient availability, resulting in higher and more stable rice yields over time. Furthermore, microbial interactions in the rhizosphere help suppress soil-borne pathogens, reducing the need for chemical pesticides. These functions of soil microbiota not only support the immediate needs of crop production but also contribute to the long-term sustainability of agricultural ecosystems by maintaining soil health and reducing the environmental impact of farming practices (Das et al., 2019; Liu et al., 2020).

8.2 Role in enhancing ecosystem services and biodiversity

Soil microbiota are integral to the delivery of ecosystem services that are essential for sustainable agriculture, including nutrient cycling, soil formation, and the regulation of greenhouse gases. The diverse microbial communities in rice paddies facilitate key processes such as methane oxidation, which is critical in mitigating the global warming potential of rice cultivation. Moreover, the presence of a rich microbial diversity enhances soil resilience to environmental disturbances, such as drought and flooding, by maintaining the functional stability of soil ecosystems.

This resilience is crucial for sustaining agricultural productivity in the face of climate change. Additionally, by supporting a wide range of biological processes, soil microbiota contribute to the conservation of biodiversity within agricultural landscapes. The preservation of microbial diversity is essential not only for maintaining the ecological balance but also for safeguarding the ecosystem services that are vital for human well-being (Saikia et al., 2019; Jiao et al., 2022).

8.3 Policy recommendations for integrating microbiota management in agricultural practices

To fully realize the potential of soil microbiota in promoting sustainable rice farming, it is essential to develop policies that support the integration of microbiota management into agricultural practices. Governments and agricultural agencies should prioritize research and development programs that focus on understanding the complex interactions between soil microbiota and crop plants, as well as the effects of different farming practices on these interactions. Policies should encourage the adoption of sustainable farming practices, such as conservation tillage, organic farming, and the use of biofertilizers, which enhance microbial diversity and soil health (Saikia et al., 2019; Liu et al., 2020).

Additionally, extension services and farmer training programs should be established to educate farmers about the benefits of microbiota management and provide them with the tools and knowledge needed to implement these practices effectively. Financial incentives, such as subsidies for organic amendments and microbial inoculants, could also be introduced to encourage farmers to adopt sustainable practices that enhance soil microbiota. By integrating these strategies into national and regional agricultural policies, it will be possible to promote more sustainable and resilient agricultural systems that are better equipped to meet the challenges of the future (Barea, 2015; Edwards et al., 2019).

9 Concluding Remarks

This paper has explored the multifaceted role of soil microbiota in rice cultivation and its implications for agricultural sustainability. Soil microbiota, including bacteria, fungi, and archaea, play crucial roles in nutrient cycling, organic matter decomposition, and the suppression of soil-borne diseases. These microorganisms contribute to essential processes such as nitrogen fixation and phosphorus solubilization, which are critical for maintaining soil fertility and crop productivity. The management practices employed in rice cultivation, including the use of fertilizers, pesticides, and tillage, have significant effects on the structure and function of soil microbial communities. Sustainable practices that incorporate organic amendments and reduced chemical inputs have been shown to enhance microbial diversity and resilience, leading to better soil health and sustained crop yields. Advances in microbial inoculant technologies, the use of biofertilizers and biopesticides, and the development of microbial consortia offer promising tools for enhancing soil health and crop productivity. These innovations can reduce the reliance on chemical inputs, mitigate environmental impacts, and contribute to the sustainability of rice farming systems.

The importance of soil microbiota in promoting sustainable rice cultivation cannot be overstated. These microorganisms are the foundation of soil health, driving processes that are essential for maintaining nutrient availability, improving soil structure, and supporting plant health. By fostering a diverse and active microbial community, sustainable farming practices can enhance the resilience of rice ecosystems to environmental stresses, reduce the need for chemical inputs, and ensure long-term productivity. The interactions between rice plants and their associated microbiota are critical for optimizing nutrient use efficiency and minimizing the environmental footprint of rice farming. As such, the integration of soil microbiota management into agricultural practices is vital for achieving the goals of sustainable agriculture and food security in the face of global challenges such as climate change and population growth.

Looking ahead, the future of global agriculture will increasingly depend on our ability to harness the potential of soil microbiota for sustainable food production. Further research is needed to deepen our understanding of the complex interactions between soil microorganisms and crop plants, particularly in diverse and dynamic field conditions. Advances in biotechnology, such as the development of tailored microbial consortia and the use of genetic engineering to enhance microbial traits, hold great promise for improving crop productivity and resilience. Moreover, the widespread adoption of microbiota-based management practices will require supportive policies, farmer education, and access to affordable microbial products. As these practices become more mainstream, they have the potential to transform agriculture by reducing dependency on synthetic inputs, enhancing ecosystem services, and contributing to global food security. The integration of soil microbiota management into agricultural systems represents a crucial step toward building a more sustainable and resilient global food system.

Acknowledgments

We would like to thank two anonymous peer reviewers for their suggestions on my manuscript.

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.

References

Babin D., Deubel A., Jacquiod S., Sørensen S.J., Geistlinger J., Grosch R., and Smalla K., 2019, Impact of long-term agricultural management practices on soil prokaryotic communities, Soil Biology and Biochemistry, 129: 17-28.

https://doi.org/10.1016/J.SOILBIO.2018.11.002

Barea J., 2015, Future challenges and perspectives for applying microbial biotechnology in sustainable agriculture based on a better understanding of plant-microbiome interactions, Journal of Soil Science and Plant Nutrition, 15: 261-282.

https://doi.org/10.4067/S0718-95162015005000021

Batista B.D., and Singh B., 2021, Realities and hopes in the application of microbial tools in agriculture, Microbial Biotechnology, 14: 1258-1268.

https://doi.org/10.1111/1751-7915.13866

Bernaola L., Cange G., Way M., Gore J., Hardke J., and Stout M., 2018, Natural colonization of rice by arbuscular mycorrhizal fungi in different production areas, Rice Science, 25: 169-174.

https://doi.org/10.1016/J.RSCI.2018.02.006

Chen D., Yuan L., Liu Y., Jianhua J., and Hou H., 2017, Long-term application of manures plus chemical fertilizers sustained high rice yield and improved soil chemical and bacterial properties, European Journal of Agronomy, 90: 34-42.

https://doi.org/10.1016/J.EJA.2017.07.007

Chen X., Henriksen T., Svensson K., and Korsaeth A., 2020, Long-term effects of agricultural production systems on structure and function of the soil microbial community, Applied Soil Ecology, 147: 103387.

https://doi.org/10.1016/j.apsoil.2019.103387

Chialva M., Ghignone S., Cozzi P., Lazzari B., Bonfante P., Abbruscato P., and Lumini E., 2020, Water management and phenology influence the root-associated rice field microbiota, FEMS Microbiology Ecology, 96(9): fiaa146.

https://doi.org/10.1093/femsec/fiaa146

Das J., Sultana S., Rangappa K., Kalita M., and Thakuria D., 2020, Endophyte bacteria alter physiological traits and promote growth of rice (Oryza sativa L.) in aluminium toxic and phosphorus deficient acid inceptisols, Journal of Pure and Applied Microbiology, 14: 627-639.

https://doi.org/10.22207/jpam.14.1.65

Das S., Gwon H., Khan M.I., Van Nostrand J.V., Alam M., and Kim P., 2019, Taxonomic and functional responses of soil microbial communities to slag-based fertilizer amendment in rice cropping systems, Environment International, 127: 531-539.

https://doi.org/10.1016/j.envint.2019.04.012

Ding L.J., Cui H., Nie S., Long X., Duan G., and Zhu Y.G., 2019, Microbiomes inhabiting rice roots and rhizosphere, FEMS Microbiology Ecology, 95(5): fiz040.

https://doi.org/10.1093/femsec/fiz040

Edwards J.A., Santos-Medellín C., Nguyen B., Kilmer J., Liechty Z.S., Veliz E., Ni J., Phillips G., and Sundaresan V., 2019, Soil domestication by rice cultivation results in plant-soil feedback through shifts in soil microbiota, Genome Biology, 20: 1-14.

https://doi.org/10.1186/s13059-019-1825-x

Edwards J., Johnson C., Santos-Medellín C., Lurie E., Podishetty N., Bhatnagar S., Eisen J., and Sundaresan V., 2015, Structure, variation, and assembly of the root-associated microbiomes of rice, Proceedings of the National Academy of Sciences, 112: E911-E920.

https://doi.org/10.1073/pnas.1414592112

Harman G., and Uphoff N., 2019, Symbiotic root-endophytic soil microbes improve crop productivity and provide environmental benefits, Scientifica, 2019(1): 9106395.

https://doi.org/10.1155/2019/9106395

Inubushi K., Yashima M., Hanazawa S., Goto A., Miyamoto K., Tsuboi T., and Asea G., 2020, Long-term fertilizer management in NERICA cultivated upland affects soil bio-chemical properties, Soil Science and Plant Nutrition, 66: 247-253.

https://doi.org/10.1080/00380768.2019.1705738

Jiao S., Qi J., Jin C., Liu Y., Wang Y., Pan H., Chen S., Liang C., Peng Z., and Wei G., 2022, Core phylotypes enhance the resistance of soil microbiome to environmental changes to maintain multifunctionality in agricultural ecosystems, Global Change Biology, 28: 6653-6664.

https://doi.org/10.1111/gcb.16387

Jiao S., Xu Y., Zhang J., Hao X., and Lu Y., 2019, Core microbiota in agricultural soils and their potential associations with nutrient cycling, mSystems, 4: 10.

https://doi.org/10.1128/mSystems.00313-18

Liu J., Song Y., Tang M., Lu Q., and Zhong G., 2020, Enhanced dissipation of xenobiotic agrochemicals harnessing soil microbiome in the tillage-reduced rice-dominated agroecosystem, Journal of Hazardous Materials, 398: 122954.

https://doi.org/10.1016/j.jhazmat.2020.122954

Lupatini M., Korthals G., de Hollander M., Janssens T., and Kuramae E., 2017, Soil microbiome is more heterogeneous in organic than in conventional farming system, Frontiers in Microbiology, 7: 2064.

https://doi.org/10.3389/fmicb.2016.02064

Mallano A.I., Zhao X., Wang H., Jiang G., Sun B.Y., and Huang C., 2022, Divergent taxonomic responses of below-ground microbial communities to silicate fertilizer and biofertilizer amendments in two rice ecotypes, Frontiers in Agronomy, 4: 1071890.

https://doi.org/10.3389/fagro.2022.1071890

Nam B., Lee H.J., and Choi Y.J., 2023, Organic farming allows balanced fungal and oomycetes communities, Microorganisms, 11: 1307.

https://doi.org/10.3390/microorganisms11051307

Nivelle E., Verzeaux J., Habbib H., Kuzyakov Y., Decocq G., Roger D., and Tétu T., 2016, Functional response of soil microbial communities to tillage, cover crops and nitrogen fertilization, Applied Soil Ecology, 108: 147-155.

https://doi.org/10.1016/J.APSOIL.2016.08.004

O’Callaghan M., Ballard R., and Wright D., 2022, Soil microbial inoculants for sustainable agriculture: Limitations and opportunities, Soil Use and Management, 38: 1340-1369.

https://doi.org/10.1111/sum.12811

Okonji C., Sakariyawo O., Okeleye K., Osunbiyi A.G., and Ajayi E., 2018, Effects of arbuscular mycorrhizal fungal inoculation on soil properties and yield of selected rice varieties, Journal of Agricultural Sciences, 63: 153-170.

https://doi.org/10.2298/JAS1802153O

Panwar A.S., Ansari M.A., Ravisankar N., Babu S., Prusty A.K., Ghasal P.C., and Meena A.L., 2022, Effect of organic farming on the restoration of soil quality, ecosystem services, and productivity in rice–wheat agro-ecosystems, Frontiers in Environmental Science, 10: 972394.

https://doi.org/10.3389/fenvs.2022.972394

Rao V., 2018, Microbial transformations implicit with soil and crop productivity in rice systems, In Sustainable Agriculture Reviews, 57-72.

https://doi.org/10.1016/B978-0-444-63987-5.00004-9

Rothenberg S., Anders M., Ajami N., Petrosino J., and Balogh E., 2016, Water management impacts rice methylmercury and the soil microbiome, The Science of the Total Environment, 572: 608-617.

https://doi.org/10.1016/j.scitotenv.2016.07.017

Saikia R., Sharma S., Thind H.S., and Singh Y., 2019, Tillage and residue management practices affect soil biological indicators in a rice–wheat cropping system in north‐western India, Soil Use and Management, 36: 157-172.

https://doi.org/10.1111/sum.12544

Seenivasagan R., and Babalola O.O., 2021, Utilization of microbial consortia as biofertilizers and biopesticides for the production of feasible agricultural product, Biology, 10(11): 1111.

https://doi.org/10.3390/biology10111111

Sergaki C., Lagunas B., Lidbury I., Gifford M., and Schäfer P., 2018, Challenges and approaches in microbiome research: from fundamental to applied, Frontiers in Plant Science, 9: 1205.

https://doi.org/10.3389/fpls.2018.01205

Tahat M.M., Alananbeh K.M., Othman Y.A., and Leskovar D.I., 2020, Soil health and sustainable agriculture, Sustainability, 12(12): 4859.

https://doi.org/10.3390/su12124859

Tang M.J., Lu F., Yang Y., Sun K., Zhu Q., Xu F.J., Zhang W., and Dai C., 2021, Benefits of endophytic fungus phomopsis liquidambaris inoculation for improving mineral nutrition, quality, and yield of rice grains under low nitrogen and phosphorus condition, Journal of Plant Growth Regulation, 41: 2499-2513.

https://doi.org/10.1007/s00344-021-10462-8

Wang W., Zhai Y., Cao L., Tan H., and Zhang R., 2016, Endophytic bacterial and fungal microbiota in sprouts, roots and stems of rice (Oryza sativa L.), Microbiological Research, (188-189): 1-8.

https://doi.org/10.1016/j.micres.2016.04.009

Yadav A., 2018, Microbial inoculants for sustainable agriculture, International Journal of Current Microbiology and Applied Sciences, 7: 800-804.

https://doi.org/10.20546/IJCMAS.2018.705.097

Zhang M., Wang Y.Y., Hu Y.Y., Wang H., Liu Y., Zhao B., Zhang J., Fang R., and Yan Y., 2022, Heterosis in root microbiota inhibits growth of soil-borne fungal pathogens in hybrid rice, Journal of Integrative Plant Biology, 65(4): 1059-1076.

https://doi.org/10.1111/jipb.13416