1 Introduction

Soybean (Glycine max) is an important crop because of its high protein content and its ability to be made into a wide variety of food and industrial products. Soybean plays a large role in agriculture around the world, especially in places where it is a staple food, and it helps a lot in local economies. Soybean also works with bacteria called Rhizobia, and this partnership is very important for soybean to grow well and have high yields. Rhizobia help soybeans absorb nitrogen from the air, which reduces the need for too much fertilizer, making agriculture more environmentally friendly (He et al., 2020).

Biological nitrogen fixation (BNF) is a natural process in which some bacteria turn nitrogen (N₂) from the air into ammonia that plants can use. This helps farmers use less fertilizer, saving money and protecting the environment. The cooperation between soybean and Rhizobia is a good example of biological nitrogen fixation. Rhizobia live in the nodules of soybeans and fix nitrogen while getting carbon and other nutrients from the soybeans. If we can figure out how this relationship works, we hope to make soybeans more productive and agriculture more sustainable (López et al., 2019; Brear et al., 2020; Zhang et al., 2020).

This study is mainly aimed at understanding the molecular signals when soybeans and rhizobia cooperate, especially those related to nitrogen fixation. We also studied what genes and biochemical processes regulate this relationship and how environmental changes affect them. Finally, we are also exploring ways to improve the biological nitrogen fixation ability of soybeans. By gaining a deeper understanding of these complex interactions between soybeans and rhizobia, we hope to help breeders breed soybean varieties with stronger nitrogen fixation capabilities, so that agriculture can go further and be more environmentally friendly.

2 Symbiotic Mechanism of Soybean and rRhizobium

2.1 Symbiosis start stage

At the beginning, the small hairs (root hairs) on soybean roots will recognize and stick to rhizobia. This process requires some special signals, which are called Nod factors. When rhizobia encounter flavonoids secreted by soybean roots, they will start to produce Nod factors. For example, Rhizobium fredii USDA257 will start to produce Nod factors when it encounters a substance called genistein. These Nod factors deform the root hairs, allowing bacteria to attach better. After the plant recognizes these signals, it will also initiate a series of reactions to help the bacteria hold on to the root hairs (Oldroyd et al., 2011).

2.2 Formation of nodules and infection threads

After the bacteria successfully attach, they will induce the soybean roots to grow a small tube called infection thread. This small tube allows the bacteria to enter the root cells smoothly. This process requires many genes in the plant and bacteria to cooperate. Nod factors play a very important role in making root hairs bend and infection filaments grow (Masson-Boivin and Sachs, 2018). In Rhizobium fredii, there are two very important genes, nodD1 and nodD2, which can help bacteria secrete signals to further promote the formation of nodules. In addition, the nodABC genes are responsible for the synthesis of Nod factors, which are essential for nodule development and nitrogen fixation (Holland et al., 2023).

2.3 Maturation of nitrogen-fixing nodules

When bacteria successfully enter the root cells, they are encapsulated in a small capsule called a symbiont. In the symbiont, the bacteria slowly transform into a special form that can fix nitrogen, called a bacteroid. As the nodules mature, a lot of communication between the plant and the bacteria is required to ensure the efficiency of nitrogen fixation. During this process, the plant also allows the bacteria to undergo terminal differentiation, which, although it makes the bacteria lose their vitality, can greatly improve the effect of nitrogen fixation (Oldroyd et al., 2011). However, environmental conditions are also important. For example, if the salt content is too high, it will affect key genes such as GmNSP1, thereby hindering the formation of nodules.

2.4 Signal transduction during symbiosis

The successful symbiosis between soybeans and rhizobia is inseparable from a complete set of complex signal transduction systems. At the beginning, flavonoids secreted by soybean roots stimulate rhizobia to produce Nod factors. Special receptors on soybean root hairs can recognize these Nod factors and then initiate a series of reactions. These reactions cause the root hairs to curl up and help the infection threads grow out (Oldroyd et al., 2011).

3 Molecular Signals Regulating Symbiosis

3.1 The role of flavonoids in rhizobium activation

Soybean roots secrete some flavonoids, such as genistein. They can attract rhizobia (such as Rhizobium fredii USDA257) and make them active. These flavonoid signals can activate the nodD1 and nodD2 genes in the rhizobia to produce and release Nod factors. Nod factors are particularly important when nodules are first formed. They can cause root hairs to bend, and other cellular changes help rhizobia infect soybean roots and start a symbiotic relationship (Holland et al., 2023).

3.2 How Nod factors and their receptors interact

Nod factors are special small molecules that rhizobia produce only after receiving flavonoid signals. They bind to specialized receptors on soybean roots, such as GmNFR1α. This binding triggers a series of signaling reactions that cause root hairs to bend, infection threads to form, and finally nodules to grow slowly. This process requires a good match, and other molecules will help, such as GmBI-1α. It can work with GmNFR1α to regulate the formation and function of nodules (Lepetit and Brouquisse, 2023).

3.3 Effects of plant hormones on symbiosis

Several hormones in plants, such as auxin, cytokinin and ethylene, also affect the symbiosis between soybean and rhizobia. Auxin mainly plays a role when nodules are just beginning to form, and it can cause the cells in the root cortex to divide and differentiate. Cytokinin is very important when nodules mature, and it can regulate some genes related to nitrogen fixation. Ethylene sometimes inhibits the formation of nodules and acts as a "brake". There must be a good balance between hormones to allow the symbiotic relationship to proceed smoothly (Lepetit and Brouquisse, 2023).

3.4 Symbiotic gene regulation

The process of controlling the expression of symbiotic genes is quite complex, requiring many regulatory proteins and signal pathways. For example, the transcription factor GmNSP1 activates a bunch of symbiotic genes after the roots receive Nod factor signals. GmNSP1 also needs to cooperate with other proteins to bind to the gene promoter and drive the gene to start working. If you encounter environmental stress such as high salt, the stress signal will activate some kinases, such as GmSK2-8, which will modify GmNSP1 and prevent it from binding to DNA. In this way, plants can flexibly adjust the formation and function of nodules according to internal and external environments and improve the efficiency of nitrogen fixation (Gavrin et al., 2021; Wu and Qiu, 2024).

4 Advances in Understanding Nitrogen Fixation

4.1 Key genes involved in nitrogenase activity

In recent years, scientists have discovered many important genes while studying the process of nitrogen fixation between soybeans and rhizobia. Among them, the GmNSP1 gene is particularly important. It is related to how rhizobia infect soybeans, how nodules grow, and the expression of symbiosis-related genes. Studies have found that in high-salt environments, the two transcription factors GmNSP1a and GmNSP1b bind to a kinase called GmSK2-8. In this way, their activity is inhibited, resulting in a decrease in the efficiency of nodulation and nitrogen fixation (He et al., 2020).

There is also an important gene family called SymRK. The two genes GmSymRKα and GmSymRKβ are also critical in the symbiosis between rhizobia and soybeans. Using RNA interference technology, it was found that GmSymRKβ plays a more significant role in nodulation and mycorrhizal infection than GmSymRKα (Indrasumunar et al., 2015). In addition, a gene called MucR1 in soybean rhizobia is also very important. MucR1 mainly regulates the expression of transport proteins for elements such as iron, molybdenum and sulfur, which are important for nitrogenase. However, MucR1 does not directly affect the expression of nitrogen fixation genes (Jiao et al., 2016).

In addition, a gene called GmNNL1 in soybean affects whether certain Bradyrhizobium strains can coexist with soybeans. GmNNL1 can bind to an exogenous protein called NopP to initiate an immune response, thereby preventing root hairs from being infected. However, if the function of GmNNL1 is lost, it can promote root hair infection, increase the number of nodules, and improve nitrogen fixation efficiency (Jiao et al., 2016). These findings tell us that the mechanism of symbiotic nitrogen fixation between soybean and rhizobia is very complex. Understanding the role of these genes is very helpful to improve the nitrogen fixation ability of soybean under different environments.

4.2 Effects of environmental and genetic factors on nitrogen fixation efficiency

The nitrogen fixation effect of soybean and rhizobia is affected by environmental and genetic factors. For example, a high salt environment will greatly inhibit this process. Under salt stress, the GmSK2-8 kinase in soybeans will increase. It will bind to GmNSP1a and GmNSP1b, affecting their ability to activate symbiotic genes. As a result, nodule formation is reduced (He et al., 2020). Light is also important. When the aboveground part of soybeans senses light, some mobile factors, such as GmSTF3/4 and GmFTs, will be produced. These factors are transmitted to the roots, helping to activate the expression of nodulation factors and connecting the aboveground and underground signals together (Wang et al., 2021).

In addition, the genes of the rhizobia themselves, such as nodD1 and nodD2, are also critical. They regulate the strain's response to flavonoid signals secreted by soybeans and help nodule formation (Contador et al., 2020). Genetic factors of soybeans themselves are also important, such as the GmVTL1a gene. The iron transport protein it encodes is expressed on the symbiotic membrane, ensuring that nitrogenase can get enough iron to fix nitrogen smoothly (Brear et al., 2020).

4.3 The role of microbiota in enhancing nitrogen fixation

The microbiota in soybean roots and nodules also helps nitrogen fixation. In particular, rhizobia such as Bradyrhizobium can improve nitrogen fixation efficiency. Inoculation with suitable rhizobia can increase the number of beneficial bacteria in the nodules and improve nitrogen fixation (Brear et al., 2020). If inoculated with other beneficial bacteria, such as Azospirillum brasilense, it can also affect the root microbiota. However, sometimes these microorganisms will compete with each other, which may reduce the number of rhizobia in the nodules (Chen et al., 2018). In addition, hydrogen sulfide (H2S) and rhizobia work together to help plants accumulate more biomass and delay leaf senescence (Zhang et al., 2020). In addition to rhizobia, other root microorganisms, such as growth-promoting bacteria and biocontrol bacteria, can also make soybeans healthier and indirectly improve nitrogen fixation (Bender et al., 2020).

5 Case Study: How to Make Soybeans Better at "Fixing Nitrogen" through Genetic Engineering

5.1 How to choose this case

This time we chose a case about modifying soybean genes so that they can better fix nitrogen in the air. When choosing, we mainly looked at several points: for example, which genes are particularly important when soybeans and rhizobia work together, how these genes affect the growth and function of nodules, and whether soybeans can be more productive and more environmentally friendly after the genes are modified (Huo et al., 2019). We pay special attention to those studies that can explain the mechanism and regulation of nitrogen fixation.

5.2 What kind of genetic modification was studied specifically

One method is particularly interesting, which is to control a gene called GmSK2-8 in soybeans. This gene belongs to the GSK3 class of kinases. Simply put, it will add phosphate to another important transcription factor GmNSP1, making it work poorly. The result is that when there is salt, nodules are difficult to form and nitrogen fixation becomes worse. Studies have found that if some of the genes of GmSK2-8 and its relatives are knocked out, soybeans can grow more nodules and fix more nitrogen in a salty environment (Huo et al., 2019). This shows that regulating some stress response genes can indeed make soybeans more resistant to environmental stress and have better nitrogen fixation.

5.3 What are the benefits of this change for soybeans

After modifying GmSK2-8, soybeans performed better in high-salt soil. There were more nodules, higher nitrogenase activity, and faster nitrogen fixation. This allowed soybeans to grow stronger and produce more seeds in salty soil (He et al., 2020). In addition, some people have found that if soybeans are allowed to express a small heat shock protein called GmHSP17.9, nodules can develop better and nitrogen fixation capacity can be taken to a higher level (Yang et al., 2021). In general, these modifications have improved the ability of soybeans themselves on the one hand, and on the other hand, they can use less fertilizers and make agriculture greener.

5.4 Inspiration for future breeding

These studies have great inspiration for future breeding. After finding key genes such as GmSK2-8 and GmHSP17.9, scientists can use them as targets to select soybeans that are better at fixing nitrogen through marker-assisted breeding or genetic engineering. In the future, breeding can consider improving salt tolerance and symbiotic efficiency, which can not only increase grain production but also protect the environment (Ye et al., 2021). Moreover, if these genetic modifications are used together with other agricultural technologies, the utilization rate of nitrogen can be even higher. Continuing to study the molecular details of the partnership between soybeans and rhizobia will also be particularly important for sustainable agriculture (Holland et al., 2018).

6 Applications and Challenges of Improving Soybean-Rhizobium Symbiosis

6.1 Application of molecular breeding and biotechnology tools

Now, scientists use molecular breeding and biotechnology to improve the cooperation ability of soybeans and rhizobia, especially to make nitrogen fixation more efficient. Researchers have found a number of DNA markers related to efficient symbiosis, which makes the selection of new soybean varieties faster and more accurate. For example, they used germplasm resources from different places to breed high-yield soybeans in Africa and Australia (Dwivedi et al., 2015). In addition, some important genes and quantitative trait loci (QTL) related to symbiotic nitrogen fixation have also been found, which helps breeders select soybeans that are more resistant to environmental stress (Dwivedi et al., 2015). For example, there is a small heat shock protein called GmHSP17.9, which plays a major role in promoting nodule development and nitrogen fixation (Yang et al., 2021). This also shows that biotechnology can help soybeans and rhizobia "cooperate" better.

6.2 Challenges of field application and environmental adaptation

Although breeding and technical means have made a lot of progress, the cooperation between soybeans and rhizobia still encounters many problems in actual planting. One big problem is that they are particularly sensitive to environmental stress, such as salt damage and heavy metal pollution. For example, there is a GSK3-like kinase called GmSK2-8, which inhibits nodule formation under salt stress (He et al., 2020), so we need to breed more stress-resistant soybeans. Similarly, if there are heavy metals such as lead and cadmium in the soil, the cooperation between legumes and rhizobia will also deteriorate. Although some people have found that spraying nitric oxide (NO) or hydrogen sulfide (H₂S) can reduce the impact (Fang et al., 2020), the problem has not been completely solved. In addition, some rhizobia strains, such as Rhizobium fredii USDA257, can only cooperate with specific soybean varieties, which also makes it more difficult to promote and apply (Yang et al., 2021).

6.3 Balancing ecological impacts and yield targets

When improving the relationship between soybeans and rhizobia, we must also consider ecological protection and yield improvement. Although improving nitrogen fixation efficiency can make soybeans grow better and have higher yields, the impact on the environment cannot be ignored. For example, studies have found that by regulating symbiosis, the accumulation of arsenic in soybeans can be reduced, reducing the threat to human health (Ye et al., 2021). In addition, combining the nitrogen fixation process with the removal of pollutants such as polychlorinated biphenyls (PCBs) may also allow soybeans to help "clean up" the environment (Wang et al., 2018). However, the introduction of genetically modified soybeans may also bring some unexpected ecological problems, so while pursuing high yields, careful evaluation and supervision are also needed to prevent new damage to the environment.

7 Conclusion and Future Outlook

The study of soybean and rhizobium symbiosis has revealed many key signals and mechanisms that affect nitrogen fixation. For example, GSK3-like kinases GmSK2-8 can inhibit symbiotic signals and nodule formation by adding phosphate to GmNSP1. This inhibition is particularly evident when the salt content is high, making it more difficult for GmNSP1 to bind to symbiotic genes. In addition, the Nod factor produced by USDA Rhizobium 257 has also been studied in detail, and it has been found that its structure is very complex, and flavonoids (such as genistein) can help its production.

In addition, studies have found that light-regulated mobile factors such as GmSTF3/4 and GmFTs can link above-ground light signals with underground symbiotic signals to promote nodule growth. Hydrogen sulfide (H₂S) has also been shown to work with rhizobia to help soybeans better utilize and distribute nitrogen when nitrogen is scarce. Iron transport is also important, especially through the GmVTL1a protein, so that iron can reach the symbiont smoothly and help fix nitrogen. In addition, the study also tells us that different varieties of soybeans have their own special genes when nodules are formed, and endopoly (increase in the number of chromosomes in the cell) is also important for the development of nodules.

In the future, the study can be further deepened to see how symbiotic signals are suppressed under various stresses (such as salt, drought, etc.). Studying GmSK2-8 and its relatives may find new ways to improve nodulation and nitrogen fixation. Flavonoids and other plant signals are also worth careful study in helping Nod factor production and secretion, which may make symbiosis more efficient. The combination of light signals and symbiotic signals is also promising, and the use of light signal regulation may also improve nitrogen fixation.

In the future, the study can be further deepened to see how symbiotic signals are suppressed under various stresses (such as salt, drought, etc.). Studying GmSK2-8 and its relatives may find new ways to improve nodulation and nitrogen fixation. Flavonoids and other plant signals are also worth careful study in helping Nod factor production and secretion, which may make symbiosis more efficient. The combination of light signals and symbiotic signals is also promising, and the use of light signal regulation may also improve nitrogen fixation.

In general, applying the soybean-rhizobium symbiosis mechanism to global agriculture has the opportunity to significantly increase crop yields and soil health. Based on these new findings, we can breed more stress-resistant and efficient soybean varieties. Through genetic engineering or traditional breeding methods, optimizing the expression of key genes such as GmSK2-8, GmNSP1, and GmVTL1a can allow soybeans to successfully form nodules and fix nitrogen normally under different environments. At the same time, the use of flavonoid treatment and light management technology can further improve symbiotic efficiency and yield. The combination of H₂S and rhizobia provides new ideas for nitrogen utilization and nutrient redistribution, and is particularly suitable for application in soils with low nutrients. Combining these advanced molecular technologies with traditional agricultural methods is expected to create a more robust and high-yield planting system, contributing to global food security and environmental protection.

Acknowledgments

The authors sincerely thanks Dr. Zhang for carefully reviewing the initial draft of the manuscript and providing detailed revision suggestions. The author also extends deep gratitude to the two anonymous peer reviewers for their valuable comments and suggestions on the initial draft of this study.

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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