1 Introduction

The rhizosphere, the narrow region of soil influenced by root secretions and associated soil microorganisms, is a hotspot for microbial activity and interactions. This zone is critical for plant growth and productivity due to the complex microbial communities it harbors, including bacteria, fungi, and archaea. These microorganisms form symbiotic relationships with plant roots, which can be mutualistic, commensal, or pathogenic. For instance, arbuscular mycorrhizal (AM) fungi and rhizobia bacteria are well-known symbionts that enhance nutrient uptake and nitrogen fixation, respectively (Tsiknia et al., 2020; Wang et al., 2020). The dynamic interactions within the rhizosphere are influenced by root exudates, which can shape the microbial community composition and function (Zhalnina et al., 2018). Understanding these interactions is essential for comprehending the ecological and evolutionary processes that govern plant health and soil fertility.

Tree-microbe interactions in the rhizosphere are particularly significant due to their long-term impact on forest ecosystems and their role in carbon sequestration, nutrient cycling, and soil structure maintenance (Bulgarelli et al., 2015; Shi et al., 2016). Trees, with their extensive root systems, interact with a diverse array of microorganisms that can influence their growth, health, and resilience to environmental stresses. For example, the symbiotic relationships between trees and mycorrhizal fungi are crucial for nutrient acquisition and stress tolerance. The microbial communities associated with tree roots can act as a barrier against pathogens, enhancing the tree's immune responses (Li et al., 2021). By studying these interactions, researchers can develop strategies to improve forest management, enhance tree productivity, and mitigate the effects of climate change.

This study will provide a comprehensive overview of the molecular mechanisms and ecological significance of tree-microbiome interactions, analyzing the diversity and functions of microbial communities in the tree rhizosphere. It will explore the molecular codes and signaling pathways involved in tree-microbiome symbiosis and discuss the ecological impacts of these interactions on forest ecosystems, as well as their potential applications in sustainable forestry and agriculture. The study will also highlight recent advances in research methodologies, including omics technologies and bioinformatics tools, which have enhanced our understanding of these complex interactions.

2 Types of Microbial Symbionts in the Rhizosphere

2.1 Mycorrhizal fungi

Mycorrhizal fungi form a symbiotic relationship with plant roots, facilitating nutrient exchange and enhancing plant growth. Arbuscular mycorrhizal (AM) fungi are particularly significant as they help in the uptake of phosphorus and other essential nutrients. These fungi penetrate the root cortical cells, forming arbuscules that increase the surface area for nutrient exchange. The symbiosis between AM fungi and plants is crucial for the assembly of root-associated microbial communities, which in turn promotes the accumulation of beneficial bacteria such as rhizobia in the rhizosphere. This interaction is vital for the overall health and productivity of plants, especially in nutrient-poor soils (Wang et al., 2020).

2.2 Nitrogen-fixing bacteria

Nitrogen-fixing bacteria, such as rhizobia, play a critical role in converting atmospheric nitrogen into a form that plants can utilize. These bacteria form nodules on the roots of leguminous plants, where they fix nitrogen through a symbiotic relationship. The presence of AM fungi can enhance the colonization and effectiveness of rhizobia, leading to improved nitrogen fixation and plant growth. This tripartite interaction between plants, AM fungi, and nitrogen-fixing bacteria is essential for sustainable agriculture and ecological balance (Kour et al., 2019; Hakim et al., 2021).

2.3 Plant growth-promoting rhizobacteria (PGPR)

Plant Growth-Promoting Rhizobacteria (PGPR) are a diverse group of bacteria that colonize the rhizosphere and enhance plant growth through various mechanisms (Kumar et al., 2022). PGPR can be classified into extracellular and intracellular types based on their location relative to the plant roots. They promote plant growth by producing phytohormones, solubilizing phosphorus, and producing siderophores that chelate iron. PGPR can induce systemic resistance in plants, making them more resilient to biotic and abiotic stresses. The use of PGPR in agriculture offers an eco-friendly alternative to chemical fertilizers and pesticides, contributing to sustainable agricultural practices.

3 Molecular Interactions Between Trees and Symbionts

3.1 Signal exchange and recognition

3.1.1 Root exudates as chemical signals

Root exudates play a crucial role in the initial stages of tree-microbe interactions by acting as chemical signals that mediate communication between plant roots and soil microorganisms. These exudates, which include a variety of organic acids, sugars, amino acids, and secondary metabolites, are secreted by plant roots into the rhizosphere. They serve multiple functions, such as altering soil properties, inhibiting the growth of competing plants, and regulating microbial communities (Zhalnina et al., 2018; Handakumbura et al., 2021; Korenblum et al., 2022). For instance, plants like Avena barbata release specific aromatic organic acids that are preferentially consumed by rhizosphere bacteria, thereby shaping the microbial community composition. Root exudates can be modulated by biotic stress, leading to changes in the rhizospheric microbial community that enhance plant stress tolerance (Sharma et al., 2023).

3.1.2 Microbial receptor mechanisms

Microorganisms in the rhizosphere possess specialized receptor mechanisms to detect and respond to the chemical signals emitted by plant roots. These receptors enable microbes to recognize specific compounds in root exudates, facilitating the establishment of symbiotic relationships. For example, rhizobia and arbuscular mycorrhizal (AM) fungi have evolved receptor systems that detect flavonoids and strigolactones, respectively, which are key signals for initiating symbiosis (Rasmann and Turlings, 2016). The ability of microbes to sense and respond to these signals is critical for their colonization and interaction with plant roots, ultimately influencing plant growth and health.

3.1.3 Mutual recognition and binding processes

The mutual recognition and binding processes between trees and their microbial symbionts involve a series of molecular interactions that ensure compatibility and successful symbiosis. These processes often begin with the recognition of root exudates by microbial receptors, followed by the activation of signaling pathways that lead to the expression of symbiosis-related genes. For instance, the establishment of AM symbiosis involves the activation of an ancestral signaling pathway in plants, which is also utilized for legume-rhizobia symbiosis (Figure 1) (Wang et al., 2020). This pathway facilitates the formation of specialized structures, such as arbuscules and nodules, where nutrient exchange occurs. The mutual recognition and binding are essential for the formation of a stable and functional symbiotic relationship.

Figure 1 AM symbiosis is required to assemble a normal root-associated microbiota in native soil (Adopted from Wang et al., 2020)

The study by Wang et al. (2020) demonstrated how arbuscular mycorrhizal (AM) symbiosis promotes the legume-rhizobium symbiosis by regulating the rhizosphere microbial community, and revealed the regulatory role of plant genotype in this symbiotic relationship. This process provides nutrients to the plants and enhances their growth and ecological functions.

3.2 Molecular pathways of symbiosis formation

The formation of symbiotic relationships between trees and microbes involves complex molecular pathways that regulate the development and maintenance of these interactions. These pathways include the perception of microbial signals by plant receptors, the activation of downstream signaling cascades, and the expression of genes involved in symbiosis. For example, the establishment of AM symbiosis requires the activation of a common symbiosis signaling pathway, which involves the perception of fungal signals by plant receptors and the subsequent activation of calcium signaling and transcriptional responses. Similarly, the formation of legume-rhizobia symbiosis involves the recognition of rhizobial Nod factors by plant receptors, leading to the activation of signaling pathways that promote nodule formation and nitrogen fixation (Tsiknia et al., 2020; Wang et al., 2020).

3.3 Genetic basis of symbiotic compatibility

The genetic basis of symbiotic compatibility between trees and their microbial symbionts is determined by the presence of specific genes that regulate the recognition, signaling, and development of symbiotic structures. These genes are often conserved across different plant species and are essential for the establishment of symbiosis. For instance, genes involved in the common symbiosis signaling pathway, such as those encoding receptor-like kinases and calcium-dependent protein kinases, are required for both AM and legume-rhizobia symbioses. Additionally, genetic variation in both plants and microbes can influence the efficiency and stability of symbiotic interactions, highlighting the importance of genetic compatibility for successful symbiosis (Lagunas et al., 2015). Understanding the genetic basis of symbiotic compatibility can inform strategies for improving plant-microbe interactions in agricultural and ecological contexts.

4 Ecological Functions of Symbiotic Microbes

4.1 Nutrient acquisition and recycling

Symbiotic microbes play a crucial role in nutrient acquisition and recycling within the rhizosphere. Mycorrhizal fungi and nitrogen-fixing bacteria are particularly significant in this context. These microbes enhance plant mineral nutrition by converting unavailable nutrients into forms that plants can absorb. For instance, plant growth-promoting rhizobacteria (PGPR) convert essential nutrients like nitrogen, phosphorus, and zinc into available forms, thereby improving soil fertility and plant growth (Jacoby et al., 2017; Huang, 2024). The interaction between soil microbes and plants significantly affects soil microbial structure and function, which in turn influences nutrient cycling and availability (Dou et al., 2023). The presence of these beneficial microbes can reduce the need for synthetic fertilizers, promoting sustainable agricultural practices.

4.2 Enhancing tree resilience to stress

Symbiotic microbes also enhance tree resilience to various biotic and abiotic stresses. Plants under stress conditions, such as drought, tend to assemble beneficial microbes in their rhizosphere to maximize survival and growth. For example, specific bacterial taxa in the root microbiome are associated with increased drought tolerance in plants (Fitzpatrick et al., 2018). Moreover, the rhizosphere microbiome acts as an indirect layer of the plant immune system, providing a barrier against pathogen invasion and inducing systemic resistance. The co-evolution of plants with arbuscular mycorrhizal (AM) fungi and rhizobia further supports plant resilience by promoting nutrient exchange and enhancing microbial community stability in the rhizosphere.

4.3 Role in soil structure and health

Symbiotic microbes contribute significantly to soil structure and health. The activities of PGPR and other beneficial microbes improve soil structure by producing cell lytic enzymes, secondary metabolites, and stress-alleviating compounds (Figure 2) (Hakim et al., 2021). These activities enhance soil aggregation, porosity, and water retention, which are critical for maintaining soil health. The microbial community structure in the rhizosphere influences soil properties and processes, such as carbon biomass and enzyme activity, which are essential for soil fertility and ecosystem stability (Elsheikh et al., 2021). The diversity and composition of microbial communities in the rhizosphere are shaped by plant and soil types, which in turn affect soil health and quality. By promoting beneficial microbial interactions, plants can positively influence soil structure and health, leading to more sustainable and productive ecosystems (López-Lozano et al., 2020).

Figure 2 The benefits of PGPR-mediated rhizosphere engineering to the plant growth (Adopted from Hakim et al., 2021)

5 Case Studies of Tree-Microbe Interactions

5.1 Symbiosis in forest ecosystems

In forest ecosystems, the symbiotic relationships between trees and rhizosphere microbes play a crucial role in nutrient cycling and carbon sequestration. For instance, the interaction between Pinus tabuliformis and Quercus variabilis with their respective rhizosphere microbial communities has been shown to significantly influence soil organic carbon (SOC) sequestration. The bacterial order Rhizobiales and the fungal order Russulales were identified as key taxa driving carbon sequestration in these tree species, respectively. This highlights the importance of specific microbial taxa in enhancing the ecological functions of forest ecosystems (Figure 3) (Song et al., 2020). Arbuscular mycorrhizal (AM) fungi, which form symbiotic relationships with about 80% of terrestrial plant species, are critical for plant growth and stress tolerance. The molecular regulation of AM symbiosis involves complex signaling pathways between the fungi and host plants, which are essential for maintaining forest health and productivity (Ho-Plágaro and García-Garrido, 2022).

Figure 3 Experimental device for sampling (Adopted from Song et al., 2020)

The experimental results indicate that different tree species and their root locations have distinct effects on microbial communities. For example, carbon sequestration in Pinus tabuliformis primarily occurs at the root tips, while in Quercus suber, it is mainly concentrated in the middle part of the roots. These differing strategies may reflect variations in nutrient acquisition and adaptation to different soil conditions. Nitrogen-fixing bacteria in Pinus tabuliformis promote carbon sequestration through nitrogen fixation, whereas Quercus suber relies on fungi from the genus Russula for nutrient exchange. The experimental setup, as shown in the figure, employed stainless steel boxes and mesh screens that allowed soil gases and moisture to pass through while preventing fine soil particles from entering, ensuring interactions between the root system and the surrounding microorganisms. These experimental devices enabled the study to simulate different soil and ecosystem states, observing the succession of rhizosphere microbial communities and their impact on carbon sequestration.

5.2 Rhizosphere interactions in agroforestry

In agroforestry systems, the interactions between legume plants and their microbial symbionts, such as rhizobia and AM fungi, are vital for improving soil fertility and crop yields. Studies have shown that the presence of AM fungi can enhance the accumulation of rhizobia in the rhizosphere, thereby promoting nodulation and nitrogen fixation in legume plants. This synergistic relationship between AM fungi and rhizobia can be leveraged to develop sustainable agricultural practices that reduce the need for chemical fertilizers (Wang et al., 2020). The complex multi-species interactions in the legume rhizosphere, including non-symbiotic microbes, play a significant role in plant growth and performance. Understanding these interactions can inform the development of integrated technologies and strategies for efficient use of beneficial microbes in agroforestry (Tsiknia et al., 2020).

5.3 Unique symbiotic systems in extreme environments

In extreme environments, such as arid zones, the symbiotic interactions between plants and rhizosphere microbes are crucial for plant survival and adaptation. For example, the rhizosphere microbial communities of Agave lechuguilla in the oligotrophic Cuatro Cienegas Basin exhibit significant differences from bulk soil communities. These rhizosphere microbes, which include plant growth-promoting bacteria, help the plant cope with harsh environmental conditions by enhancing nutrient uptake and stress resistance (López-Lozano et al., 2020). Similarly, the invasive tree species Acacia dealbata in South Africa has been found to enrich its rhizosphere with beneficial microbial taxa, particularly Bradyrhizobium species, which play a key role in nitrogen fixation and plant growth promotion. This microbial enrichment likely contributes to the invasiveness and ecological impact of A. dealbata in novel environments (Kamutando et al., 2018).

6 Advances in Molecular Techniques for Studying Symbiosis

6.1 Genomics and metagenomics approaches

Genomics and metagenomics have revolutionized our understanding of microbial symbiosis in the rhizosphere. These techniques allow for the comprehensive analysis of microbial communities and their functional potential. For instance, shotgun DNA sequencing has been employed to investigate the rhizospheric microbiomes of invasive tree species like Acacia dealbata, revealing an enrichment of genes associated with plant growth-promoting traits, particularly those involved in nitrogen metabolism and membrane transport systems (Kamutando et al., 2018). Similarly, metagenomic approaches have been used to study the functional potential of rhizospheric microbiomes in various contexts, including their role in biogeochemical cycling and plant productivity (Kotoky et al., 2018).

6.2 Transcriptomics and proteomics studies

Transcriptomics and proteomics provide insights into the active metabolic pathways and interactions between plants and their microbial symbionts. Metatranscriptomics, for example, has been utilized to profile microbial communities in the rhizosphere, offering a view of the relative abundance and composition of actively transcribed genes. This approach has been instrumental in understanding the molecular interactions that underpin plant-microbe symbiosis and their ecological significance (Bharti et al., 2021). Proteomics, on the other hand, has been used to identify and quantify proteins involved in these interactions, shedding light on the functional roles of different microbial taxa in the rhizosphere (Lagos et al., 2015).

6.3 CRISPR and gene editing technologies

CRISPR and other gene editing technologies have opened new avenues for studying and manipulating microbial symbionts in the rhizosphere. These tools allow for precise modifications of microbial genomes, enabling researchers to dissect the genetic basis of symbiotic traits and their contributions to plant health and productivity. For example, CRISPR has been used to engineer beneficial traits in rhizobial bacteria, enhancing their nitrogen-fixing capabilities and overall fitness in the rhizosphere (Burghardt, 2019). Gene editing technologies hold promise for developing microbial inoculants tailored to specific environmental conditions, thereby improving agricultural sustainability (Balasubramanian et al., 2020).

7 Challenges and Future Perspectives

7.1 Complexity of rhizosphere interactions

The rhizosphere, a dynamic zone of root-soil interactions, is characterized by a complex web of interactions among plants, microbes, and the soil environment. This complexity poses significant challenges in understanding and predicting the outcomes of these interactions. For instance, mutualistic relationships between legumes and their symbionts, such as rhizobia and arbuscular mycorrhizal (AM) fungi, are influenced by a multitude of factors including crop species, genotype, and environmental variables. The intricate network of microbial interactions within the rhizosphere further complicates this scenario, as evidenced by the high network complexity and extensive mutualistic interactions among rhizosphere bacteria (Shi et al., 2016). The presence of other microorganisms can modulate the fitness and symbiotic performance of rhizobia, adding another layer of complexity to these interactions (Agudelo et al., 2023). Understanding these multifaceted interactions requires a holistic approach that considers the overlapping mechanisms and their evolutionary and ecological dynamics.

7.2 Integrating multidisciplinary approaches

To address the challenges posed by the complexity of rhizosphere interactions, integrating multidisciplinary approaches is essential. Advances in molecular and bioinformatics tools have significantly enhanced our understanding of symbiotic interactions in the rhizosphere (Tsiknia et al., 2020). For example, quantitative microbiota profiling (QMP) has revealed how AM symbiosis impacts the assembly of root-associated microbiota and promotes rhizobia accumulation in the rhizosphere (Ganesh et al., 2022). The use of synthetic microbial communities (SynComs) has emerged as a promising strategy to study the outcomes of multiple biotic interactions in a controlled manner. By combining genomic technologies, network analysis, and experimental procedures, researchers can gain a more comprehensive understanding of the molecular pathways and ecological principles governing plant-microbe interactions. This integrated approach can also inform the development of new technologies and practices for improving plant health and productivity.

7.3 Future research directions in tree-microbe symbiosis

Future research in tree-microbe symbiosis should focus on several key areas to advance our understanding and application of these interactions. There is a need to unravel the molecular mechanisms underlying plant-microbe interactions, particularly those involving AM fungi and rhizobia, to facilitate the development of reliable technologies for engineering the rhizosphere (Balasubramanian et al., 2020; Ho-Plágaro and García-Garrido, 2022). Exploring the functional potential of rhizospheric microbiomes, such as those associated with invasive tree species, can provide insights into the roles of specific microbial taxa in promoting plant growth and adaptation to novel environments (Kamutando et al., 2018). Investigating the eco-evolutionary dynamics of rhizobia and other symbionts in complex biotic environments can reveal new aspects of their interactions and inform the development of beneficial inoculants for agricultural applications. Systematic and standardized studies using SynComs can help bridge knowledge gaps and enhance our understanding of the mechanisms governing multiple interactions in the rhizosphere (Marín et al., 2021). By addressing these research directions, we can harness the potential of tree-microbe symbiosis for sustainable agriculture and ecosystem management.

Acknowledgments

We would like to express our gratitude to Dr. K. Jin from Instituteof Life Sciences, Jiyang College, Zhejiang A&F University for her suggestions on this 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.

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