The most prevalent microbial population in soil, soil bacteria, have a major influence on plant health, soil texture, the nutrient cycle, and biodiversity. As seen in Figure 6, they primarily affect soil structure and plant growth in the following ways: (1) By secreting enzymes that convert organic materials into nutrients that plants may use, bacteria take part in the breakdown of organic matter in the soil. For example, different proteases and polysaccharide hydrolases can be released by Bacillus subtilis and Bacillus licheniformis (Bais et al., 2004; Lee et al., 2022). Cellulomonas uda is a wet cellulose bacterium belonging to the Cellulomonas genus that can break down complex macromolecular organic materials into simpler compounds (Pérez-Avalos et al., 2008; Ontañon et al., 2021). Bacteria are also frequently employed to break down organic contaminants in soil. As an instance, phenolic compounds can be broken down by the Flavobacterium genus (Larsbrink et al., 2016), and polycyclic aromatic hydrocarbons (PAHs) can be broken down by the Bacillus and Pseudomonas genera (Saeed et al., 2022). These soil bacteria's decomposition processes contribute to the soil ecosystem's balance, soil environment purification, and soil quality improvement. (2) Soil bacteria aid in the cycling of nutrients, such as potassium, phosphorus, and nitrogen. Bacillus mucilaginosus Krass, for instance, has the ability to break down feldspar and convert potassium components that are insoluble into soluble nutrients (Ahmad et al., 2016; Tallapragada and Matthew, 2021). Some types of soil bacteria, including those genera Erwinia (Kim et al., 1998; Maldonado et al., 2020), Pseudomonas (Alsohim et al., 2014; Oteino et al., 2015; Hamdali et al., 2021), Agrobacterium (Belimov et al., 1999; Yu et al., 2011; Zheleznyakov et al., 2022), and Bacillus (Ramírez and Kloepper, 2010), can change insoluble phosphate into soluble phosphorus that plants can use, which helps plants grow. (3) Beneficial bacteria can form symbiotic relationships with plants, providing nutrients to promote their growth and development. For example, Rhizobium forms symbioses with legume plants, while phosphorus-solubilizing microorganisms form symbioses with plant roots. They change nitrogen and phosphorus that plants can't directly absorb into forms that plants can use for growth through nitrogen fixation (Chabot et al., 1996; Chebotar et al., 2001; Tokala et al., 2002; Tilak et al., 2006; Figueiredo et al., 2008) and phosphorus solubilization actions (Chabot et al., 1993; Purnomo et al., 2005; Badawi, 2010; Turan et al., 2012; Berde et al., 2021; Lelapalli et al., 2021), respectively. (4) Soil bacteria can also suppress pathogens and reduce the occurrence of plant diseases. For example, Streptomyces (Bressan and Figueiredo, 2008; Cordovez et al., 2015; Guo et al., 2020) and Bacillus subtilis (Li et al., 2013; Sidorova et al., 2018) can produce antibiotics to inhibit pathogens. Bacillus can make plants produce antimicrobial peptides, antioxidants, and other chemicals that help plants defend themselves against pathogens and stop their growth (Chakraborty et al., 2006; Ren et al., 2012; Revilla-Guarinos et al., 2014; Ahmed et al., 2022). Rhizobium can make secondary metabolites that can affect plant signaling systems in a direct or indirect way. This can cause plants to make good bacteria and become resistant to disease (Zehnder et al., 2001). Plants can protect themselves and get induced systemic resistance from molecules made by Pseudomonas bacteria. These molecules include salicylic acid and volatile organic compounds (Bigirimana and Höfte, 2002; Pieterse et al., 2003; Siddiqui and Shaukat, 2003). Bacillus (Huang et al., 2014, 2015) and Pseudomonas (Karnwal, 2011) bacteria have been widely used in biocontrol and are known as biocontrol bacteria. (5) Some soil bacteria can produce plant hormones such as indole acetic acid (IAA), gibberellins, and cytokinins. They promote plant growth by influencing physiological processes such as plant growth, flowering, and fruit development. Streptomyces and Micromonospora can produce gibberellins (Bottini et al., 2004), and PGPR-like Bacillus can produce IAA (Pishchik et al., 2002; Zou et al., 2010). Research has shown that Bacillus subtilis WW1211 can promote plant growth by regulating coenzyme biosynthesis and redistribution (Wang et al., 2021b). (6) Soil bacteria can also improve soil structure and texture. Bacteria like Pseudomonas aeruginosa, Bacillus subtilis, and Chromobacterium violaceum can work together to make polysaccharide adhesives that stick to soil particles, help soil aggregates form, improve soil structure, make soil more aerate and hold on to water, and make soil more fertile (Martens and Frankenberger, 1992). In fact, a single soil bacterium can perform multiple functional roles simultaneously. Some examples are Pseudomonas, which can help with nutrient cycling and plant defense mechanisms for biocontrol while also helping plants grow (Jacobson et al., 1994); Streptomyces, which can make antibiotics to stop pathogens; and they produce gibberellins, which can help plants grow (Solá et al., 2021). To sum up, soil bacteria play a collective role in promoting plant growth, shaping soil structure, and participating in ecological processes. Their interactions with plants and other microorganisms have significant impacts on plant and soil ecosystems. The interplay of these mechanisms collectively maintains the balance and stability of ecosystems.

External environmental factors frequently drive the mechanisms by which soil bacteria affect plants and soil. People often use environmental factors to induce bacteria to promote certain ecological processes in order to enhance ecosystem functionality. For example, the cadmium-induced rapeseed Xanthomonas campestris has shown adaptive resistance and cross-resistance to Zn. This characteristic can alleviate the toxicity of Zn in soil to plants, reduce the harm of metal to plants, and maintain the functionality of soil ecosystems (Banjerdkij et al., 2003). In addition, adding bioorganic fertilizers can stimulate the quantity of Pseudomonas in the soil. Pseudomonas can play a role in biological control and enhance the suppression ability of plant diseases (Tao et al., 2020). Another example is that biochar made from tobacco straw can alter the rhizosphere bacterial community, allowing growth-promoting bacteria to flourish and promote cherry growth (Yang et al., 2022). However, remarkably, adding organic fertilizers can also stimulate the growth of pathogenic bacteria (Tariq et al., 2022). Thus, when artificially inducing certain ecological processes, it is important to have a thorough understanding of the types of bacteria involved. Deepening the understanding and research of these mechanisms of soil bacteria can help in artificially regulating ecological processes and applying them to agricultural production. This will better harness the role of bacteria in enhancing ecological functionality and promoting beneficial ecological functions and services for humans.

Although there are some similarities and distinctions, the methods by which soil fungi affect plants and soil are similar to those of bacteria. As seen in Figure 6, they mostly have the following effects on soil and plants: (1) Fungi aid in the breakdown of soil organic matter by reducing complex organic molecules to simpler ones and hastening the organic matter's mineralization process. For example, Paecilomyces lilacinus 112 can secrete hydrolytic enzymes to break down organic matter (Constantin et al., 2022). (2) Soil fungi can convert nutrients such as phosphorus and iron, which plants cannot directly obtain, into available chemical substances (Cao et al., 2015). For example, the Penicillium genus can break down insoluble phosphates (Whitelaw et al., 1999; Wakelin et al., 2006; Gómez-Muñoz et al., 2018; Sang et al., 2022), which boosts crop output. (3) In order to provide plants with nutrients and water, soil fungi establish a mycorrhizal symbiosis with plant roots and mycelial networks are responsible for achieving this symbiotic relationship. Fungi that require organic carbon from plants for energy, which is produced through photosynthesis, such as AMFs, are essential for ecological processes. With 80% of terrestrial plants, AMF can create an arbuscular mycorrhizal symbiosis and help plants grow, take up water and nutrients, and maintain healthy soils by regulating the cycling of nutrients (Lee et al., 2014; Mansur et al., 2019). Through competing for nutrients and space, the mycorrhizal symbiosis between AMF and plant roots can make plants more resistant to disease, fight soil-borne pathogens, make plant communities better able to handle stress from outside sources, and improve plant growth and soil quality. This helps restore ecosystems that can take care of themselves (Barea et al., 2011; Pickett et al., 2022). According to Bianciotto et al. (2018), AMF is a crucial component of ecosystems, and its scarcity or absence can reduce the ecosystems' ability to function as efficiently as possible. Hence, using AMF can recover damaged mining ecosystems, which has been applied extensively (Wang, 2017). (4) Some soil fungi can control diseases by producing antibiotics or metabolites harmful to plant pathogens. For example, the Trichoderma genus releases volatile organic compounds that activate the plant's defense mechanism against powdery mildew (Yao et al., 2016; Lazazzara et al., 2021; Cabral-Miramontes et al., 2022). They protect plant health by competing for nutrients with pathogens or inhibiting their growth. In addition, some soil fungi mediate the production of signaling molecules to activate plant defense responses, induce the plant's immune system, enhance its resistance to pathogens, and reduce the occurrence of diseases. For instance, endophytic insect-pathogenic fungi can affect wheat growth through immune responses and related hormone signaling pathways (González-Guzmán et al., 2022). Trichoderma atroviride is a fungus that lives inside strawberry trees and protects them from plant pathogens by releasing acids that break down cellulase, proteins, and other compounds that kill pathogens (Martins et al., 2022). (5) Most soil rhizosphere fungi can secrete auxins, such as IAA, to promote plant growth. In the Takalar District, 17 different types of fungi were found to produce IAA. These included Trichoderma, Fusarium, Aspergillus, Penicillium, and Gliocladium (Larekeng et al., 2019). Among them, Trichoderma produced the most IAA. In summary, soil fungi play a significant role in providing nutrients to plants, enhancing plant immune systems, decomposing organic matter, and improving soil structure. Through their interactions with plants and other soil microorganisms, they have important effects on plant and soil ecosystems. The synergistic effects of these mechanisms maintain the balance and stability of soil ecosystems.

However, the impact of soil fungi on plants and soil is not always beneficial. Research has shown that parts of fungi are a major source of pathogenic organisms. For example, Fusarium oxysporum, a devastating soil-borne pathogen, is a major source of plant diseases (Rekah et al., 2001; Lisboa et al., 2015; Goncharov et al., 2022). Phytophthora capsici, a polyphagous plant pathogen, can infect dozens of plant species (Saltos et al., 2022). Plectosphaerella melonis, a common pathogen of cucurbits in the United States and Spain, can infect plants such as gourds, peppers, tomatoes, basil, and parsley (Tsekhmister and Kyslynska, 2022). As a result, it is essential to differentiate between beneficial fungi and pathogenic fungi when studying the mechanisms of fungal impact on plants and soil.

Compared to bacteria and fungi, our understanding of archaea is relatively limited, and current research still mainly focuses on isolating and identifying new archaeal taxa. However, existing research has shown that the roots and rhizosphere of plants create both anaerobic and aerobic microhabitats. These areas are perfect for MA and AOA organisms because they help release methane and are involved in the nitrogen cycle (Bomberg and Timonen, 2009; Pump and Conrad, 2014; Moissl-Eichinger et al., 2018). Consequently, as seen in Figure 6, soil archaea also affect plants and soil in different ways: (1) The decomposing activity of archaea can convert organic matter into nutrient substances that plants can absorb and use, promoting soil nutrient cycling. As an example, AOA can break down organic micropollutants in riverbanks, turning them into small molecules that help the cycle of nutrients and affect plant growth (Zhao et al., 2022). (2) Archaea can facilitate the cycling of substances such as nitrogen, phosphorus, sulfur, and carbon, as well as produce Fe carriers, providing the required nutrients for plant growth. For example, AOA changes ammonia into nitrite during aerobic conditions. During anaerobic conditions, they work with nitrite-oxidizing bacteria to reduce nitrite to nitrogen dioxide during denitrification. This changes how nitrogen is changed on Earth, as seen in Figure 7 for the process (Li et al., 2020; Kraft et al., 2022; Martens-Habbena and Qin, 2022). Archaea provide plants with the necessary nitrogen source through nitrification, promoting plant growth and development. Meanwhile, they also reduce nitrogen gas through denitrification, reducing nitrogen elements in ecosystems. These two processes interact with each other, regulating the nitrogen cycling process in ecosystems and maintaining ecosystem stability. For instance, the new DPANN archaea found in hydrothermal vents take in nitrogen and sulfur and break down amino acids and nucleic acids in the environment. This helps the cycling of nitrogen, phosphorus, and other elements (Cai et al., 2021). MA, on the other hand, turns compounds into methane in the absence of oxygen, which helps the cycling of carbon in nature (Evans et al., 2018). Moreover, halophilic archaea exhibit functional characteristics related to phosphorus and iron production, and they may promote plant growth by enhancing the ability of plants to uptake iron (Dave et al., 2006; Al-Mailem et al., 2010). (3) Archaea can produce plant hormones such as IAA, which affect plant growth. For instance, Sulfolobus acidocaldarius, a type of thermophilic microorganism, has been seen to make 1,000 times more IAA than other plant extracts (White, 1987). Additionally, metagenomic analysis of marsh vegetation provides evidence that archaea carry genes for synthesizing auxins, further supporting the notion that archaea can promote plant growth. (4) Archaea activate plant defense mechanisms in multiple ways, enhancing immune responses and protecting vegetation health. For example, archaeal volatile organic compounds (VOCs) can induce resistance in plants. According to research by Ryu et al. (2003) and Song et al. (2019), Nitrosocosmicus oleophilus MY3 produces VOCs that aid in the growth of Arabidopsis thaliana. This suggests that the mechanisms by which archaea promote plant growth may be similar to those of PGPR. Also, archaea can talk to bacteria through intercellular signaling, and they do this by making chemicals like N-acyl-L-homoserine lactones, which affect plant growth and make plants defend themselves (Gao et al., 2019). Besides, archaea can help plants adapt to abiotic stress environments. Some Euryarchaeota genus members, like Methanosarcina, can stabilize the harmful metal mercury (Hg), which means that plants can still grow even when heavy metals are present (Ma et al., 2019; Zhang and Wang, 2020); Halophilic archaea can alleviate salinity, enhance crop tolerance, promote plant growth, and reduce the impact of environmental stress (Naitam et al., 2023). In general, soil archaea have big effects on plant growth and soil quality. They do this by breaking down organic matter, nitrifying and denitrifying, making plant hormones, and starting up plant defense systems. They play crucial roles in soil ecosystems, maintaining soil health and plant-soil ecosystem stability.

Microorganisms can be used to purify soil contaminated with heavy metals and organic compounds through their processes of dissolution and degradation, which improves soil quality and promotes ecosystem functionality to restore damaged ecosystems and a clean soil environment. For instance, functional bacterial strains can remediate contaminated soil. Researchers have found that the bacteria Paracoccus aminovorans HPD-2 and Azotobacter chroococcum HN can break down PAHs into smaller inorganic compounds, which lowers the amount of organic pollution in the soil (Wang et al., 2023). Haloarchaea colonized in the rhizosphere of halophytes, in cooperation with other rhizobacteria, can effectively degrade crude oil. Utilizing these rhizosphere microbial mechanisms can remediate oil-contaminated, high-salt environments. Additionally, some good bacteria and fungi can help plants fight off pathogens, lessen the damage that metals do to plants, increase the production of hormones and enzymes that help plants grow, and work with plants to clean up polluted soils (Ma et al., 2016). As an example, gene expression is changed by plant growth-promoting bacteria (PGPB) such as Bacillus paranthracis NT1 and Bacillus megaterium NCT-2 to help Solanum nigrum L. get rid of cadmium (Cd), making Cd less harmful to plants and opening the door for PGPB and plants to work together to clean up heavy metal-contaminated soils (Chi et al., 2022). AMF that lives in harmony with plants can stop uranium from moving through soils and plant roots, which stops uranium from moving from roots to shoots and effectively cleans up soils that are contaminated with this metal (Fomina et al., 2020; Wang et al., 2022a). Some types of Brevibacillus can make IAA, which, along with AMF, pulls Zn out of the growth medium. This makes Zn-contaminated soils less toxic and helps plants grow (Vivas et al., 2006a,b). Through various mechanisms, these microorganisms efficiently remediate contaminated soils in an environmentally friendly manner, greatly benefiting ecosystem functionality.

In agricultural production, based on the principle of microorganisms promoting plant growth, beneficial microorganisms can be cultured in vitro and made into biological fertilizers and microbial agents, which can be applied to improve crop yield, promote local ecosystem functions when needed, and assist in the restoration and rebuilding of ecosystems. For instance, some beneficial microorganisms can be used to produce biological fertilizers: nitrogen-fixing bacteria can convert atmospheric N₂ into NH₃ that can be utilized by plants, reducing the use of nitrogen fertilizers in agriculture (Shantharam and Mattoo, 1997; Urquiaga et al., 2012; Smercina et al., 2019; Hu et al., 2021); Bacillus subtilis N11 with strong plant colonization ability can effectively control banana wilt disease and serve as a new type of bio-organic fertilizer (Zhang et al., 2011); Rhizobium and Pseudomonads genera can be used as natural biological fertilizers to promote plant growth (Liu et al., 2020b); Beneficial microorganisms can also be selected and cultured in vitro to produce functional strains that can be expanded for use as microbial agents. Microbes like the members of Bacillus genus and nitrogen-fixing bacteria can help woody cuttings stay alive and grow in nurseries. They can also help them avoid pathogens and encourage lateral branching (Plugatar et al., 2019). Penicillium can break down phosphates, make gibberellins and plant growth regulators to help plants grow, and be used as a bio-inoculant to boost crop yield (Nunes et al., 2022). Some non-pathogenic fungi can also be made from nanoparticles that can effectively control plant diseases, kill bacteria, and lower the toxic effects of metals in the soil. These nanoparticles are commonly used in agriculture as nano-insecticides, nano-fungicides, and nano-herbicides (Alghuthaymi et al., 2015; Cao et al., 2020). However, as certain organic fertilizers can also promote the growth of pathogenic fungi, caution should be exercised when using biofertilizers (Tariq et al., 2022). This method should only be employed properly and efficiently after a thorough understanding of the characteristics and processes of microorganisms.

Utilizing the characteristics and mechanisms of microorganisms, we can produce pesticides and eliminate nitrogen and phosphorus, which not only maintains the health of vegetation and enhances vegetation productivity but also environmentally and economically purifies the environment, effectively maintaining the stability of the ecosystem. Some strains from the genera Pseudomonas, Bacillus, and Trichoderma have been good at controlling various fungal diseases to reduce the damage that pathogens cause to plants. For example, (a) Arabidopsis thaliana plants that are colonized with Pseudomonas fluorescens are protected from pathogen invasion (Wang et al., 2022b); (b) Bacillus amyloliquefaciens hmb33604 is resistant to potato late blight (Fan et al., 2021); (c) the strain of Trichoderma genus LZ42 releases volatile organic compounds that inhibit tomato seedling wilt (Rao et al., 2022). Additionally, the antagonistic interactions between different microbial species can also suppress the growth of pathogens. For example, the antagonistic effect between Streptomyces violaceus G10 and Fusarium oxysporum effectively controls plant diseases (Getha and Vikineswary, 2002); the combination of Penicillium and Bacillus genera can antagonize the infection of Fusarium oxysporum in banana plants (Win et al., 2021). These beneficial microorganisms can be formulated into biological pesticides for the biocontrol of plant diseases, reducing the likelihood of vegetation being infected by pathogens. In terms of eliminating nitrogen and phosphorus elements, microorganisms can reduce environmental pollution (such as water eutrophication) through degradation and participation in element cycling, which indirectly promotes plant growth and maintains the stability of the ecosystem. For instance, AOA nitrification and denitrification processes reduce wastewater nitrogen levels, which aids in the resolution of water pollution issues (Yang et al., 2021). According to Kurt et al. (2017), this technique has also been applied to clean industrial wastewater and encourage the sustainable use of water resources. However, due to their slow growth and sensitivity to their surroundings, AOA can only survive in environments with high levels of ammonia and nitrogen, which indicates that further investigation and study are required (Hu et al., 2023). Under aerobic circumstances, biological phosphorus removal can be accomplished via the physical adsorption and precipitation of microorganisms (Massoompour et al., 2022). Based on the above content, the principles of microorganisms provide us with an effective way to maintain ecosystem stability and environmental cleanliness.