Soil Microbiome: Diversity, Benefits and Interactions with Plants

Abstract

Plant roots aid the growth and functions of several kinds of microorganisms such as plant growth-promoting rhizobacteria, mycorrhizal fungi, endophytic bacteria, actinomycetes, nematodes, protozoans which may impart significant impacts on plant health and growth. Plant soil–microbe interaction is an intricate, continuous, and dynamic process that occurs in a distinct zone known as the rhizosphere. Plants interact with these soil microbes in a variety of ways, including competitive, exploitative, neutral, commensal, and symbiotic relationships. Both plant and soil types were found to have an impact on the community diversity and structure of the rhizosphere, or vice versa. The diversity of microorganisms in soil is thought to be essential for the management of soil health and quality because it has different plant growth-promoting or biocontrol effects that could be very advantageous for the host plant and alter plant physiology and nutrition. The composition of microbial community is influenced by soil and plant type. Besides these beneficial microbes, the soil also harbors microorganisms that are detrimental to plants, competing for nutrients and space, and causing diseases. Numerous microorganisms have antagonistic activity and the ability to defend plants from soil-borne diseases. The study of the soil microbiome is essential for formulating strategies for transforming the rhizosphere to the benefit of the plants. This review pays special emphasis on the types of microbial populations in the soil and how they influence plant growth, nutrient acquisition, inter-relationships between soil microbes and plants, stress resistance, carbon sequestration, and phytoremediation.

1. Introduction

The environmental conditions in soil are dynamic and constantly changing. Due to the diverse nutrients and vital components in humus, the soil is home to a variety of microorganisms. Fungi, bacteria, viruses, actinomycetes, blue-green algae, protozoa, etc., are among the many soil microorganisms present in the rhizosphere. These microorganisms provide a number of functions, including the biodegradation of contaminants, preservation of soil structure, and circulation of biogenic elements that supply nutrients to plants. The rhizosphere is the region of soil around the roots of plants where the properties of soil are affected by the activities of the root. The conservation of biological diversity and ecosystems depends greatly on microbial diversity. Plant–microbial interactions are essential for ecosystem functioning. In addition to helping a plant embed in the ground, absorb water and ions, store nutrients, the root system interacts closely with a range of soil microbial populations [1]. Microbial interactions with roots can be symbiotic, associative, or serendipitous in nature and can involve endophytic or free-living microorganisms. Symbiotic associations include diazotrophs with legumes and mycorrhizal fungi. Interactions between soil microorganisms and roots have profound implications for nutrition and growth [2]. Lorenz Hiltner first introduced the term “rhizosphere”, and he has referred to it as a microenvironment in which the bacteria that thrive there (bacteriorhiza) can engage and have a substantial impact on plant nutrition [3]. Moreover, Hiltner proposed that “the composition of the rhizosphere microbiota relies on the resilience of plants against disease” [4]. In comparison to the bulk soil, the rhizosphere typically exhibits higher levels of bacterial activity, diversity, and abundance [5]. This is due to the fact that root exudates contain a wide range of phenolic chemicals, organic acids, amino acids, sugar and other small molecules that act as chemo-attractants, which attract and favor the formation of plant-specific microbiota [6,7,8,9]. Depending on the type of plant species, roots produce specific chemical compositions of exudates to attract particular microbial communities [10,11]. The rhizosphere is influenced by these root exudates by altering how the soil’s biochemistry is made up and also providing a suitable environment for the growth of specific soil microorganisms [12]. These compounds include organic acids, sugars, amino acids, polyphenols, flavonoids, hormones, and nutrients that serve as sources of food for the microorganisms around the roots [13]. Compounds released in root exudates are carbohydrates, amino acids, organic acids, flavonols, sugars, lignins, coumarins, anthocyanins, fatty acids, proteins, enzymes, indole compounds, glucosinolates, allomones and aurones. It is generally recognized that the primary method by which plant roots produce compounds is a passive process mediated by three distinct pathways: diffusion, ion channels, and vesicle transport. Small polar and uncharged molecules are transported through lipid membranes’ permeability through diffusion. Compounds like sugars, amino acids, and carboxylate anions are transported across membranes with the help of proteins; their direction of movement is determined by the electrochemical gradient that allows them to pass from the cytoplasm of intact root cells [14]. Different plant species, associated genotypes, and elements of root exudates have an impact on the structure and organization of the rhizospheric microbiome [15,16]. The particular selection of rhizospheric microbial populations may be seen in plant-specific root exudates for example the cucumber plant secretes citric acids from its roots, which influenced the attraction of Bacillus amyloliquefaciens, and the banana plant secreted fumaric acid from its roots, which attracted Bacillus subtilis towards roots and resulted in the formation of biofilms [17].

Numerous microbial species that serve a variety of purposes and affect plant growth can be found in the rhizosphere. They assist in the cycling of nutrients, protecting plants against biotic and abiotic stressors, and some can even function as phytopathogens [18]. Along with increasing the availability of nutrients for the roots, rhizosphere bacteria may also increase plant growth by producing phytohormones, which promote plant tolerance to biotic and abiotic stressors [19] by producing osmo-protective substances in the cytoplasm under saline stress conditions, such as trehalose, exopolysaccharides, proline, quaternary ammonium compounds and volatile organic molecules [20,21]. Soil salinity affects plant growth and yield, causes an imbalance in soil nutrients, reduces nutrient uptake, and raises negative osmotic pressure on plant cells [22].

Numerous studies have revealed that soil microorganisms, including endophytic and rhizospheric bacteria, encourage plant growth and survival in abiotic stress conditions [23]. Potential benefits of endophytes and aboveground microbiota include enhanced disease resistance, reduced stress, and stimulation of plant development [24]. Utilizing beneficial microbes has become more popular in place of synthetic and chemically based insecticides and fertilizers [25]. Protection against diseases is aided by the inoculation of seeds with beneficial microbes with the ability to colonize roots [26]. Beneficial microbes can indirectly alleviate plant nutrient deficiency stress by increasing antioxidant enzyme activity, protecting plants from stress-induced ROS accumulation [27]. Overall, soil microbes play a crucial role in mitigating the negative effects of abiotic stresses on plants by improving soil structure, enhancing nutrient availability, producing growth-promoting substances, and inducing systemic resistance, soil microbes can help plants better tolerate water scarcity and maintain their productivity under drought conditions. In this review, we have compiled the various benefits of soil microbiota on plants such as how soil microbes help in the growth and development of plants through phytohormone production, help in the uptake of nutrients, and mutual symbiotic associations of mycorrhizae. The diversity of soil microbes in the rhizosphere plant growth-promoting bacteria, fungi, endophytes and various types of positive and negative interactions between plants and soil microbes is discussed. The role of soil microbiota in macro and micronutrient uptake, carbon sequestration to increase soil organic carbon, phytoremediation, and the interaction of biochar with microbes is highlighted. This review also emphasizes how soil microbes play a role in biotic and abiotic stress resistance in plants.

2. Diversity of Soil Microbes in Rhizosphere

Soil harbors a diversity of microbes such as plant growth-promoting bacteria, endophytes, fungi, actinomycetes, protozoans, etc. (Figure 1).

2.1. Plant Growth-Promoting (Rhizo)Bacteria (PGPR or PGPB)

In 1978, Kloepper came to coin the term “plant growth-promoting rhizobacteria” (PGPR) [28]. PGPR or PGPB are a significant group of beneficial, root-colonizing bacteria thriving in the plant rhizosphere. PGPBs are described as symbiotic or free-living bacteria in soil that can effectively inhabit the roots and have advantageous effects on the host plant. Rhizospheric bacteria, which are often found around plant roots, and endophytic bacteria both have been shown to have the ability to act as PGPBs [29]. The key difference is that once established within the tissues of the host plant, endophytic PGPB are no longer susceptible to the whims of shifting soil conditions [29]. Temperature, soil pH, moisture content, and the population of soil bacteria that may compete for binding sites on the host plant’s root surface are among the changing conditions that may hinder the function and growth of rhizospheric PGPB [30].

Rhizobacteria that encourage plant growth can be categorized as extracellular plant growth-promoting rhizobacteria (ePGPR) that reside in the rhizosphere, or in intercellular spaces in the root cortex, and the intracellular plant growth-promoting rhizobacteria (iPGPR) that exist inside the root cells [31]. It is estimated that ~2–5% of rhizobacteria act as PGPR [32]. They are a useful group of rhizosphere microorganisms that can assist plant development through a variety of mechanisms which includes synthesis of ACC (1-aminocyclopropane-1-carboxylate) deaminase, nutrient uptake, increased root volume, phytohormone synthesis, siderophore synthesis, biological N₂ fixation, phosphorous solubilization, and the introduction of systemic tolerance genes, accumulation of stress-related metabolites like glycine betaine, poly-sugars, proline, various volatile organic compounds (VOC), upregulation of antioxidants enzymes as catalase (CAT), ascorbate peroxidase (APX), superoxide dismutase (SOD), glutathione (GSH), ascorbic acid (AsA), glutathione reductase (GR) and α-tocopherol [33,34,35,36].

The major taxonomic groups of PGPB belong to Proteobacteria and Firmicutes [37,38]. The most explored genera of Firmicutes and Proteobacteria for promoting plant development are Bacillus and Pseudomonas, respectively. Strains ascribed to the genera Rhizobium, Achromobacter, Azospirillum, Azotobacter, Pseudomonas, Burkholderia, Acinetobacter, Serratia, Enterobacter, Pantoea and Rahnella are the major representative’s genera of the phylum Proteobacteria [39,40,41]. Strains ascribed to the genera Staphylococcus, Oceanobacillus, and Paenibacillus are the major representative genera of the phylum Firmicutes [41]. PGPR also interact with other microorganisms such as arbuscular mycorrhizal fungi, to support plant growth [42]. Bacillus and Pseudomonas species are widely investigated PGPRs [43]. Rhizobacteria from certain genera are the most efficient Arthrobacter, Azospirillum, Alcaligenes, Bacillus, Azotobacter, Bradyrhizobium, Burkholderia, Flavobacterium, Serratia, Enterobacter, Streptomyces, Pseudomonas, Rhodococcus, Mesorhizobium, Klebsiella, etc. [44]. Symbiotic nitrogen-fixing rhizobia are classified into 36 species distributed among seven genera (Allorhizobium, Bradyrhizobium, Azorhizobium, Mesorhizobium, Rhizobium, Methylobacteriu, and Sinorhizobium) [45]. Some important non-symbiotic nitrogen-fixing bacteria include Achromobacter, Alcaligenes, Acetobacter, Arthrobacter, Azospirillum, Azomonas, Azotobacter, Beijerinckia, Bacillus, Clostridium, Derxia, Corynebacterium, Enterobacter, Klebsiella, Herbaspirillum, Rhodopseudomonas, Pseudomonas, Rhodospirillum, and Xanthobacter [46].

2.2. Fungi

Fungi are eukaryotic, heterotrophic organisms that help in nutrient cycling, decomposition of debris, increase nutrient availability in soil and helps in plant growth [47].

Mycorrhiza

Mycorrhizae are fungi that grow in symbiotic association with plant roots. Mycorrhizal fungi can be found living within the cortex of a plant’s root, on the surface of the root, or surrounding the root’s epidermal cells. These fungi’s roots produce hyphae that spread out into the soil, where they scavenge for minerals that promote plant growth, particularly phosphates and nitrates. On the basis of structure and function, four main mycorrhizal types have been described namely Ectomycorrhizae, Endomycorrhizae, Ericoid and Orchidaceous types [48]. The term “arbuscular mycorrhiza” (AM) refers to a particular kind of mycorrhiza in which the symbiotic fungus enters the cortical cells of the roots of vascular plants to create arbuscules.

A type of symbiotic association known as an ectomycorrhiza develops between the roots of different plant species and a fungal symbiont, or mycobiont. The Hartig net forms when hyphae (typically coming from the inner region of the mantle enclosing it) infiltrate the root of the plant host. In order to create a network connecting the outer cells of the root axis, the hyphae penetrate and develop in a transverse direction to the axis of the root [49]. The area where the fungus and root cells connect is where the exchange of nutrients and carbon takes place [50]. These associations are exceedingly prevalent in the plant kingdom. According to studies, fungus from the Glomeromycota group form AMs with 74% of all plant species, orchid mycorrhizae are present in 9% of plants, 8% of plants are entirely non-mycorrhizal, 7% have inconsistent non-mycorrhizal and mycorrhizal interactions, 2% form EM (Ectomycorrhizas) associations and 1% of plants form ericoid mycorrhizas [51,52]. Ectomycorrhizas associations are the most commonly found in, Pinaceae, Fagaceae, Betulaceae, Salicaceae, Junglandaceae, Myrtaceae, and Ericaceae. The majority of mycorrhizal fungi belong to ascomycetes and basidiomycetes [53].

2.3. Plant Growth-Promoting Fungi (PGPF) in Soil

Rhizosphere fungi are plant-associated fungi that utilize nutrients produced by a host plant to establish plant rhizospheric fungal interactions that are essential to the growth of healthy ecosystems and the sustainability of the environment [54]. Many PGPF species such as Trichoderma, Fusarium, Talaromyces, Phytophthora and Penicillium, are known to enhance plant growth, their innate immunity and some important secondary metabolites [55]. PGPF can both promote systemic resistance and act as a biocontrol agent against phytopathogens. The mineralization of the major and minor elements necessary to sustain plant development and production is the possible mechanism of action for PGPF. Additionally, PGPF creates defense-related enzymes, induced resistance, and phytohormones to prevent or stop the invasion of harmful bacteria, or in other words, to support plants under stress [56].

2.4. Endophytes

A group of microorganisms that dwell inside the tissues of plants and have “closer” interactions with them without harming them are known as endophytes. The wide majority of plants include endophytes [57]; in fact, every plant species that has been examined is known to house microbial endophytes. An endophyte-free plant is extremely uncommon in nature [58]. Broadly, the endophytes can be grouped into systemic and non-systemic. Non-systemic endophytes are facultative and transient, and their population size and species richness change with time. Under difficult environmental conditions, they can also switch between mutualism to parasitism. Conversely, mutualist systemic endophytes have closely developed with the plant host [59]. Endophytes perform diverse functions in the host plant including nutrient acquisition, phytohormone and siderophore production, protection from abiotic stresses and biotic [60].

2.4.1. Fungal Endophytes

Numerous fungi colonize the roots of plants including endophytic and mycorrhizal fungi. The fungal endophytic relationships unlike mycorrhizal symbioses lack specialized structures for nutrient exchange, synchronized development, and substantial advantages for both individuals [61]. The most well-known members of the wide group of fungi that make up root-endophyte interactions are the dark septate endophytes. Endophytes can infiltrate and colonize host plant tissues either through vertical seeding or horizontal transfer. The recognition and attraction of endophytes by the host plant are mediated by chemical signals such as root exudates and signaling molecules. Endophytes employ various strategies such as motility and cell wall degradation to actively colonize plant tissues and also modulate plant physiology and biochemistry to their advantage. Once inside the plant, endophytes can produce compounds that stimulate plant development and aid plants in coping with stress [62]. The influence of fungal root endophyte colonization shows a full spectrum of variation from harmful to beneficial [63]. Numerous host plants have been reported to naturally comprise fungus endophytes [64]. Basidiomycetes groups were found to be the most dominant endophytes among fungi. While some blatantly benefit the host plants, others might impair plant performance [65,66]. The degree to which the roots have been colonized by fungi may differ, indicating the adaptability of both the individual fungi and the endophytes as a whole. Colonization is frequently extensive, inter- or intracellular, and occasionally restricted to the cortex or epidermis [67]. The common genera of endophytic fungi include Aspergillus, Chaetomium, Bipolaris, Cladosporium, Fusarium, Diaporthe, Alternaria, Mucor, etc.

2.4.2. Bacterial Endophytes

Rhizobacteria are known as endophytic bacteria that colonize their host plant [68]. The most prevalent bacterial endophyte genera include Pseudomonas, Burkholderia, Bacillus, Micrococcus, Stenotrophomonas, Pantoea, and Microbacterium [69]. Taxonomically, they are classified into 16 phyla with more than 200 taxa. The majority of them belong to the three phyla: Actinobacteria, Proteobacteria and Firmicutes [70]. Through interactions with other bacteria, some endophytic bacteria, such as nitrogen-fixing rhizobia, increase the positive effects of other beneficial bacteria. Under both normal and stressful conditions, bacterial endophytes directly benefit plants by aiding them in acquiring nutrients and promoting growth by modulating growth hormones [71]. They can also indirectly promote plant growth by antagonizing phytopathogens or enhancing plant defensive response by producing siderophores, chitinases, and proteases [72,73]. When compared to many rhizospheric bacteria, endophytic bacteria typically have stronger positive effects on host plants as residing inside plant tissues allows them to be in close contact with the host plants to readily exchange nutrients [74].

3. Rhizosphere as the Hotspot for Plant–Microbe Interaction

The interactions between plants and microbes are universal and are crucial for the health of both the partners as well as soil. It is a complex process in which the plants interact with diverse heterotrophic microorganisms and can share an intimate relationship from symbiosis to parasitism. The rhizosphere, the area adjoining the plant roots, is a microenvironment where key plant–soil–microbe interactions take place between plant roots and soil-microorganisms in a variety of ways that can be beneficial, harmful, or neutral [75]. It is richer in microbes than the surrounding soil, perhaps one of the ecosystems with the highest levels of biodiversity on the planet [76], with 10 to 100 times more microbes than the bulk soil [77] that contain up to 1011 microbial cells per gram root [78]. Plant-associated microbes are referred to as the second genome of the plant [79]. More than 80% of interactions in the rhizosphere are positive, indicating that the rhizosphere has a greater potential for mutualistic associations [80]. The activities like respiration, gas exchange, nutrient and water uptake are concentrated in the rhizosphere, as labile carbon and other nutrients are localized here [81]. The distinct characteristics of the rhizosphere are primarily caused by rhizodeposition, which refers to the process by which plant roots release various organic compounds such as sugars, amino acids, organic acids, polysaccharides, vitamins, and secondary metabolites into the soil surrounding the roots [82]. The microbial communities that grow by utilizing these root exudates form a niche for themselves thereby helping in recruiting other microbes and creating a new niche for themselves [83]. The root exudates, especially low molecular weight molecules, are used as substrates for energy requirements by microbes of the rhizosphere, which causes enhancement of microbial activity and biomass [82,84].

4. Types of Interactions

Understanding plant–microbe interactions is critical in recognizing the effects microbes impart on plants and vice versa. Different types of plant–microbe interactions in the rhizosphere are illustrated in Figure 2.

4.1. Beneficial Plant–Microbe Interactions

4.1.1. Legume-Rhizobia Symbiosis

Plant–rhizobia endosymbiotic interactions occur when leguminous plants develop specialized root nodules that house the rhizobia, the most common Gram-negative alpha-proteobacteria [85]. Rhizobia and legume roots have a symbiotic association that fixes atmospheric nitrogen by the activity of nitrogenase [86]. Rhizobia include several genera, which include Rhizobium, Azorhizobium, Mesorhizobium, Bradyrhizobium, Ensifer, etc. [87]. The nodules are very complex structures, where a number of processes operate and interplay at different stages. When compatible microorganisms in the soil recognize plant signals, the process of nodule formation begins. After this, Nod factors are produced, which sets off a gene cascade that causes bacterial infection and cell division. Bacteria migrate from the nodule primordium to the root hair cells through an infection thread, where they develop into bacteroids that fix atmospheric nitrogen [88]. A symbiosome membrane that encloses the bacteroids creates a microaerobic environment for nitrogen fixation [89,90]. Rhizobia also exhibit endosymbiotic association with non-leguminous plant Parasponia [91].

4.1.2. Actinobacteria-Actinorhizal Plants Symbiosis

Plants that establish nitrogen-fixing root nodule symbiosis with the actinobacteria are known as actinorhizal. It is well documented that Actinomycetes such as Frankia sp. associate with a wide range of actinorhizal plants [92]. Actinorhizal plants include over 200 species belonging to 24 genera and 8 families (Casuarinaceae, Betulaceae, Myricaceae, Elaeagnaceae, Coriariaceae, Rhamnaceae, Datiscaceae and Rosaceae) [93]. Frankia infects actinorhizal plants either intracellularly via root hair penetration or intercellular penetration [94]. The Actinobacteria-actinorhizal plants’ symbiosis led to the formation of actinorhizal nodules, where the bacteria are hosted intracellularly and perform atmospheric nitrogen fixation. The root exudates released by the host plant increase the growth of Frankia and favor the infection and nodulation process [95]. On the basis of physiological and structural differences between actinorhizal and legume root nodules, actinorhizal symbioses appear to be less developed and less effective in nitrogen fixation than legume–rhizobia symbioses [89]. Actinorhizal nodules are modified lateral roots with a central vascular system, as opposed to legume nodules, which are stem-like organs with peripheral vascular systems [96].

4.1.3. Cyanobacteria–Plant Symbiosis

Even though cyanobacteria are widespread, very few of them establish symbiotic associations with eukaryote hosts. By far, the genus Nostoc of cyanobacteria is the most commonly seen in association with land plants [97]. Cyanobacteria are known to colonize different plant organs, either intracellularly as in Angiosperms or extracellularly as in Gymnosperms, Pteridophytes and Bryophytes [92].

Bryophytes, which include mosses, hornworts and liverworts, get infected with heterocystous cyanobacteria [98]. The cyanobacteria associated with moss are mostly epiphytic [99]. All hornworts have endophytic cyanobacterial symbioses [100], whereas only two liverwort genera exhibit this symbiotic relationship [101]. The majority of plant–cyanobacteria symbioses are facultative, meaning that either partner can be cultured alone; nonetheless, plants in the wild almost always form symbiotic relationships with cyanobacteria [97]. The sole instance of a cyanobacteria–plant symbiosis where the cyanobiont is constantly linked with the host and passed down from generation to generation is the pteridophyte Azolla. The transmission of the cyanobacteria to the offspring of both asexual and sexual reproduction maintains the link between Azolla and its cyanobiont [102]. In gymnosperms, cycads develop coralloid roots that become infected with heterocystous cyanobacteria, mostly belonging to the genus Nostoc; however, Calothrix spp. have occasionally been noted [103]. Between the inner and outer cortical layers, there is a mucilage-filled region where the cyanobionts reside. The infection by cyanobacteria causes morphological changes that increase the area of contact between plant cells and the cyanobiont to improve the exchange of nutrients [104]. The only known symbiosis between angiosperms and cyanobacteria is the Gunnera-Nostoc symbiosis. This is a true endosymbiosis, where the Nostoc cells are found between the host cell wall and the plasmalemma [97]. Cyanobacteria enter Gunnera plants through specialized stem glands located at the base of each leaf stem. The mucilage produced by these glands contains chemical signals that encourage the formation of hormogonia, which are attracted to the plant through chemotaxis. Once inside the Gunnera cells, the cyanobacteria occupy the spaces between the plasmalemma and cell wall, forming a symbiotic interface where nutrient exchange occurs between the partners [98,105].

4.1.4. Mycorrhizal Associations

In mycorrhizae, hyphae spread out from the root into the surrounding soil, significantly increasing the surface area for nutrient and water absorption. The fungus receives sugars from the plant in exchange for mobilizing the nutrients into the plant, creating a mutually beneficial relationship [106]. Based on their interactions and location in plant roots, mycorrhiza can be grouped into ecto- and endomycorrhizae.

Endomycorrhizae, also called arbuscular mycorrhizae (AM), is one of the oldest and most widespread associations between plant roots and fungi. In this, the fungal partner is always a member of the Glomeromycota. AM Fungi have developed an efficient way to obtain inorganic nutrients from soil, but they are unable to grow independently of their hosts. Nutrient exchange takes place in highly branched hyphae called arbuscules, which penetrate into the cortical cells. Approximately 70–80% of all vascular plant species harbor in their roots a multifunctional symbiosis with AM fungi. AM fungi are reported to have synergistic interactions with soil microorganisms like nitrogen fixers, phosphate solubilizers and other PGPRs [107,108].

In ectomycorrhizae, the fungus, usually a member of Basidiomycota or sometimes an Ascomycota, forms a sheath (mantle) outside the root. The exchange of nutrients takes place through the Hartig net, which is an intercellular network of hyphae in the root cortex, but fungal hyphae do not penetrate the cells. These dual soil–plant inhabitants are efficient at deriving nutrients saprotrophically from soil organic matter, where they live transitorily, and biotrophically from plants, during mutualistic interactions. These fungi are effective at obtaining nutrients both biotrophically from plants during mutualistic interactions and saprotrophically from soil organic materials, where they live transitorily [109].

4.2. Harmful Interactions

4.2.1. Plant–Pathogen Interaction

There are four main groups of plant pathogens: fungi, nematodes, bacteria, and viruses [110]; among these, fungi and nematodes are the major phytopathogens [19]. Similar to plant–fungal mutualistic interactions, pathogens also utilize chemical signals in the early steps of host recognition and infection. Phytohormone signaling, pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI), and effector-triggered immunity (ETI), are three ways that the plant combats these infections [111]. Based on their modes of nutrition, the phytopathogens can be broadly divided into two groups, necrotrophs and biotrophs. Although, limiting the nutrition supply, biotrophs maintain the host’s vitality, and harm the host very little. Whereas necrotrophs use a variety of virulence tactics to kill host plant cells and absorb their nutrients for growth and reproduction [112].

Fungi pose the biggest threat to the health of plants of all the plant–pathogenic microbes. Only a small number of soil pathogenic fungi are biotrophic, and the majority are necrotrophic [113]. These exist in soil as chlamydospores, oospores, microsclerotia, or sclerotia [114]. In addition to various pathogen effector molecules, fungi also release enzymes that break down cell walls, and toxic secondary metabolites to speed up the infection process [115].

4.2.2. Antimicrobial Root Exudates

Plant root exudates function as antimicrobials to fight off pathogens in the rhizosphere by enlisting beneficial bacteria strains or suppressing harmful microbial strains. A variety of secondary metabolites found in plant root exudates aid plants in their defense against microbial diseases [116]. The root exudates showing antimicrobial properties include indole, benzoxazinone, terpenoids, flavonoids, phenolics and isoflavonoids [117]. Jasmonic acid, jasmonates, salicylic acid and abscisic acid signaling networks play a vital role in controlling plant defense responses against pathogens and pests [118]. The protein composition in rhizosphere changes in response to pathogenic interactions as antimicrobial chemicals build up in the rhizosphere [119]. The rhizobiome aids in suppression of disease as beneficial and pathogenic microbes fiercely compete for available nutrients [120]. Overall, antimicrobial root exudates are an important defense mechanism for plants, helping to protect them from soil-borne pathogens and maintaining the health of the soil microbiome.

5. Role of Soil Microbes on Plant Growth

Soil microorganisms play a role in promoting plant growth through both direct and indirect means (Figure 3). Within a plant-soil subsystem, plants play a crucial role by acting as primary energy sources. They provide nutrients and carbon through root exudates and litter deposits, nourishing the heterotrophic microbial communities [121]. However, various biotic (related to living organisms) and abiotic (related to non-living factors) stresses can hinder plant growth. Under biotic and abiotic stress conditions, microorganisms have the ability to stimulate the synthesis of indole-3-acetic acid (IAA) or activate the transcription of ACC synthase genes. This, in turn, leads to the production of low-molecular-weight osmolytes such as glycinebetaine, proline and other amino acids. Additionally, microorganisms contribute to plant growth under stress by facilitating mineral phosphate solubilization, nitrogen fixation, producing organic acids and synthesizing key enzymes like ACC-deaminase, chitinase and glucanase. These microbial activities have the potential to enhance plant growth and alleviate the impact of abiotic stresses [122].

Plant growth-promoting microorganisms (PGPM) play a vital role in enhancing plant growth by stimulating the production of gibberellin, facilitating seed germination, and promoting the growth of various plant parts such as stems, leaves, flowers, and fruits. These microorganisms have the ability to infiltrate the plant roots and provide benefits to their host plants [123]. The presence of PGPM results in the stimulation of cytokinin production, leading to improved root development, enhanced vascular cambium activity, facilitated cell differentiation and reduced apical dominance [124]. Numerous studies highlight the role of beneficial microbes in promoting plant growth [125,126]. These findings underscore the significance of advantageous microbial interactions in supporting plant growth and development. Plant growth-promoting bacteria (PGPB) have been recognized for their capability to enhance plant growth and provide protection against diseases and abiotic stresses [29,127,128]. PGPB that contain ACC deaminase act as sinks for ACC (1-aminocyclopropane-1-carboxylate), resulting in reduced ethylene production by the plant in response to environmental stress. This reduction in ethylene production limits the plant’s stress response, thus decreasing its susceptibility to stress [29]. PGPB play a significant role in the adhesion and colonization of roots, influencing important processes for soil survival, growth, and function [129]. In nutrient-poor calcisol soil, the bacterial strains Pseudomonas alcaligenes, Bacillus polymyxa and Mycobacterium phlei have been found to significantly enhance plant growth and improve the uptake of essential nutrients such as nitrogen (N), phosphorus (P), and potassium (K) [130]. These bacteria contribute to the improvement of nutrient availability in challenging soil conditions, supporting plant growth and nutrient uptake. A study to compare the effects of inoculating wheat seedlings with two strains of Bacillus spp., namely 12A and 25A was carried out [131]. The results indicated that the 12A strain significantly improved various growth parameters, including root length, surface area, and biomass, shoot dry weight, and phosphorus content. Azotobacter promoted the germination of Capsicum annuum (Bell pepper) seeds [132]. Furthermore, phytase-producing bacteria from the genera Tetrathiobacter, Bacillus, and Advenella were observed to enhance the growth of Indian mustard and significantly increase the P content [133,134]. Overall, these studies demonstrate the positive effects of bacterial inoculation on plant growth and nutrient uptake, particularly in terms of root development, biomass, phosphorus content, and seed germination.

Bacterial and fungal strains can release K from silicate minerals like mica, biotite, and orthoclase, enhancing mineral weathering and increasing K solubilization in soil this is achieved through acidolysis, chelation, and exchange reactions, with microbe-secreted organic acids playing a crucial role in these reactions [135,136]. Many bacterial and fungal species in the rhizosphere release sulfur from sulfate esters and sulfonates through mineralization and enzyme complexes, with ssu gene cluster (being prevalent in bacteria AM fungi, also enhance plant fitness in Cu deficient and toxic conditions, particularly by Glomus mosseae in white clover plants, by extending extraradical mycelia for more nutrients and enhance plant Zn nutrition in low soil Zn conditions and protect plants from excessive accumulation at high Zn availability in various plant species like red clover, medick or burclover and tomato [137]. Major types of beneficial soil organisms and their functions are listed in

Table 1. Major types of beneficial soil microbes and their functions.

Types of Microbes	Subtype	Examples	Function	References
Plant growth-promoting bacteria (PGPB)	Plant growth-promoting rhizobacteria (PGPR)	Azotobacter, Azospirillum, Acetobacter, Bacillus, Diazotrophicus, Herbaspirillum, Burkholderia, Rhizobium Paenibacillus, and Bradyrhizobium	Auxin production, increase root length and number of lateral roots	[138]
		Achromobacter xylosoxidans, Gluconobacter diazotrophicus, Acinetobacter calcoaceticus, Rhizobia, Azotobacter spp., Bacillus spp., Herbaspirillum seropedicae, Azospirillum spp., Azotobacter, Pseudomonas, Rhizobium, Arthrobacter, Bacillus pumilus Agrobacterium, Clostridium, Flavobacteirum, and Bacillus licheniformis	Production of GAs (gibberellins)	[139,140]
		Pseudomonas, Azospirillum, Rhizobium, Azotobacter, Bacillus, and Arthrobacter	Cytokinins production	[141]
		Frankia casuarinae, Frankia irregularis, Frankia inefficax, and Frankia saprophytica		[142]
		Bacillus cereus	Bioremediation, production of amylase, remediation of industrial waste	[143]
		Bacillus subtilis	Bioremediation (Degrading xenobiotics and allelochemicals)	[143]
		Pseudomonas aeruginosa	Bioremediation (Cellulase production, heavy metals uptake	[143,144]
		Bacillus thuringiensis, and Pseudomonas sp. Lk9	Bioremoval of, Cu, Zn, Cd in metal amended media	[145]
		Acinetobacter, Achromobacter, Enterobacter, Ralstonia, Agrobacterium, Burkholderia, Alcaligenes, Azospirillum, Bacillus, Pseudomonas, Serratia, and Rhizobium	Produce ACC-deaminase, which controls ethylene levels and lessens growth inhibition induced on by elevated ethylene levels	[146]
		Pseudomonas putida, Escherichia coli, and Agrobacterium tumefaciens	Deamination of ACC deaminase that regulates ethylene level	[147]
Endophytes	Proteobacteria	Pantoea, Pseudomonas spp., Duganella, Kosakonia, Klebsiella, Massilia, Bordetella, Salmonella, and Serratia	IAA, Siderophores, ACC deaminase production, nitrogen fixation phosphorus/potassium solubilization, and trace metal tolerance	[138,148,149]
	Firmicutes	Bacillus paralicheniformis, Bacillus, Micrococcus, Staphylococcus, and Exiguobacterium	Nitrogen fixation, ACC deaminase, amylase, IAA, lipase cellulase, protease production, phosphate solubilization	[150]
	Actinobacterium	Curtobacterium, Microbacterium, Nocardia, Sediminihabitans, and Frankia	IAA production, nitrogen fixation fungicidal and bactericidal activities	[138,149]
Fungi	Ectomycorrhiza	Amanita, Boletus, and Ramaria	Soil aggregation, carbon cycle and plant productivity, nitrogen and phosphorus acquisition, decomposition, seedling survival regulation of plant diversity (reduction and stimulation)	[51]
	Arbuscular mycorrhiza	Glomus, Funneliformis, and Gigaspora	Carbon cycle plant productivity, nitrogen acquisition, plant phosphorus uptake, seedling survival	[151]
	Ericoid mycorrhiza	Rhizoscyphus ericae		[152]
	Orchid mycorrhiza	Armillaria mellea, Epulorrhiza, and Rhizoctonia solani	Carbon cycle plant productivity, Plant nitrogen phosphorus uptake acquisition, seedling survival	[153]
	PGPF	Aspergillus, and Penicillium spp.	Helps in phosphate mobilization	[154]
	Endophytes	Colletotrichum tropicale	Increase plant immunity	[155]
	Antagonists	Trichoderma sp., and Gliocladium	Production of antibiotics, phytotoxins and lytic enzymes	[156]

.

The arbuscular mycorrhizal fungi (AMF) play a crucial role in supporting plant growth, especially in adverse environmental conditions. They facilitate complex communication interactions between the plant and the fungus, leading to various benefits. These include enhanced photosynthetic rates, improved gas exchange-related traits, and increased water uptake for the host plants [157]. AMF form a mutually beneficial symbiotic relationship with plants, enabling them to overcome challenging environmental conditions and promote their growth and survival. AMF contribute to the improvement of soil quality by modifying its structure and texture, leading to enhanced plant health [158,159]. The establishment of a hyphal network between AMF and plant roots significantly enhances the root system’s capacity to explore a larger soil surface area, thereby promoting plant growth [160]. Additionally, AMF play a vital role in improving plant nutrition by increasing the availability and transport of several nutrients [161]. These symbiotic interactions between AMF and plants have a positive impact on soil health, plant growth, plant productivity, and nutrient uptake under environmental stresses [162,163,164,165], like drought [166,167,168], salinity [169,170,171] and heavy metals [172,173,174].

The utilization of Funneliformis mosseae and Rhizophagus intraradices under varying stress conditions resulted in significant increases in dry biomass and enhancements in leaf physiological parameters [175,176]. Under drought stress, the application of AMFs such as Glomus clarum, Glomus mosseae and Gigaspora margarita significantly improved soybean (Glycine max L.) growth and yield under drought conditions [168]. Furthermore, AMF enhance photosynthesis, activate antioxidant enzymes, regulate cell osmotic balance, and positively affect the growth, nutrient uptake, water status, and drought tolerance in Cinnamomum migao [177,178]. The hyphae of these microbes possess the remarkable ability to infiltrate soil pores that are typically inaccessible to plant root hairs. This unique capability allows them to efficiently absorb water and nutrients from the soil. Consequently, this alteration in the plant–water relationship leads to a substantial enhancement in water utilization efficiency, ultimately resulting in the maximization of crop yields [179]. Furthermore, the application of AMF species such as Funneliformis mosseae and Claroideoglomus etunicatum has proven effective in mitigating the detrimental effects of salinity stress. They induce non-enzymatic antioxidant responses, leading to the accumulation of flavonoids in both roots and shoots, as well as phenols in roots. These biochemical changes enhance various growth parameters and concurrently reduce root cell damage in Moldavian balm (Dracocephalum moldavica) [180]. The arbuscular mycorrhizal fungus (Funneliformis constrictum) reduced oxidative stress and enhanced salt tolerance in maize plants, resulting in significantly increased plant biomass and photosynthetic pigments [181]. Thus, AMF help in enhancing plant resilience in saline environments.

In plants, metal toxicity disrupts nutrient and water uptake, causing oxidative damage and inhibit growth [182]. AMF alleviate the impact of heavy metals by storing them in vacuoles, aiding their attachment to fungal cell walls, enhancing the removal of reactive oxygen species (ROS), supporting metal chelation, and promoting the formation of glomalin-induced soil metal complexes [172,183,184]. The inoculation of Funneliformis mosseae with soybean plants under heavy metal-containing soil led to the retention of HMs primarily in the roots, resulting in a significant reduction in the translocation of copper (Cu), lead (Pb), and zinc (Zn) by 21.8%, 57.6% and 67.3%, respectively, within the aerial portion of the plant. It also boosted overall plant productivity by 59.1% [185]. Similarly, Rhizophagus irregularis was found to significantly alleviate the phytotoxic effects of beryllium while enhancing growth and photosynthesis in ryegrass and chickpea plants [173]. These findings underscore the efficient growth and benefits that plants can derive from their association with AMF.

Fungal endophytes, such as Phialemonium dimorphosphorum, demonstrated their capacity to enhance herbage yield and improve the nutritional value of Trifolium subterraneum and Poa pratensis [186], also effective in promoting the growth of rice plants [187,188]. Furthermore, the inoculation of Scytalidium lignicola, a type of dark septate endophytic (DSE) fungi, has been observed to have profound effects, including enhanced root growth, increased plant survival under cadmium stress, and a significant increase in shoot biomass [189]. Moreover, it is well-established that soil algae establish symbiotic relationships with plant roots, leading to the release of hormones that stimulate root growth [190,191,192]. This, in turn, facilitates the activities of other beneficial microorganisms associated with the plant’s root system [193].

6. Suppression of Soil Borne Diseases by Beneficial Soil Microorganisms

Soil microbiota exerts a pivotal influence on augmenting the suppressive properties of natural soil, thus enhancing its ability to inhibit soil-borne phytopathogens [194]. The efficiency of water and nutrient intake is decreased by soil-borne phytopathogens [195]. These pathogens cause diseases including root rot, damping-off, and wilts that directly affect plant growth and survival [196]. Since the 1970s, researchers have explored how soil bacteria inhibit soil-borne pathogens. The suppressive attributes can be elucidated by the collective antimicrobial effects exerted by molecules and microorganisms, or through mechanisms involving antagonistic interactions between pathogens and microbes. The bacteria, including Paenibacillus, Bacillus, and Pseudomonas; actinomycetes such as Streptomyces, and filamentous fungi like Aspergillus, Trichoderma, Penicillium and Gliocladium, constitute the biocontrol-based microbiome that can activate all pathways involved in disease suppression [194].

The combination of plant-associated soil/root microbes is known as the phytomicrobiome, and when combined with the plant, they form a holobiont. These associated microbes engage in various types of relationships with plants, including exploitative, competitive or neutral interactions [197]. PGPR encompass a diverse array of microbes that are closely associated with a broad spectrum of plant species. These microbes exert beneficial effects on plants, including promoting growth and mitigating stress conditions [198]. Throughout the evolutionary process of plants adapting to terrestrial environments, PGPR have co-evolved alongside their respective host plant species, leading to the establishment of mutually beneficial and synergistic relationships [124]. For instance, strains like Bacillus subtilis, B. amyloliquefaciens, and Pseudomonas stutzeri have been demonstrated to be effective in root colonization and significantly suppress the pathogen Phytophthora capsici [199]. The application of Bacillus subtilis effectively suppressed the fruit infection caused by Penicillium sp. and Rhizopus stolonifer at the post-harvest stage [200]. In greenhouse settings, specific strains of B. amyloliquefaciens were found to exhibit notable inhibition against wilt disease caused by Fusarium oxysporum [201]. The detrimental effects of one or more phytopathogens can be alleviated or prevented by pathogen-controlling PGPR [202]. Numerous studies have provided evidence for the efficacy of combining PGPR to enhance biological control against diverse plant diseases by inducing systemic resistance (ISR) [203] and through antagonistic effects against specific plant pathogens [204]. The induction of ISR by PGPB is often associated with the upregulation of genes involved in the ethylene and jasmonic acid pathways [205].

Fungi facilitate the establishment of the root system by defending the plant from pathogens, acting directly or indirectly as biocontrol agents, and providing plant resistance [206,207,208,209]. Mycorrhizal fungi enhance the chemical and physical characteristics of the root-zone environment by modifying the anatomical and morphological features of plant roots. Hence, this results in the activation of several defense and disease resistance mechanisms in the plants [210]. Multiple studies have provided evidence that mycorrhizal plants possess defense mechanisms against soil-borne pathogens [211,212,213,214,215].

AMF has the potential to mitigate the damage caused by various pathogens such as bacteria, fungi, nematodes and others in plants like Lycopersicon esculentum, Cucumis sativus, Cucumis melo, Olea europaea, Citrus reticulata, Fragaria ananassa, Medicago truncatula, Solanum tuberosum, Zea mays, Musa nana and more. Additionally, it can also lead to a reduction in the use of pesticides, as highlighted in various studies [216,217,218,219,220,221]. Numerous studies have provided evidence that over 30 species of AMF are capable of effectively controlling soil-borne diseases in plants [222,223]. A specific AMF species called Rhizophagus intraradices can activate defense-related genes when banana plants are infected by Fusarium oxysporum f. sp. cubense, effectively suppressing wilt disease and promoting plant growth [224]. It was observed that R. irregularis was able to alleviate the symptoms and decrease seedling mortality caused by Fusarium oxysporum f.sp. dianthi in Dianthus caryophyllus seedlings [225]. The symbiotic relationship between fungi and plant roots improves the plant’s ability to resist fungal infections that specifically target the roots [226,227,228].

Previous studies have provided evidence that rhizosphere bacteria exhibit effective antagonistic properties against a wide range of fungal pathogens [229,230,231]. Bacterial endophytes isolated from Glycyrrhiza uralensis (licorice), such as Bacillus atrophaeus and Bacillus mojavensis, have exhibited antifungal properties [232]. Similar investigations have identified numerous instances of fundal endophytes exhibiting antibacterial properties [233,234,235,236,237,238].

7. Role of Soil Microbes in Carbon Sequestration

Soil holds the largest carbon reservoir on Earth, exceeding the combined carbon content of the atmosphere and vegetation [239,240]. The loss of carbon from the soil to the atmosphere has significant and wide-ranging impacts across various aspects of our world [241]. Soil organic matter (SOM) encompasses a mixture of inorganic compounds, including carbonates and lime, along with organic fractions that involve the decomposition of animals, plants, and microorganisms [242]. SOM is characterized by its division into two primary components: the active fraction accounting for approximately 35% and the passive fraction constituting about 65% [243]. The active fraction comprises living organisms, along with deceased animals and plant remnants, rich in easily decomposable carbohydrates and proteins. Conversely, the passive fraction denotes soil constituents that exhibit greater resistance to microbial breakdown [243].

Carbon sequestration involves the extraction of carbon dioxide from the atmosphere and its incorporation into soils, thereby increasing the storage of soil organic carbon. This process is facilitated by photosynthetic organisms, such as plants or autotrophs, which uptake CO₂ from the atmosphere, contributing to carbon sequestration [241]. However, through the respiration process of both autotrophic and heterotrophic organisms, the sequestered carbon is eventually released back into the atmosphere [244]. Microbial communities present in the soil play a crucial role in both soil carbon emission and carbon sequestration processes [245]. Therefore, as carbon and energy sources, microbes use various organic and inorganic forms of carbon [246]. Bacterial and fungal inoculants [241], mycorrhizae, microalgae, copiotrophs and oligotrophs [247] play key roles in carbon sequestration in soil ecosystems. Approximately 8% of the total atmospheric carbon is released annually by terrestrial ecosystems and the atmosphere itself through processes such as net primary production and terrestrial heterotrophic respiration, primarily driven by microbial activity [246]. These natural processes contribute to the dynamic exchange of carbon between terrestrial environments and the atmosphere.

The microbial contribution to carbon sequestration is influenced by various factors, including microbial biomass, microbial community structure, microbial by-products, and soil characteristics such as texture, clay mineralogy, pore size distribution, and aggregate dynamics [248,249,250]. The interplay between these factors determines the extent of microbial involvement in the process of carbon sequestration in soils. Rhizosphere microorganisms in forests are essential to the sequestration of carbon in terrestrial ecosystems [251]. Roots and the interactions between roots and rhizo-microorganisms are major contributors to the presence of soil organic carbon (SOC) [252,253]. The sequestration of SOC is regulated by the interplay of competition and symbiotic relationships between plant roots and soil microorganisms [254]. Additionally, soil microbes play a vital role in the succession of plant communities and exert an influence on carbon sequestration processes [255,256]. Bacteria are more abundant in soil compared to fungi [241]. Several bacterial species, including Bacillus pumilus, B. cereus, B. mucilaginosus and B. pasteurii, have the potential to play a role in the carbon cycle and the process of carbon sequestration [257,258,259]. Pseudomonas fluorescens, a bacterium known for promoting plant growth, shows potential in carbon sequestration and climate change mitigation [260]. In the carbon sequestration process, the bacterial order Rhizobiales and the fungal order Russulales played significant roles for Pinus tabuliformis and Quercus variabilis, respectively [251]. When it comes to carbon sequestration, fungi demonstrate superior performance compared to bacteria in the creation and preservation of organic matter within the soil [261,262]. The diversity of fungal species and the amount of fungal biomass present have an impact on the capacity of fungi to accumulate carbon in the soil [263,264]. Fungal necromass serves as the primary microbiological contributor to stable soil organic matter, accounting for a larger proportion (70.7%) compared to bacterial necromass (25.9%) [262]. Arbuscular mycorrhizal fungi play a role in carbon sequestration in the soil by transferring photosynthates from host plants to intraradical hyphae and then extraradical hyphae, eventually releasing them into the soil matrix [265]. The extent of AMF’s contribution to soil carbon sequestration is influenced by factors such as the amount of hyphal biomass produced, the turnover time of accumulated hyphal biomass, and the role of these fungi in stabilizing the formation of soil aggregates [266]. Glomalin, a glycoprotein synthesized in the cell walls of mycorrhizal fungi, is known for its high persistence in the soil, even after the death of hyphae [267,268]. Glomalin has been associated with the long-term storage of carbon and nitrogen and the promotion of soil aggregate stability [267]. Carbon sequestration is impacted by glomalin in two different ways: (1) it assists in the formation of soil aggregates, which in turn has an impact on carbon sequestration; (2) it is resistant to decomposition, which renders it stable in soils for a prolonged time [241].

Microalgae and cyanobacteria are key contributors to the food chain within the diverse soil microbiota, showcasing their remarkable adaptability to thrive even in adverse conditions such as dry, semi-arid, and wetland ecosystems [269,270]. Photosynthetic microorganisms known as microalgae have a natural ability to fix carbon dioxide (CO₂) 10 to 50 times more quickly than terrestrial plants can in order to produce oxygen (O₂) [271]. Prokaryotic (cyanobacteria) and eukaryotic (green algae, euglenoids, and diatoms) organisms are the primary photosynthetic microorganisms comprising the immensely diverse group known as microalgae [272,273]. Arthrospira, Aphanizomenon, Dunaliella, Chlorella, and Nostoc are among the representative genera of microalgae mentioned [274]. These genera serve as typical examples within the world of microalgae. Cyanobacteria, a type of microalgae, play a crucial role in the interactions among plants and microbes within natural ecosystems [275]. Despite being widespread in soil ecosystems, microalgae and cyanobacteria have received limited attention regarding their potential contributions [269,276]. Microalgae provide soil-borne microbes with photosynthates, serving as a nutritional source of fixed carbon [277,278]. A collaborative relationship among cyanobacteria, bacteria, and eukaryotic microalgae contributes to the provision of organic carbon (OC) necessary for plant growth [279,280]. Additionally, this coalition is involved in the fixation of atmospheric nitrogen (N₂) [281,282]. Research has shown the potential use of microalgae for the sequestration of CO₂ from flue gas emissions generated by power stations and cement industries [283].

Biochar is a substance formed through the thermochemical breakdown of biomass, occurring at temperatures between 300 and 1000 °C, in the absence of oxygen. This process can take place via pyrolysis or gasification and is employed to harness energy from biomass [284]. Biochar, with its pore structure, surface area, and ion adsorption capacity, can modify soil properties like surface area, porosity, and density [285]. It boosts microbial biomass and increases carbon and nitrogen levels in soil [286]. Biochar’s influence on soil microorganisms is primarily due to its ability to alter the soil environment [287], leading to increased species diversity and soil fertility [288,289]. This could impact soil ecological health and agricultural productivity [290].

Biochar amendments can improve plant nutrient absorption and crop yields, especially in soil lacking essential nutrients [291]. Soil microorganisms play a crucial role in soil fertility maintenance and climate dynamics [292]. Biochar can enhance plant health and growth by enhancing nutrient absorption [293], suppressing soil-borne pathogens [294,295] and promoting saprotrophic microorganism proliferation over fungal pathogens [296]. This occurs through the provision of easily accessible carbon sources, enhancing saprotrophs’ competitive edge against pathogens. The underlying mechanisms for disease suppression can be explained as follows: (1) the microorganisms stimulated by biochar compete with pathogens for carbon resources, produce substances harmful to pathogens, or even parasitize them [296,297]; (2) biochar indirectly boosts the plant’s systemic resistance by supplying nutrients, improving root structure, and enhancing the colonization of arbuscular mycorrhizal fungi [298]. Biochar provides habitats for soil microorganisms to colonize [299,300].

Biochar provides a conducive micro-environment for mycorrhizal growth and their interactions with plant roots [301]. The application of biochar into the soil as an amendment can enhance the abundance and infection rate of AMF by modifying soil characteristics and influencing microbial activity [299,302,303]. The synergistic combination of biochar and AMF exerts a more substantial influence on plant growth, root morphology, physiological attributes and soil enzymatic functions [304].

8. Phytoremediation

Phytoremediation is an emerging technique that involves growing plants on contaminated soil to break down or sequester the toxins. Rhizoremediation, also known as “bio-augmentation,” is the employment of rhizospheric bacteria to increase soil metal bioavailability and consequently promote phytoremediation [305]. Rhizoremediation involves several soil microorganisms, which are crucial. Bacteria that stimulate plant development provide biosurfactants that aid metal mobility and ultimately phytoremediation of hazardous metals. Pseudomonas aeruginosa BS2 produces di-rhamnolipid, increasing the mobility and solubility of lead and cadmium [306]. Metal-resistant bacteria from the genus Neorhizobium and Bacillus reduced the bioaccumulation of cadmium in polished rice and the bioavailability of the metal in soil [307]. The inoculation of plants with particular and adapted microbes has grown in popularity for the phytoremediation of metal-polluted soils [308]. PGPR, when grown in contaminated soils with metals, have been shown to have the ability to reduce phytotoxicity induced by metals and increase plant biomass production. Despite the PGPR’s effect on plant growth and the potential for heavy metal in contaminated soils, phytoremediation has been investigated widely [309].

9. Nutrient Acquisition

Nitrogen-fixing bacteria convert N₂ to NH₃ using nitrogenase, which is a complex enzyme that the nitrogenase gene encodes (nif) to produce biological nitrogen, which is utilized by plants. Microbes that cohabit with plant roots produce 80% of the total organic nitrogen that is fixed biologically. Non-symbiotic nitrogen fixers play a crucial role in the accumulation of a large amount of nitrogen in nature. Due to concentration gradient nitrogen is secreted into the host cytoplasm, which is converted into biological nitrogen in the bacterial cytoplasm [305]. Up to 90% of nitrogen requirements in plants can be met by rhizobia, which develop symbiotic associations with the legumes of the host [310]. Some PGPB are metal-resistant and capable of generating compounds that directly support plant growth, such as the solubilization or transformation of mineral nutrients, the production of organic acids, siderophores, phytohormones and antioxidant enzymes [71,145]. By producing low molecular weight organic acids like gluconic and citric acid, or by releasing protons and producing chelating compounds, inorganic P can be solubilized. On the other hand, the synthesis of the enzymes phosphomonoesterase, phosphodiesterase and phosphotriesterase, which catalyze the hydrolysis of phosphoric esters, culminates in the mineralization of organic phosphorus [311,312]. Specifically, in P-poor soils, phosphate-solubilizing bacteria represent a sustainable and environmentally acceptable approach to increase P availability for plants. Bacteria have evolved the ability to synthesize low-weight molecules (between 500 and 1500 Da) known as siderophores, which have a high affinity for Fe³⁺ in order to cope with a limited amount of available Fe³⁺. A receptor located on the cell membrane recognizes the Fe-siderophore complex, also known as ferrisiderophore, where the siderophore binds to Fe³⁺. The internalization of the ferrisiderophore, which is subsequently transformed into Fe²⁺ at the membrane level and discharged inside the cell, is made possible by the ferrisiderophore’s uptake to a membrane receptor [313].

In root nodules, symbiotic N₂ fixation takes place where the specialized environment supports bacterial N₂ fixation and the bacteroids acquire organic nutrients from plants in return for ammonia (NH₃) [314,315]. Non-nodulating diazotrophs can also enhance plant N uptake. For instance, the nitrogen-fixing cyanobacterium Nostoc punctiforme inoculation caused rice roots to exhibit nitrogenase activity and encouraged plant development under nitrogen-deficient conditions [316]. Microbes produce organic acids like citric and gluconic acid, which can liberate immobilized inorganic P by precipitating P-containing anions [317]. Soil acidification releases P from precipitates through the production of soluble hydrogen or dihydrogen phosphates. Non-specific acid phosphatases catalyze the majority of microbial mineralization of organic P [318], while phytases hydrolyze phytate [319,320], the most ubiquitous organic phosphorus molecule in soil [320]. Myo-inositol, a myo-inositol-containing species, is known for its P-solubilizing capabilities, drawing Bacillus megaterium species these processes contribute to the mineralization of organic P in soil [321]. Table shows the various roles of soil microbes in nutrient acquisition (

Table 2. The various functions of microbes in nutrient acquisition.

Type of Nutrient	Microbes	Function	References
Nitrogen	Allorhizobium, Rhizobium, Frankia, Azorhizobium, Mesorhizobium, Sinorhizobium, Bradyrhizobium, Azoarcus, Achromobacter, Burkholderia, and Herbaspirillum, Sinorhizobium, Neorhizobium, and Pararhizobium	Symbiotic nitrogen fixation (conversion of nitrogen into ammonia)	[41,322,323,324]
	Azotobacter and Azospirillum	Non-symbiont nitrogen fixation and can also solubilize phytate
Phosphate	Bacillus, Rhizobium, and Pseudomonas aeruginosa	Predominantly manufacturs acid phosphatases that aid in the mineralization of organic phosphorus in soil, phosphate-solubilizing bacteria play a crucial role in the solubilization of insoluble forms of phosphorus	[312]
	Achromobacter, Flavobacterium, Agrobacterium, Mycobacterium, Gluconacetobacter, Bacillus, Enterobacter, Erwinia, Pseudomonas, and Serratia		[325]
Siderophores	Chryseobacterium spp., Pseudomonas sp., Serratia marcescens, and Streptomyces sp.	It binds to iron, phytopathogens are prevented from growing on the host plant. The iron is subsequently released from the siderophore either by reduction to the ferrous state (Fe2+) or by cleavage of the siderophore molecule once the now-soluble iron-siderophore complex has been bound and imported by receptor molecules on the surfaces of bacteria or plants	[326,327,328]

).

10. Role of Soil Microbes in Combating Abiotic Stress

Abiotic stress is a term that refers to non-living elements that adversely affect a plant’s ability to grow and develop. Adverse climatic conditions, leading to abiotic stresses, are significant factors contributing to a decline in plant productivity. The primary abiotic stresses include drought, extreme temperatures (both low and high), salinity, flooding, and nutrient deficiencies [329]. Approximately 90% of the world’s arable land is believed to be susceptible to one or more environmental stress factors, leading to a significant 70% reduction in yield for key crops [330]. The negative effects on crop productivity are accelerating exponentially as a result of both the direct and indirect consequences of abiotic stress factors. To address the detrimental consequences of abiotic stresses, utilizing microbes proves to be a potent, environmentally sound, and economically sustainable approach [331,332]. The focus on PGPM is growing among agronomists and environmental advocates, as they are considered potential candidates for creating a viable, environmentally friendly, and sustainable alternative to traditional practices [145].

Several microorganisms play a significant role in growth by the fixation of atmospheric nitrogen, the production of bioactive compounds, such as vitamins, hormones, and enzymes [333,334,335]. Plant growth-promoting rhizobacteria (PGPRs) and plant-growth-promoting fungi (PGPFs) are examples of some microorganisms that help to mitigate abiotic stress. These microorganisms mitigate abiotic stress by adopting various strategies such as phytohormone production, lowering ethylene oxide levels, upregulation of dehydration response, and the induction of genes encoding antioxidant genes. Some studies revealed that the enhanced growth of plants under abiotic stress by microorganisms is due to the activation of primary metabolisms, leading to increased plant growth, improved photosynthesis, better uptake of nutrients, and higher antioxidant enzyme activity [336,337,338]. The crosstalk between microbial and plant hormones serves as a mechanism through which plants enhance their tolerance to abiotic stress [339].

Numerous plant species can interact with mycorrhizal and/or endophytic fungi, which help significantly in the adaptation of these plants to a variety of environmental stresses [340]. In many regions of the world, salt stress has an impact on the growth and productivity of plants. Salt stress occurs when the concentration of salt (mainly sodium and chloride ions) in the soil exceeds the threshold level tolerated by plants. The accumulation of salt in plant tissues disrupts the normal physiological and biochemical processes of the plant leading to a reduction in growth, quality and yield. More than 6% of the world’s land is affected by soil salinization, reducing agricultural output on 22–33% of all cultivated and irrigated agrarian land [341]. Soil salinity will endanger almost 50% of arable land by the year 2050 [342]. In drought stress, plants experience a prolonged period of water scarcity, resulting in reduced growth, development and yield. Causes of this stress are various environmental factors such as low precipitation, soil water deficit and high temperature. In response to drought stress, plants activate an array of physiological and biochemical mechanisms to maintain water balance and prevent damage to their cells and tissues. Droughts have risen dramatically in recent years, threatening global food security. Soil-borne microorganisms can colonize the plant’s endo-rhizosphere/rhizosphere and induce drought tolerance by producing phytohormones, volatile compounds, exopolysaccharides (EPS), osmolytes antioxidants, suppressor or inducing stress-responsive genes and altering root morphology [322]. Reduced nutrient diffusion and bulk water-soluble nutrient flow caused by drought stress reduce the amount of chlorophyll in a variety of plant species. By producing various phytohormones like indole-3-acetic acid (IAA), gibberellic acid (GAs), abscisic acid (ABA), and cytokinins (CK), as well as by reducing ethylene levels by ACC deaminase, rhizobacteria stimulated plant drought tolerance mechanisms. In addition, bacterial compounds such as bacterial exo-polysaccharides induce systemic tolerance [343]. Some microbes that help in overcoming stress conditions are listed in

Table 3. Soil microbes in plants combating different abiotic stresses.

Stress Type	Microorganisms	Plant	Effect	References
Salt stress	Enterobacter sp. P23	Rice seed	IAA-production	[344]
	Ensifer meliloti	Medicago truncatula	Improved IAA production	[345]
	Azospirillum brasilense NH	Durum wheat	Enhanced the IAA production	[346]
	Acinetobacter calcoaceticus SE370, Promicromonospora sp. SE188, and Burkholderia cepacia SE4	Cucumber	Increase proteins, reduced sugars, antioxidant enzymes and ribonuclease production	[347]
	Dietzia natronolimnaea STR1 and Bacillus amyloliquefaciens RWL-1	Wheat and rice	Changes ABA signaling and auxin cascades	[348,349,350,351]
	Pseuodomonas putida, Pseuodomonas stutzeri, and Stenotrophomonas maltophilia	Coleus	Enhances production of gibberellins and IAA	[352]
	Pseudomonas extremorientalis TSAU20	Tomato	Enhances level of proline	[353]
	Bacillus subtilis	Acacia gerrardii	Increases proline levels and sustain balance of water in plant tissues	[354]
	Bacillus subtilis	Arabidopsis	Reduce the activity of high-affinity potassium ion transporters (HKT1) to avoid excessive Na+ ion absorption by plant tissues and to keep ions in balance	[355]
	Pantoea agglomerans strain KL	Rice	Increases length roots and shoots, increases fresh and dry weight, chlorophyll content, and reduces proline and melondialdehyde (MDA); It also improves ACC deaminase activity and increases the synthesis of ammonia, phosphate, and exopolysaccharide	[356]
	Chryseobacterium gleum sp. SUK	Wheat	By increasing ACC deaminase activity, IAA, siderophore, ammonia, and hydrogen cyanide production, the root and shoot length, fresh and dry weight, chlorophyll, proteins, amino acids, phenolics, flavonoids, and potassium ion content improved	[20]
	Enterobacter cloacae ZNP-3	Wheat	By promoting the formation of ACC deaminase, phosphate solubilization, IAA, and HCN (hydrogen cyanide), the root and shoot length, fresh and dry weight, chlorophyll content, and potassium ion uptake are all increased. MDA, sodium ion uptake, H2O2 and O2 are decreased	[357]
	Enterobacter cloacae, and Paenibacillus xylanexedens	Canola	By increasing ACC deaminase activity and IAA production, root length increase	[358]
	Bacillus cereus Pb25	Mung beans	Increase in fresh and dry weight of root, shoot and nodule, potassium, chlorophyll content, phosphorous, nitrogen level, enhance ACC deaminase activity, phosphate solubilisation, IAA and siderophore production	[359]
	Bacillus megaterium, Pseudomonas fluorescens, and Variovorax paradoxus	Cucumber		[360]
	Pseudomonas fluorescens 002	Maize		[361]
	Serratia sp. SL-12	Wheat		[362]
	Streptomyces venezuelae ATCC 10712	Rice	Reduction in Na+ ion contents, ethylene and accumulation of proline, relative water content, chlorophyll content, malondialdehyde and K+ ions	[363]
	Rahnella aquatilis HX2	Maize	ACC-deaminase production	[364]
	Bradyrhizobium japonicum (KY940048)	Greengram	Production of 2,3-dihydroxybenzoic acid (2,3-DHBA) and ACC deaminase	[365]
	Pseudomonas frederiksbergensis OB139, and Pseudomonas vancouverensis OB155	Red pepper	Decrease in ethylene and increased the plant growth	[366]
	Enterobacter aerogenes LJL-5, and Pseudomonas aeruginosa LJL-13	Alfalfa	Phosphate solubilisation, ACC deaminase and siderophore production, plant biomass increase	[367]
	Methylobacterium oryzae CBMB20	Rice	Improved photosynthesis and ACC deaminase production	[368]
	Nostoc flagelliforme	Arabidopsis	Enhancement in seed germination and shoot growth of transgenic plants	[369]
	Curtobacterium albidum strain SRV4	Rice	Production of IAA, hydrogen cyanide (HCN) and nitrogen (N2) fixation, Increase in plant height, carotenoid content, antioxidant enzyme activity, dry weight, chlorophyll content, potassium ion uptake and decrease in sodium ion uptake	[370]
	Pseudomonas sp. strain AK-1	Soybean	Upregulation of different genes in shoots and down-regulation in roots	[371]
	Bacillus licheniformis SA03	Chrysanthemum	Help in mediation of ABA levels in plants	[372]
	Trichoderma harzianum	Cucumber	Increased ROS scavenging activity and stabilized osmotic stress	[373]
	Bacillus spp., Alcaligenes spp., Proteus spp., and Aneurinibacillus aneurinilyticus	Chili	Significant increase in root and shoot length	[374]
	Enterobacter sp. EN-21	Sugarcane	Plant length, fresh and dry weight, chlorophyll content, potassium ion absorption, and proline level increases	[375]
	Enterobacter sp. MN17, and Bacillus sp. MN54	Chenopodium quinoa	Improve plant water condition	[376]
	Novosphingobium sp. HR1a and Pseudomonas putida KT2440	Citrus macrophylla	Decreased stomatal conductance and transpiration rate in plants with significant decrease in the levels of abscisic acid (ABA), salicylic acid (SA) and increase in growth of plant	[377]
	Acinetobacter bereziniae IG2, Alcaligenes faecalis IG27, and Enterobacter ludwigii IG10	Pisum sativum	Lower the levels of electrolyte leakage and H2O2 contents, improvement in chlorophyll, proline content and total soluble sugar	[378]
	Pseudomonas oryzihabitans AXSa06	Solanum lycopersicum	Regulation of plant growth, activate antioxidant metabolism	[379]
	Stenotrophomonas maltophilia BJ01	Arachis hypogaea	Stimulated the growth and development, auxin production, lowers the levels of electrolyte leakage, lipid peroxidation, proline contents, total amino acids were enhanced	[380]
	Brevibacterium iodinum KNUC7183, Microbacterium oleivorans KNUC7074, and Rhizobium massiliae KNUC7586	Pepper	Increased in height of plant, dry and fresh weight, chlorophyll content, total sugar and proline contents	[381]
	Bacillus subtilis NRCB003	Medicago sativa	Enhance ACC deaminase activity	[382]
Drought stress	PGPB strain and Pseudomonas simiae AU	Soybean	Total soluble sugar concentration and gene expression associated with induced proline	[383]
	Enterobacter sp. FD17 and Burkholderia phytofirmans PsJN	Maize	Improved plant development by modifying photosynthetic activity and glucose metabolism	[384]
	Agrobacterium fabrum and Bacillus amyloliquifaciens	Wheat	Production of ACC deaminase resulting in increased grain yield and biomass	[385]
	Leclercia decarboxylata and Agrobacterium fabrum	Wheat	Increase nutrients uptake and chlorophyll contents	[386]
	Ochrobactrum pseudogrignonens eRJ12, Pseudomonas sp. RJ15, and Bacillus subtilis RJ46	Pea	Lowers ACC accumulation	[387]
	Pseudomonas fluorescens, Enterobacter hormaechei, and Pseudomonas migulae	Foxtail millet	Improvement in seedling growth and seed germination	[388]
	Psuedomonas flourescens DPB15 and Pseudomonas palleroniana DPB16	Wheat	Enhancement in root and shoot growth	[389]
	Pseudomonas aeruginosa PM389, Pseudomonas aeruginosa ZNP1, Bacillus endophyticus J13, and B. tequilensis J12	Arabidopsis thaliana	Increased phytohormones production	[390]
	Streptomyces pactum	Wheat	Accumulation of ABA and upregulation of drought resistant genes	[391]
	Azospirillum lipoferum	Juglans regia	Increase in secondary metabolites and activity of peroxidase enzyme which helps in plant growth	[392]
	Azotobacter chroococcum	Mentha pulegium	Stimulate biosynthesis of secondary metabolites	[393]
	Bacillus amyloliquefaciens	Mentha piperita	Decrease in the membrane lipid peroxidation, higher total phenolic content and enzymatic activities	[394]
	Bacillus amyloliquefaciens and Moraxella pluranimalium	Triticum aestivum	Modulation of auxin	[395]
	Bacillus cereus	Glycine max	Increase in the stomatal conductance	[396]
	Bacillus cereus and Myroides odoratimimus	Sorghum bicolor	Regulation of gene expression, production of IAA and Phosphate solubilization	[397]
	Bacillus megaterium	Solanum lycopersicum	Decrease in the expression of genes related to ethylene	[398]
	Bacillus megaterium	Cicer arietinum	Modulation of phytohormones	[399]
	Bacillus pumilus	Glycyrrhiza uralensis	Protection of chloroplast, increase in chlorophyll content, improvement in water state	[400]
	Bacillus sp.	Mucuna pruriens	Regulation of aminocyclopropane-1-carboxylate (ACC) deaminase	[401]
	Bacillus sp.	Triticum aestivum, Zea mays	Regulation of salicylic acid and IAA acid, alterations in root system architecture	[402]
	Bacillus sp. ESA 402	Sorghum bicolor	Nitrogen accumulation	[403]
	Bacillus spp.	Megathyrsus maximus	Reduced glutathione reductase activity, increased proline accumulation	[404]
	Bacillus subtilis Paenibacillus illinoisensis	Capsicuum annuum	Enhancement in the expression and activity of vacuolar H+-pumping pyrophosphatase	[405]
	Bacillus subtilis	Cicer arietinum	Regulation of phytohormones production	[406]
	Bacillus velezensis	Triticum aestivum	Reprogramming of metabolites	[407]
	Bradyrhizobium japonicum	Glycine max	Improvement in root nodulation and reduction in pod abortion rate	[408]
	Curtobacterium herbarum	Lactuca sativa	Reduction in lipid peroxidation and oxidative stress	[409]
	Gluconacetobacter diazotrophicus	Oryza sativa	Positive regulation of defence genes, increased plant biomass	[410]
	Variovorax sp. YNA59	Brassica oleracea	Sugar production, ABA production and tolerate oxidative stress like H2O2	[411]
	Bacillus subtilis HAS31	Solanum tuberosum	Significant increase in the growth attributes along with tuber weight and yield	[412]
	Arbuscular mychorrhizal fungi and PGPR	Nicotiana tabacum	Increase in chlorophyll, enhancement in phenol and flavonoids content	[413]
	Neotyphodium spp.	Lolium perenne	Increase in biomass, plant height and tiller numbers	[414]
Heavy metal stress	Pestalotiopsis spp.	Nypa fruticans	Enhancement in heavy metals tolerance including zinc (Zn), copper (Cu), lead (Pb) and chromium (Cr)	[415]
	Exophiala pisciphila	Maize	Provide tolerance against soil cadmium (Cd) toxicity	[416]
	Penicillium funiculosum LHL06	Soybean	Secretion of gibberellin	[417]
	Enterobacter spp. and Kocuria spp.	Solanum nigrum	Enhanced phytoremediation arsenic (As) tolerance	[418]
	Glomusmosseae, Rhizobium trifolii, and Brevibacillus brevis	Clover	Increase in plant biomass and P and N contents under nickel stress	[419]
	Pseudomonas aeruginosa ZN3	Wheat	Improvement in nutrient uptake, increase in leaf chlorophyll and total soluble protein under Zn stress condition	[420]
	Azotobacter chroococcum and Bacillus megaterium	Maize and Sunflower	Increase nutrient uptake in Cd stress condition	[421]
	Bacillus subtilis FBL-10	Solanum melongena	Activation of antioxidant system in plants and decrease the level of MDA and peroxide under Pb toxicity	[422]
	Bacillus subtilis STU-6	Tomato	Enhanced polyamine mediated iron remobilization under Fe (iron) deficiency	[423]
	Bacillus subtilis MF497446	Cow pea	Produce phytohormones and siderophores to induce plant growth under Cd stress	[424,425]
	Bacillus subtilis KP717559	Brassica juncea	Enhance phytoextraction by plants while producing phytohormones, HCN for plant growth under Ni, Cd and Cr stress	[426]
	Bacillus subtilis	Chick pea	Higher proline content and decrease in lipid peroxidation under Ni, Pb, Cd stress conditions	[427]
	Bacillus subtilis PBRB3	Mung bean	Increase in antioxidative enzyme activity in lead toxicity	[428]
Thermal stress	Curvularia protuberate	Dichanthelium lanuginosum	Increase tolerance at high soil temperatures	[429]
	Bacillus subtilis	Wheat	Enhanced activity of proline and antioxidants	[430]
	Bacillus tequilensis SSB07	Glycine max	Production of phytohormones, increase in length of shoot, photosynthetic pigments, leaf development and endogenous jasmonic acid, salicylic acid content	[431]
	Thermomyces lanuginosus	Cullen plicata	Change in the concentration of different antioxidants	[432]
Water logging stress	Trichoderma asperellum MAP1	Triticum aestivum	Improvement in morphological attributes of seedlings	[433]
Nutrient deprivation	Paenibacillus lentimorbus B-30488 (B-30488), Bacillus amyloliquefaciens SN13 (SN13)	Oryza sativa	Enhanced the growth of seedlings; improved concentrations, uptake, and distribution nutrient elements	[434,435]
Oxidative and Nitrosative stress	Bacillus aryabhattai SRB02	Soyabean	Enhanced the levels of IAA, jasmonic acid (JA), GA12, GA4, and GA7, resulting in longer roots and shoots	[436]
Cold stress	Pseudomonas frederiksbergensis OS211, Flavobacterium glaciei OB146, Pseudomonas vancouverensis OB155, and Pseudomonas frederiksbergensis OS261	Solanum lycopersicum Mill.	Reduction in membrane damage and activation of antioxidant enzymes and proline synthesis in the leaves	[437]
	Trichoderma harzianum	Solanum lycopersicum Mill.	Reduction in the rate of the lipid peroxidation and electrolyte leakage and enhancement in leaf water content and proline accumulation.	[438]
	Sphingomonas faeni	Finger millet and foxtail millet	Improved root and shoot growth, as well as increased biomass; enhanced antioxidant activity	[439,440]
	Bacillus spp. CJCL2, RJGP41 and Bacillus velezensis FZB42	Wheat	Regulation of abscisic acid, lipid peroxidation and proline accumulation pathways in a beneficial manner, positive regulation of phytohormones expression leading to improved plant growth	[441]
	Brevibacterium halotolerans (Sd-6), Bacillus subtilis (Ldr-2), Achromobacter xylosoxidans (Fd-2) and Burkholderia cepacia (Art-7), Trichoderma harzianum (Th)	Ocimum sanctum	Improved photosynthetic efficiency, enhanced fresh weight, improved nutrient uptake, increased accumulation of proline, starch, total phenolics, and reduced accumulation of ACC	[442]
	Kosakonia sp. CIR2 and Staphylococcus sp. CSR1T2	Rice	Higher survival rates, increased fertiility, improvement in grain length, seed weight per plant, and seed yield	[443]
Salt, drought, and cold stress	Rhizophagus irregularis SA, Rhizophagus clarus BEG142, Glomus lamellosum ON393, and Funneliformis mosseae BEG95	Arachis hypogaea L.	Higher plant growth, leaf relative water content, net photosynthetic rate, photosystem II efficiency, antioxidant enzymes activities, and K+: Na+ ratio while lower leaf relative electrolyte conductivity, malondialdehyde concentration, and the accumulation of reactive oxygen species, reduction in the damage to thylakoids and mitochondria	[444]
Flooding stress	Streptomyces sp. GMKU 336	Vigna radiata (L.) Wilczek	Enhanced plant growth and biomass, chlorophyll content, leaf area, leaf color, stimulated adventitious roots formation, and reduced ethylene levels	[445]
	Microbacterium sp. (AR-ACC2), Methylophaga sp. (AR-ACC3), and Paenibacillus sp. (ANR-ACC3)	Rice	Enhanced germination, seedling vigor index, root and shoot length and total chlorophyll contents, reduced ethylene production	[446]
	Klebsiella variicola AY13	Glycine max	Improvement in the plant growth, chlorophyll content, and the quantum efficiency of chlorophyll fluorescence	[446,447]
Heat stress	Bacillus cereus SA1	Soybean	Improved the biomass, chlorophyll content and fluorescence, increased the ascorbic acid peroxidase, superoxide dismutase, and glutathione contents, enhanced potassium gradients	[448]
	Pseudomonas composti SDT3, Aeromonas aquariorum SDT13, Bacillus methylotrophicus SMT38, Bacillus aryabhattai SMT48, Bacillus zhangzhouensis HPJ40, and Pseudarthrobacter oxydans SRT15	Vitis vinifera	Enhanced photoprotection capability and higher thermo-stability, exhibiting a significantly lower dissipation energy flux than the non-inoculated plants, Improved antioxidant mechanisms and membrane stability	[449]
	Bacillus cereus	Solanum lycopersicum	Promoted shoot, root length, leaf surface area, fresh and dry weight	[450]
	Paraburkholderia phytofirmans strain PsJN	Lycopersicon esculentum Mill.	Enhanced growth parameters, such as increased chlorophyll content and improved gas exchange, at both Normal (25 °C) and elevated (32 °C) temperatures	[451]
Drought and heat stresses	Streptomyces sp. RA04, and Nocardiopsis sp. RA07	Sorghum-bicolor	Increased growth and photosynthetic pigments, reduced reduced oxidative damage, enhanced cadmium accumulation	[452]

.

11. Conclusions

The rhizosphere harbors diverse soil microbes that are involved in crucial soil functions and are thought to be essential for maintaining soil health and vitality. Plant growth-promoting bacteria play a vital role in nutrient acquisition, antibiotic synthesis, phytohormone synthesis, stress resistance, rhizoremediation, carbon sequestration and the growth of plants directly or indirectly. Mycorrhizae also help in mineral uptake and enhance plant growth. To reduce the use of chemical fertilizers microorganisms can be used as they help in nutrient uptake and can be developed as biofertilizers to improve crop yield and also control plant pathogens. There is a need to develop new techniques for large-scale production, formulation, genetics, biochemistry, and physiological studies of PGPB. Consequently, some genetic modifications can be essential, so that PGPB do not cause any harmful effect on the environment. Several plant growth-promoting bacteria and mycorrhizae have been commercialized as biofertilizers. Soil microbes are capable of enhancing plant nutrient acquisition and thus offer environmentally benign solutions to encounter the plant nutrition requirements. However, transcriptional regulation and molecular level initiation remain unclear due to microbial factors. Some agricultural crops are inoculated with commercial PGPB, but these represent only small fractions in current worldwide agricultural practices. But there are some limitations in commercialization of PGPB that need to be addressed like the identification of crucial traits for efficient functioning and selecting PGPB strains with suitable biological activities, a greater comprehension of the benefits and the drawbacks of utilizing endophytic versus rhizospheric bacteria, a more thorough understanding of the possible interactions between PGPB, mycorrhizae and other soil fungi. Endophytic microorganisms interact with plants, often causing plants to emit ROS and causing plants to produce antioxidants and other oxidative stress defenses, leading to plants that have improved tolerance to oxidative stressors. Future research is required to better comprehend how nutrients move between bacteria and plants during the rhizophagy cycle. A deeper comprehension of the interactions between PGPB and mycorrhizae that effectively boost plant growth is required.