Green Microbe Profile: Rhizophagus intraradices—A Review of Benevolent Fungi Promoting Plant Health and Sustainability

Abstract

Arbuscular mycorrhizal fungi (AMF) such as Rhizophagus intraradices (formerly known as Glomus intraradices) are of great importance to maintaining the soil ecosystem while supporting sustainable agriculture and practices. This review explores the taxonomy of Rhizophagus intraradices, their attributes, mycorrhizal symbiosis, plant growth improvement, nutrient recycling in the soil, soil health and environmental rehabilitation, and challenges that impede the effective use of AMF in agriculture. AMF impacts soil structure by releasing organic compounds like glomalin, improving total organic carbon and water-holding capacity, and reducing water scarcity. AMF, in sustainable agriculture, not only improves crop productivity through nutrient uptake but also enhances soil fertility and plants’ resistance to so-called stress from abiotic factors as well. The integration of AMF with other beneficial microorganisms in organic farming will be powerful both to ensure long-term soil output and to protect food from bacteria. Nevertheless, chemical inputs and spatial biases of the researchers remain matters to be solved in connection with the broad feasibility of AMF use.

1. Introduction

Glomus intraradices, initially detected within a citrus plantation in Florida by Schenck and Smith [1], is categorized as an arbuscular mycorrhizal fungus (AMF) that predominantly forms its spores intraradically [2]. Following the differentiation of Glomus at a generic level within this specific species, G. Intraradices underwent a reclassification to Rhizophagus intraradices by Schüssler and Walker [3], aligning with the historical utilization of the genus name for AMF generating spores in roots [4,5]. Despite the recommendation put forth by Sieverding et al. [6] to replace Rhizophagus with Rhizoglomus, Walker et al. [7] opposed this suggestion, advocating for the preservation of the generic term Rhizophagus, albeit with an alteration of the type species to R. intraradices. Adhering to the principle of ‘existing usage’ as prescribed in recommendation 14A.1 of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) by Turland et al. [8] signifies that the current assignment, Rhizophagus intraradices, will be employed in this investigation, except in scenarios where previous designations offer added clarity. The utilization of molecular analysis of ribosomal DNA facilitated the reclassification of all arbuscular mycorrhizal fungi from the Zygomycota phylum to the Glomeromycota phylum [9].

Rhizophagus intraradices interact with the roots of plants to foster a symbiotic relationship. The balance between organisms being beneficial, mutually beneficial, or potentially detrimental for plants serves as a foundation for healthy and thriving plant communities. Formerly, the genus Glomus was transferred to the genus Rhizophagus and classified within the family Glomeraceae [2]. The spores of this fungus come in different colors, including white, cream, or yellow brown, with a median length of 40 to 140 μm. The structure of the hyphae is cylindrical or flared, and it has a width of 11 to 18 μm. It can colonize new plants by taking over their spores, hyphae, or root fragments. Despite being an ancient and very simple organism, it seems to be able to develop (undergo meiosis) and recombine genes [2].

It acts as a soil inoculant and has agricultural and horticultural significance for plants’ growth and the quality of the soil. It is common in different types of soils and performs the role of maintaining the biodiversity of the ecosystem and the normal functions of these ecosystems through the formation of a great number of networks of hyphae. This microorganism has a vital role in promoting plant health and sustainability and can help in increasing the scope of research on the topic as it is an agent involving ecological benefits and agricultural applications [10]. This article therefore aims to provide a comprehensive understanding of the multifaceted benefits of R. intraradices, emphasizing its importance in sustainable agriculture and its potential to contribute to food security and environmental health. This review systematically recapitulates all currently available information about Rhizophagus intraradices and offers an extensive introduction to its life cycle, environmental conditions, and host plant relations. This is useful to current readers who do not always have the luxury of time to go through several studies separately and decipher which findings are the most relevant to the field at the moment. Through a discussion of the search results in relation to agriculture, the current study centers its findings on the need for further research into the fungal species to improve plant health and production. From such discussions arise the probability of an increase in crop yields, better soil quality, and a decrease in the use of chemical fertilizers and pesticides. This review also highlights some of the areas where knowledge about the biology of Rhizophagus intraradices may be lacking, masking the need for further investigation. They can serve as a research agenda to direct future findings and assist with determining how funds are invested. This article consists of knowledge from different fields, including microbiology, plant sciences, ecology, and agronomy, and thus offers a broader perception of the fungi and their usefulness. But more than simply reviewing current literature, the review also presents new directions on how to implement Rhizophagus intraradices in modern agriculture. This may involve techniques for the introduction of beneficial microbes into plants, enhancing symbiosis, and expanding the application of fungi in various systems of production. Furthermore, the addition of cases or examples of existing successful uses of Rhizophagus intraradices makes it more appealing to farmers and the agricultural industry because it encourages its use and shows a desirable result. Consequently, in addition to informing readers of previous work in the field, the review also presents several valuable suggestions and points of view for those who would like to engage in further research and practice in sustainable agriculture and plant health.

2. Taxonomy and Characteristics

In

Table 1. Taxonomic classification and identification of Rhizophagus intraradices (formerly known as Glomus intraradices).

Taxonomy	Classification
Domain	Eukaryota
Kingdom	Fungi
Division	Glomeromycota
Class	Glomeromycetes
Order	Glomerales
Family	Glomeraceae
Genus	Rhizophagus
Species	R. intraradices

, R. intraradices is categorized under the Eukaryota domain, showing that it possesses nucleus-containing cells. It falls under the fungi kingdom, particularly within the Glomeromycota division, known for fungi capable of establishing mutually beneficial relationships with the roots of plants. Further classification is identified in the class Glomeromycetes, order Glomerales, and family Glomeraceae, providing detailed fungal taxonomical classification. It is then grouped under the genus Rhizophagus, with the species name R. intraradices, recognized for its important ability to form arbuscular mycorrhizal associations with plants, thereby leading to enhanced nutrient absorption and promoting plant growth.

Figure 1 depicts the spores of Rhizophagus intraradices, captured under a microscope, with three distinct spores, each exhibiting a spherical form with hues ranging from brown to yellow. The spores are surrounded by transparent, thread-like formations, likely representing fungal hyphae or other minuscule elements within the microscopic field.

Table 2. Morphological features of Rhizophagus intraradices (formerly known as Glomus intraradices).

Features	Description
Spores	Color: Pale yellow, greyish yellow.
	Shape: Elliptical with irregularities.
	Size: Generally, between 40–140 μm. Formation: Predominantly forms spores intraradically.
Hyphae	Shape: Cylindrical or slightly flared.
	Size: Width: 11–18 μm.
Distribution	Found in almost all soils, especially those populated with common host plants, and in forests and grasslands.
Colonization	Colonization peaks earlier than many other fungi in Rhizophagus, with extensive hyphal networking and intense intraradical spores associated with the older roots of host plants.
Reproduction	Colonizes new plants using spores, hyphae, or fragments of roots colonized by the fungus.

provides a summary of the morphological features, distribution, colonization behavior, and reproduction method of Rhizophagus intraradices.

Table 3. Physiological features of Rhizophagus intraradices (formerly known as Glomus intraradices).

Features	Description
Metabolism	Capable of osmotic adjustment, antioxidation, and expression of aquaporin Plasma Membrane Intrinsic Proteins, PIP genes under drought stress [11].
Meiosis and recombination	Possesses homologs of 51 meiotic genes, indicating the capability of undergoing conventional meiosis and genetic recombination [12].
Mycorrhizal association	Forms arbuscular mycorrhizal symbiosis with plant roots [2].
Growth temperature range	Mesophilic, optimum growth temperature around 25–30 °C
Growth substrate	Grows in soil, forming mycorrhizal networks with plant roots [10].
Nutrient utilization and uptake	Utilizes organic carbon compounds for growth. Can use both organic and inorganic nitrogen sources. Efficiently absorbs and transports phosphorus to the host [10].

provides an overview of the metabolic, genetic, ecological, and physiological characteristics of the organism Rhizophagus intraradices.

3. Mycorrhizal Symbiosis

Within the domain of terrestrial vegetation, mycorrhizal fungal associations are acknowledged as important breakthroughs. A mycorrhiza signifies a symbiotic association between plant roots and fungi, with plants providing carbohydrates synthesized from photosynthesis to the fungi while the fungi offer nutrients, and water, and protect the plant from diverse environmental pressures in return [13].

Mycorrhizal symbiosis’s importance in the ecosystem stems from its influence on plant productivity and diversity. While generally boosting plant productivity, mycorrhizal fungi can display diverse relationships with species, ranging from mutualism to parasitism, depending on differences in the condition of the environment [14]. Instances can occur where mycorrhizal fungi establish parasitic relationships with plants, particularly when the total benefits are greater than the cost. The complex nature of mycorrhizal symbiosis requires comprehension of the different factors affecting the functions, structure, and physiology of both the plant and fungi interacting, as well as the biotic and abiotic elements within the rhizosphere across various ecological levels [13].

The research by Zhang and Gong [2] underscores the substantial role played by mycorrhizal symbioses in facilitating revegetation and ecological restoration efforts in areas contaminated with arsenic (As). The classification of mycorrhizal relationships into four principal types, namely arbuscular mycorrhiza (AM), ectomycorrhizal (EcM) (Figure 2), ericoid mycorrhiza (ErM), and orchid mycorrhiza (OM), is based on anatomical characteristics and the identities of the partners involved [15].

Arbuscular mycorrhizae (an exemplar of arbuscular mycorrhiza is Rhizophagus intraradices), for instance, are traceable in subterranean parts of ancient plant fossils and play a crucial role in nutrient uptake by plants in exchange for photosynthate. They not only contribute significantly to plant health but can also influence the composition of plant communities. The hyphal nature of arbuscular mycorrhizae, along with their development of highly branched haustoria, facilitates efficient nutrient exchange with the host root cells [15].

A study by Ramírez-Flores et al. [10] demonstrated that maize growth under low potassium conditions was significantly enhanced through inoculation with Rhizophagus intraradices. Mycorrhizal plants exhibit denser and intricately branched root systems. The augmented content of most quantified elements in mycorrhizal plants correlates with root and overall plant growth. Nonetheless, the elevated concentrations of boron, calcium, magnesium, phosphorus, sulfur, and strontium surpass the anticipated values established solely on the size of the root system, suggesting an additional function of fungal transport in nutrient absorption. In addition to supplying nutrients, AMF also promote root development, thereby benefiting the plant host. Begum et al. [18] suggested that a higher ratio of roots to shoots indicates a significant degree of mycorrhizal efficacy. Improvements in seedling quality, manifested in growth traits compared to the control group, further validate the idea that infected seedlings enhanced their strength, resilience, growth, and subsequent performance after transplantation. The introduction of AMF, particularly R. intraradices, was considered advantageous for seedlings [19]. Moreover, studies have shown that mycorrhizal inoculation can improve crop consistency, reduce transplant fatalities, and increase the yield of various horticultural crops cultivated on soilless substrates devoid of AM fungi [20].

Studies have shown that R. intraradices helps reduce transplant shock in plant seedlings [18]. A study examined the impact of various AMF species on micropropagated grapevine plantlets. The study revealed that colonization of AMF effectively reduced stress caused by transplantation. The study observed high levels of proline in mycorrhizal plants, which is a non-protein amino acid gotten from plant tissue during unfavorable weather. Many studies support this assertion and show that proline is crucial for the regulation of osmosis and protein protection in harsh conditions [20].

The study by Pons et al. [21] examined how a mycorrhizal arbuscular fungus called Rhizophagus intraradices yields phytohormones. The researchers extracted phytohormones from methionine, including isopentenyl adenosine, indole-acetic acid, and gibberellin A4. The obtained results, to a certain extent, ought to serve as a hint that there might not only be a mutualistic interaction between the plants and arbuscular mycorrhiza but also a way for Rhizophagus intraradices to self-control. Different types of phytohormones majorly control the various stages of the arbuscular mycorrhiza symbiosis, such as the pre-symbiotic and the senescent stages, as well as those phases of interaction between plants and fungi. It stands for the realization of producing detailed explanations about AM symbiosis signaling pathways and the host–fungal hormonal interactions that are together oriented towards the benefit of both organisms.

4. Role of R. intraradices in Promoting Plant Growth

Zhang and Gong [2] elucidated in their study that the incorporation of R. intraradices effectively mitigated toxicity in R. pseudoacacia seedlings. This achievement was attained via enhancements in botanical development, modifications in root structure, alterations in phytohormonal levels and proportions, and an increase in soil glomalin concentrations. A study carried out by Ramírez-Flores et al. [10] noted that the introduction of Rhizophagus intraradices resulted in improved growth of maize under circumstances of limited potassium availability.

Roussis et al. [22] ascertained that the use of elevated levels of the AM fungus R. intraradices in nutrient solutions within a hydroponic system led to a substantial enhancement in the quality and development of processing tomato seedlings. Likewise, Roussis et al. [22] determined that Rhizophagus intraradices promoted the growth of processing tomato roots by increasing the overall root length and dry mass. Seedlings treated with the highest AMF concentration (AMF3) displayed an approximately 50% higher total root length compared to non-inoculated ones, potentially resulting in improved nutrient uptake and enhanced growth in agricultural contexts. Previous research supports these conclusions, underscoring the advantageous influence of R. intraradices on the root formation and biomass of tomato plants [23,24]. Generally, it is widely recognized that integrating inoculants during the initial stages of plant growth can promote AM symbiosis, leading to heightened plant development in the nursery and improved efficacy in the field after transplantation [18,20].

Zhang et al. [2] showed that planting seedlings with R. intraradices could help to improve several growth parameters under energy stress, thereby enabling more effective growth. AMF, which includes R. intraradices, produce a dramatic influence on the growth and root systems of plants that are grown in soils polluted by arsenic by helping in the nutrient uptake and establishment of plants. This evidences the capability of AMF, especially R. intraradices, for fostering plants thereby preventing the deleterious effects of arsenic contamination on plant health and productivity, which has also put these beneficial microbes into consideration as one of the plant ameliorators. Zhang et al. [25] revealed that the growth-promoting impact of R. intraradices was relatively inferior compared to R. intraradices and F. mosseae, which was associated with heightened mycorrhizal colonization and increased lipid utilization.

Chen et al. [26] established an adverse relationship between arbuscular colonization and root biomass, indicating an extended function of maize roots facilitated by R. intraradices. Furthermore, the positive correlation between the overall AMF colonization level and shoot biomass corroborated the notion that R. intraradices makes a beneficial contribution to maize growth. The study’s discoveries suggest that soil bacteriomes interact cooperatively with R. intraradices, impacting maize growth by regulating AMF colonization in the roots.

Xie et al. [27] observed that Rhizophagus intraradices, an arbuscular mycorrhizal fungus, enhances plant growth by associating with plant roots to enhance nutrient absorption, boost resistance against pathogens and pests, and regulate plant growth via phytohormones. R. intraradices did not exhibit a mutual enhancement of B. amyloliquefaciens population density. Simultaneous inoculation with B. amyloliquefaciens and R. intraradices led to the most significant increase in shoot weight and photosynthetic efficiency in T. repens and F. Vesca. Xie et al. [27] noted that colonization by the sole inoculation of AM fungus R. intraradices failed to stimulate the growth of the maize cultivar SY Milkytop, both in non-saline and saline conditions. Maize root biomass inoculated solely with R. intraradices was lower than that inoculated solely with bacteriomes. It is plausible that root growth is induced to recruit microbes and acquire a broader range of substances from the soil with the sole inoculation of bacteriomes.

Pons et al. [21] examine the impact of the arbuscular mycorrhizal fungus Rhizophagus intraradices on plant growth, with a focus on phytohormone production. Available reports highlight that this fungus combines the production of various phytohormones, including auxins, cytokinins, and strigolactones, which trigger major biochemical processes, such as root growth, absorption of nutrients, and stress reactions, thus boosting plant productivity. Besides, the sophisticated synergy between plants and mycorrhizal fungi, complex signaling routes, and phytohormones are in charge of growth promotion and bring about many plant growth contributions along the way. Through the convergent relationship between plants and arbuscular mycorrhizal fungus, nutrient uptake, stress tolerance, and plant health are improved, which helps increase plant growth and hence its overall productivity.

5. Nutrient Cycling and Soil Health

Soil nutrient cycling in the soil–plant system of crops relies on the effects of agronomical practices on soil conditions, especially the soil microbial population mediating soil carbon transformation (either mineralization or stabilization), the nitrogen cycle including soil nitrogen transformation, uptake and return from plants, and nitrogen losses, and the fate of other elements mediating these trade-offs, including phosphorous [28]. AMF play a pivotal role in the nutrient cycling processes occurring in ecosystems [29]. The intricate network of mycelium that they possess facilitates the transportation and delivery of nutrients, particularly phosphorus, to the plant hosts. This mechanism significantly boosts the availability of nutrients for plants, thereby enhancing their growth and utilization of nutrients. Consequently, it creates favorable conditions for the growth of various plant species. The mycelium network of AMF serves as a crucial link between the soil and the roots of plants [30,31]. It extends well beyond the range of plant roots, extensively exploring the neighboring soil in search of nutrients. Through this exploration, AMF are able to acquire phosphorus that would otherwise remain inaccessible to plants due to its limited mobility in soil. Subsequently, these fungi transfer these acquired nutrients directly to their plant hosts via specialized structures known as arbuscules [32,33]. The heightened availability of phosphorus exerts significant impacts on the growth and development of plants, as phosphorus is an indispensable element necessary for numerous physiological processes in plants, such as energy transfer and DNA synthesis. By facilitating the uptake of phosphorus, AMF empower plants to divert more energy towards growth and reproduction [34]. Furthermore, AMF also enhance the efficiency of nutrient utilization in plants by improving the absorption of other essential elements like nitrogen and potassium through the expansion of root surface area using their mycelium network. As indicated in a study by [35], this enhancement enables plants to extract a greater amount of nutrients from the soil while minimizing losses through leaching or volatilization.

Plant root systems play a crucial role in the acquisition of nutrients and water within various environments characterized by limited resources. Modifying the architecture of root systems is a strategic approach adopted by the majority of terrestrial plants to optimize their performance. Modifying the architecture of root systems is a strategic approach adopted by the majority of terrestrial plants to optimize their performance. Various terrestrial vegetation forms mutually beneficial relationships with arbuscular mycorrhizal fungi to boost the absorption of nutrients effectively [10].

A notable increase in the levels of chlorophyll, an important pigment vital for photosynthesis to occur, stems directly from the heightened absorption of nitrogen aided by arbuscular mycorrhizal fungi [36]. Moreover, the boosted supply of phosphorous in plants facilitated by these fungi may indirectly affect photosynthesis by altering the ATP-to-ADP ratio or regulating the action of the enzyme ribulose 1,5-bisphosphate (RuBP) carboxylase [37]. This finding aligns with elevated levels of phosphorous discovered in seedlings, as indicated by available data. R. intraradices is capable of improving PEPCase activity, an essential enzyme for malate production. Malate is the final product of the photosynthetic carbon reduction (PCR) cycle in C3 plants like tomatoes, emphasizing the important contribution of R. intraradices to photosynthesis [38].

However, it is important to note that, apart from enhancing nutrients and raising the rates of photosynthesis, other elements can affect the total improvement in survival and quality of seedlings. Arbuscular mycorrhizal fungi are said to trigger the synthesis of phytohormones, beyond their functions in improving the absorption of nutrients [39].

Hestrin et al. [40] illustrated that the interactions between the mycorrhizal fungus Rhizophagus intraradices and soil microbial communities have a synergistic effect on nitrogen acquisition by the model grass Brachypodium distachyon. These intricate microbial interactions result in a significant non-additive enhancement in nitrogen uptake by mycorrhizal plants from organic sources, surpassing the nitrogen acquisition of non-mycorrhizal plants cultivated without soil microbes. This newly identified multipartite relationship could contribute substantially to the annual assimilation of plant nitrogen, thus playing a critical role in global nutrient cycling and ecosystem functioning. The availability of nitrogen often limits primary productivity in terrestrial ecosystems. While arbuscular mycorrhizal fungi enhance plant nitrogen uptake, their ability to access organic nitrogen is limited. Other soil organisms that mineralize organic nitrogen into plant-usable forms may compete for nitrogen, potentially affecting plant nutrition simultaneously [40].

The maintenance of soil structure is a fundamental aspect of agricultural management. Arbuscular mycorrhizal fungi aid in the development of water-stable soil micro-aggregates by secreting a hydrophobic glycoprotein called glomalin, which acts as a robust binding agent. By accumulating glomalin on the external hyphal walls and surrounding soil particles, AMF stimulates the generation of micro-aggregates that evolve into macro-aggregates, thereby promoting soil aggregation. This results in better capability to retain water, enhanced air circulation, expanded soil capacity, and elevated levels of organic material content.

Arbuscular mycorrhizal fungi (AMF) play a crucial role in altering soil fertility, structure, and stability [41,42]. The enhancement of soil structure by AMF is facilitated by the intricate interweaving of their hyphae and the secretion of glomalin-related soil protein (GRSP), ultimately fostering the development and endurance of soil aggregates [43]. In Lane Late navel orange trees, the introduction of mycorrhizal fungi into the field resulted in varying levels of soil nutrients, contingent upon the specific AMF species involved. For instance, D. spurca exhibited no significant impact on soil nitrate nitrogen levels but did impede the availability of soil potassium while concurrently increasing soil Olsen-P and ammonium nitrogen levels. Conversely, D. versiformis led to a reduction in levels of ammonium nitrogen, nitrate nitrogen, and available potassium in the soil, while elevating the concentrations of Olsen-P. Despite these differences, the collective effect of these AMF inoculations was a notable enhancement in soil aggregate stability in Lane Late navel orange trees compared to the non-AMF control group. Similarly, in Newhall navel orange trees, the presence of D. versiformis and D. spurca resulted in heightened soil Olsen-P levels and improved aggregate stability [44]. In a different context, the inoculation of vetch with F. mosseae, D. spurca, and R. intraradices led to a significant decrease in soil Olsen-P and available potassium levels [45].

AMF plays a vital role in improving soil structure and quality. The external hyphal network aids in soil aggregation by establishing a framework in the mycorrhizosphere. AMF enhances soil structure by releasing various proteinaceous and non-proteinaceous organic compounds, with the protein glomalin being particularly efficient in binding soil particles, consequently ensuring the stability of these aggregates even six months after the network has vanished [46].

Gou et al. [47] performed a simulated erosion study and tested the hypothesis that exogenous AM fungal inoculation, namely Funneliformis mosseae, alters the gene expression and enzyme activities linked with N-cycling processes and that such change is related to N acquisition and loss. It was carried out using treatment factors of AM fungal treatments (control and AM fungal inoculation), crops (maize and soybean), and the slope of the plots. The experimental plots received natural rainfall to mimic the erosion incidences. From the findings of the experiment, the impact of AM fungi was more profound in the maize soils than in the soybean soils. In the maize soils, AM fungi enhanced the copy numbers of N-fixing and nitrifying genes and N cycling enzyme activity. The results showed that in the soybean soil, AM fungi, on average, enhanced the abundance of the N-fixing gene while reducing the nitrifying gene abundance. The interaction between the bacterial population and the N fixing gene was positively related to N uptake, but it was inversely related to N loss. Moreover, AM fungi amplified the responses of mycorrhizal colonization and moisture on the microbial parameters associated with N-cycling processes but reduced the response of the nutrients in the soil. Hence, AM fungal inoculation, thereby improving N uptake and minimizing N loss through the stimulation of N-fixing gene abundance, should preferably be utilized in low N conditions or in systems where N is restrictively competed.

Bukovská et al. [48], in a study involving two pot experiments both involving root-free compartments receiving 15N-labeled chitin, concluded that AM fungi were able to transfer proportions amounting to over 20% of N in the form of chitin to their plant hosts within 5 weeks. Moreover, the study revealed that in mycorrhizal pots, N leaching and/or volatilization losses integrated over the time period after the addition of chitin to the soil were significantly lower than in non-mycorrhizal pots, sometimes even being less than 50% of the added N. In contrast to the present hypothesis, the AM fungi chitin mineralization and N uptake rates were not slower but were at least as efficient as green manure (clover biomass) using direct 15N labeling and tracking down the N. This efficient N recycling from soil to plant observed in mycorrhizal pots was not much influenced by the structure of AM fungal communities or by the environmental conditions to which plants were subjected in the glass house, outside conditions, or under additional mineral N application. This study has shown that, in general, AM fungi could be considered an important and stable soil component in relation to several intricate processes occurring in soil, namely, organic nitrogen cycling.

Zhen et al. [49] found that arbuscular mycorrhizal fungal colonization enhanced plant mineral element uptake, especially phosphorous (P), both in lucerne hay (LH, C:N ratio of 18) and sugarcane mulch (SM, C:N ratio of 78), which was not significantly affected by water conditions in the iron (Fe) ore tailings. Symbiosis development in AM effectively prevented the accumulation of toxic levels of the supplemented nutrients (i.e., potassium and iron) in plant shoots by reducing their transport from root to shoot. Higher organic-care AM fungal ability in P uptake and the station of splitting out other elements was detected in the LH-amended tailings rather than in the SM-amended tailings. Drought reduced AM fungal capture and processes related to elemental nutrient acquisition and distribution. These outcomes have revealed how AM fungi produced a significant service involving the control of plant growth plus nutrition state on Fe ore tailings technosol, which provided an important input for the use of AM fungi in the eco-engineering of tailings into pedogenesis.

6. Environmental Restoration and Ecosystem Resilience

AMF are essential for improving the quality and health of soil through soil structure, plant physiology, and interactions with ecological systems. These factors jointly help to enhance plant functionality, growth, and productivity. Soil structure maintenance is improved by the development of soil aggregates caused by glomalin production by AMF. Physiologically, AMF changes the process of nutrient absorption, leading to an improvement in soil fertility and productivity. By adjusting the physiological conditions of a plant, AMF helps in preventing biotic (pathogens and weed plants) and abiotic (salinity, drought, extreme temperature, soil pH, and heavy metals) challenges. AMF, as a biocontrol agent, forms antagonistic associations with plant pathogens. AMF foster a collaborative effect on the performance of plants by creating advantageous relationships with other rhizosphere microorganisms and above-ground organisms [50].

A study by Sugiura et al. [46] showed that the arbuscular mycorrhizal (AM) fungus Rhizophagus intraradices can grow and produce spores independently when provided with external myristates (C:14) fatty acids. These findings challenge the conventional belief that AMF solely rely on their hosts for fatty acids during symbiosis. Rillig et al. [51] suggest that understanding the roles and functions of AM fungi on the ecosystem can be changed if fungi can come in contact with sources of carbon such as decaying plant material, litter, or other microbes apart from the ones from their host plants. This indicates that AMF can interact independently with the ecosystem of the direct host plant carbon supply through their beneficial effects on soil aggregation and carbon sequestration [52,53]. Arbuscular mycorrhization contributes to augmenting the soil organic matter content and water-holding capacity, consequently aiding in the conservation of the soil ecosystem. The elongated hyphae assume a crucial role in alleviating water scarcity in arid soil conditions and diminishing evaporation [50].

Hovland et al. [54] stated that AMF have the potential to exert significant impacts on the resilience of ecosystems and their ability to resist invasion in rangelands. The maintenance of plant community structure is facilitated by AMF through various ecological feedback mechanisms, including enhancing nutrient cycling and uptake by host plants, contributing to the stability of soil structure both physically and chemically, and mediating plant competition. These interactions between plants and AMF could play a crucial role in arid environments by supporting native plant communities in coping with stressors such as drought, grazing, and fire, while also defending against the invasion of exotic plant species. Nevertheless, invasive exotic plants might exploit their associations with native AMF communities, potentially leading to alterations in these communities. AMF have been implicated as drivers of plant community composition as well as contributors to ecosystem functionality.

7. Sustainable Agriculture and Organic Farming

Begum et al. [18] asserted that the efficient utilization of specific arbuscular mycorrhizal fungi (AMF) in relation to various crops and soils has the potential to enhance agricultural sustainability. Consequently, AMF are progressively emerging as an indispensable biological instrument for enhancing both crop yield and soil quality. Particularly within the framework of conventional agriculture, which relies heavily on chemical inputs and poses a threat to the sustainability of food security as well as human and ecosystem well-being, the adoption of alternative agricultural practices has become imperative. Hence, the integration of AMF has now become crucial within the realm of environmentally friendly and natural farming techniques. Within these agricultural landscapes, there is a notable augmentation of natural biological processes that contribute to the preservation of soil fertility. Furthermore, crops exhibit heightened intrinsic resilience to pests and diseases within such agroecosystems. Additionally, these ecosystems exhibit robust health, with the soil harboring a diverse array of organisms in these agricultural settings.

Kuila and Ghosh [55] revealed that the escalating global human population growth, in tandem with diminishing agricultural land, exerts substantial pressure on crop productivity, food security, and soil health worldwide, particularly in developing countries. Unsatisfactory land management practices, characterized by heavy dependence on chemical fertilizers and agrochemicals to boost productivity, have adverse repercussions on human health, the environment, biodiversity, and sustainability. The utilization of arbuscular mycorrhizal fungi (AMF) as a bio-fertilizer, either in isolation or in conjunction with other beneficial microorganisms, has emerged as a burgeoning research domain in the realms of agriculture and life sciences. Prior research has illustrated the favorable impacts of AMF on the nourishment, development, and yield of crops, along with enhancing soil quality, elevating biological soil fertility, and fortifying resistance to pathogens. AMF symbionts assume a pivotal role in bolstering plants’ tolerance to abiotic stresses. When utilized alongside other beneficial rhizobacteria, AM can function as a feasible substitute for chemical fertilizers in modern, sustainable organic farming systems [55].

As a bioinoculant, arbuscular mycorrhizal fungi (AMF) contribute positively to sustainable agriculture by establishing symbiotic associations with numerous crop plants [50]. Organic agriculture represents an alternative bio-agricultural approach that ensures economical and eco-friendly food production. The transition from conventional, high-input agriculture to organic farming should not solely focus on achieving immediate yield parity. Organic fertilizers are processed and utilized alongside diverse soil microbes. Implementing organic farming practices with suitable microbial blends customized to specific environmental conditions, soil attributes, and crops is imperative for ensuring yield stability across successive seasons [56]. Furthermore, this approach ensures the continual fertility of the soil and the production of safe and high-quality food products [57]. Using arbuscular mycorrhizal fungi (AMF) as a bio-inoculant provides a compelling avenue that can bring significant benefits such as sustaining the fertility of the soil, enhanced plant nutrients, and protection, thus holding considerable promise for sustainable agriculture [58].

Table 4. Benefits of Rhizophagus intraradices in promoting plant health and sustainability.

Benefits	Description
Mycorrhizal Symbiosis	Arbuscular mycorrhizae, such as Rhizophagus intraradices, substantially affect the absorption of nutrients by plants and the growth of the root system. Mycorrhizal application improves the consistency of crops, reduces transplant losses, and increases the yield of numerous horticultural crops [13,14].
Plant Growth Promotion	Inoculation with Rhizophagus intraradices improves seedling growth, root development, and biomass. Rhizophagus intraradices stimulates root growth, nutrient uptake, and growth parameters under different environmental conditions. Combined inoculation with Rhizophagus intraradices and other microbes can increase shoot weight and photosynthetic efficiency [2,10,22].
Nutrient Cycling	Mycorrhizal fungi such as Rhizophagus intraradices affect photosynthesis by improving nutrient absorption by plants, leading to changes in chlorophyll levels and the availability of phosphorus. Arbuscular mycorrhizal fungi help in obtaining nitrogen from organic material, affecting nitrogen cycling and ecosystem functioning [38,40].
Environmental Restoration and Ecosystem Resilience	Mycorrhizal fungi such as Rhizophagus intraradices play a crucial role in soil health, plant physiology, and ecological interactions, improving the function of plants and ecosystem resilience. Arbuscular mycorrhizal fungi enhance soil organic matter content and water retention, thereby preventing the scarcity of water and improving the preservation of the soil ecosystem [46,51].
Sustainable Agriculture and Organic Farming	Arbuscular mycorrhizal fungi are important in sustainable agriculture for improving plant nutrition, growth, and stress tolerance. Mycorrhizal fungi can function as bio-fertilizers, enhancing soil quality, fertility, and resistance to pathogens, thereby improving organic farming practices [50,55,56].

highlights the various benefits of Rhizophagus intraradices in promoting plant health and sustainability.

8. Agro-Ecological Relevance of Glomeromycota and R. intraradices

(a)

Plant growth promotion based on nutrient solubilization and phytohormones

Arbuscular mycorrhiza fungi, particularly through species such as Rhizophagus intraradices, have an important contribution to the dissolution of various nutrients that are in the soil to make them available to the plant. This is particularly the case with phosphorus, which is an essential micronutrient that is immobilized in the soil in relatively stable forms of organic and inorganic phosphorus. These fungi stretch greatly past the root region, making the surface area for the uptake of these nutrients larger. They break up organic and inorganic complex phosphorus compounds into simpler forms that plants can favorably assimilate [59]. Rhizophagus intraradices also access the levels of many phytohormones, which are organic compounds that control plant growth processes. Phytohormones such as indole-3-acetic acid (IAA), gibberellic acid (GA), and abscisic acid (ABA) are regulated in the presence of R. intraradices [21]. This fungus causes higher IAA levels, which stimulate root elongation and branching, resulting in an increase in the surface area of the roots. Through its influence on plant hormone regulation, the fungus helps the plant gain better access to the soil and nutrients [60]. The effect of the fungal-induced ABA and GA reduction may further assist the plant in managing stressful conditions and continuing to grow, even under suboptimal conditions [61]. Rhizophagus intraradices enhances the root architecture and improves solubilization. It also helps maintain an optimal balance of phytohormones, a vital compound that is used in regulating the growth of plants [2]. R. intraradices play a role in the formation of glomalin-related soil proteins that have a significant role in the agglomeration forces of the soil particles. These proteins also help in the processes of carbon and metal ion storage enhancement, which belongs to the non-negligible ecological advantages of this symbiosis [62]. This is true since beneficial members of ecosystems are known to help increase yields and contribute to overall stability. They develop the structure of the soil due to the release of glomalin, which is a glycoprotein that helps in holding the soil particles, thereby preventing soil erosion and enhancing water retention. This also has consequences for carbon storage, as plants with mycorrhizal associations can store more carbon, which helps to protect the climate [63].

• (b) Mycorrhiza–plant interaction: yielding plant disease biocontrol

Glomeromycota and Rhizophagus intraradices are specific mycorrhizal fungi that can benefit plant growth and development through enhanced nutrient uptake and defense against diseases. Relating to disease biocontrol, mycorrhizal fungi are regarded as having a protective function. They can improve the plant’s ability to repel numerous pathogens, from fungi and bacteria to nematodes [64].

Mycorrhizal fungi with a network of hyphae can occupy the surface of roots in a way that pathogens cannot easily compete for the space. They prevent pathogens from infecting the plant roots by occupying this location and using up the nutrients needed by the pathogens, leading to their inhibition [65].

The mutualistic mutualism between the mycorrhizal fungi and the plant results in a systemic rearrangement of the immune system of the plant, improving its defense against diseases [66]. According to Dutta and Ghosh [67], in addition to serving as an efficient biofertilizer, mycorrhizae provide plants with some measure of immune system called Mycorrhiza-Induced Resistance (MIR). This immunity is useful against most airborne and soil-transmitted diseases. Plant receptor protein complexes, or pattern-recognition receptors, detect the Effector Proteins (EP) and Microbe-Associated Molecular Patterns (MAMPs) in mycorrhizae since these are closely linked to possible pathogens. Consequently, the MAMP-Triggered Immunity response (MTI) is induced in plants and limits the subsequent penetration of pathogens. It provides short-term and long-term protection in plants with systemic acquired resistance and induced systemic resistance. During this process, defense-related genes become induced for various pathogens, and antipathogenic second metabolites are synthesized. They also change plant root exudation to recruit beneficial microbes, which also provide induced systemic resistance and form consortiums [67].

Fungal mycelium forms a complex, dense network around the roots and is thus considered to be a first line of defense against pathogens. This barrier does not only arrest the physical invasion by pathogens but also facilitates a less hostile environment for the pathogens [68]. It is known that the root exudates are altered in their chemical composition in the presence of mycorrhizal fungi. These alterations may allow for the synthesis of products that are lethal or non-permissive to pathogens; hence, the chances of disease establishment are eliminated [64]. Mycorrhizal fungi can effectively elicit plant defense mechanisms where the plant starts to produce chemical compounds like phytoalexins, pathogenesis-related proteins, and enzymes like chitinase and glucanase. These compounds have the ability to protect against a range of pathogen species, offering broad-spectrum action [69].

The mutualism underlying the interaction between mycorrhizal fungi and plants not only enhances plant growth and health but also forms a disease management strategy. Thus, the use of mycorrhizal fungi for biocontrol in the agro-ecological system reduces chemical pesticide reliance, in line with sustainable agriculture. This synergy is particularly relevant in the case of organic farming since it employs it in the case of managing plant diseases in a natural and sustainable manner, leading to increased crop yield and minimized ecological impact. The mycorrhizal fungi can therefore be used to highlight an integrated pest management technique that is both efficient and sustainable.

• (c) Mycorrhiza–microorganisms interaction

The hyphae of these arbuscular mycorrhizal (AM) fungi have more area for contact with other microbes and act as a major route of transport of energy-rich plant assimilations to the soil [55]. Using different AM fungi, soil leachates, and model microbial communities, Jin et al. [70] described organic P conditions where AM fungi may preferentially attract P-mobilizing bacteria to the exclusion of other types of bacteria. Standardly, they found out that the isolate Streptomyces sp. D1 had a privileged interaction with either the carbon source derived from the fungus, which was obtained by the bacterium capable of converting organic P into inorganic P, or the bacterial community that lives on the surface of hyphae, which can be at least partially controlled by the bacterium of the genus Streptomyces. This is done mainly by limiting the activity of bacteria that have low P-mineralizing potential, thus allowing AM fungi to access P [70,71].

Mycorrhizal helper bacteria (MHB) are a subset of those beneficial bacteria that function to improve mycorrhizal formation. These can support mycorrhizal fungi growth, enhance the uptake of nutrients by plants, and also safeguard the plant from diseases [72]. Yang et al. [73] sampled 45 kinds of bacterial strains from the rhizosphere soil of Vaccinium uliginosum and selected MHB strains by aiming at dry-plate confrontation and the promotion of extracellular bacterial metabolites. The growth rate of Oidiodendron maius 143, an ericoid mycorrhizal fungal strain, was enhanced by 33.33 and 77.77% for bacterial strain L6 and LM3 exposure, respectively, as revealed by the dry plate confrontation assay. Moreover, L6 and LM3 caused a profound enhancement in the extracellular production of biomass, which facilitated the growth of O. maius 143 mycelial filaments in other wells at a mean growth rate of 40.9 and 57.1%, respectively. Compared with the control group, the cell wall-degrading enzyme activities and the genes of O. maius 143 increased distinctly. In this case, strains L6 and LM3 were considered the most probable MHB strains due to a relatively low number of differences. Furthermore, the co-inoculated treatments resulted in improved blueberry growth, nitrate reductase, glutamate dehydrogenase, glutamine synthetase, and glutamate synthase activity in blueberry leaves, and enhanced nutrient acquisition in blueberries. From the results of the physiological tests and the 16Sr DNA gene molecular analysis, strain L6 was identified as Paenarthrobacter nicotinovorans and strain LM3 was identified as Bacillus circulans. The results of the metabolomics analysis showed that mycelial exudates provide rich substrates, including sugar, organic acid, and amino acid, which could effectively promote the growth of MHB. Thus, the growth of L6 and LM3 and O. maius 143 is self-promoting, and the co-inoculation of L6 and LM3 and O. maius 143 can promote the growth of blueberry seedlings and provide theoretical guidance for the exploration of the mechanism of the ericoid mycorrhizal fungi-MHB-blueberry symbiotic relationship. It provided the technical premise for the comprehensive development of biocontrol strain resources and the formulation of biological fertilizer [73].

Berrios et al. [74] gathered soil cultures in Bishop pine forests over a climate-latitude gradient of the California coast, separated the cultures based on their proximity to EcM colonized roots, analyzed the microbial communities by amplicon sequencing, and established linear regression models demonstrating the effect that selected bacterial phylotypes have on the density of EcM fungi. Moreover, they used transcriptome data to confirm the direction of these associations and to unveil which genes EcM-synergist bacteria induce during tripartite symbioses, as well as using greenhouse experiments. According to the outcome, ectomycorrhizas (that is, roots where the bacteria colonize) promote the presence of conserved bacterial species across climatically diverse locales. Here, they unveiled relationships between phylogenetically distinct EcM synergists and plant and fungal growth and reported that EcM synergists and antagonists differ in gene expression profiles. All in all, they help define the general processes that enable diverse and expansive multipartite symbioses, which shed light on how plants evolve within complex environments [74].

• (d) Mycorrhiza–soil interaction

Yu et al. [75] find that both AMF infection rates and the number of AMF spore species are increasing before emergent plants, proving that there is higher competitive mutualism between both AMF and plants. Concentrations of carbon (C), nitrogen (N), and phosphorous (P) in the above-ground biomass and in the root stock and the C/N and C/P ratios differ significantly in those four emergent plants. Furthermore, the infection frequency of AMF positively affected the shoot N concentration, negatively affected the aboveground and total biomass N (p < 0.05), and positively affected arbuscular mycorrhiza formation rate and versicular formation. The rate of AMF after root infection affected root N and root N/P. Regarding the relationship of the AMF infection characteristics with the soil properties, total C, total N, total P, and oxidation–reduction potential (ORP) showed a significant correlation with the parameters studied. Hence, the main conclusions drawn from this study are that redundancy and path analysis supported the notion that the quantity of soil C, N, and P and the ORP directly influenced the concentration and ratio of these macronutrients in plants. However, it might also control the direction of change in plant ecological stoichiometry through shifting the AMF mycorrhiza. Accordingly, our data emphasize that both the reciprocal exchange between AMF and soil are involved in the determination of plant ecological stoichiometry, and, therefore, these partners can be considered to have integral properties when analyzing the interactions between plant and soil [75].

Fall et al. [76] opined that AMF help to enhance fertility on the ground and that they improve the fertility of the soils surrounding plant roots. AMF are beneficial to the soil by synthesizing organic acids and glomalin, help prevent soil erosion, reduce binding between heavy metals and soil particles, aid in carbon formation, and improve macroaggregation of soil particles. AMF also attracts the bacteria that precipitate the alkaline phosphatase mineralization, which is a soil enzyme that relates to the availability of organic phosphorus. Besides, AMF predetermine the composition, richness, and functionality of the microbial consortium in the soil by competing or cooperating with disparate partners. All these activities of the AMF play a role in raising the fertility levels of the soil [76].

AMF affect the structure of the soil in a beneficial way. The AMF are located abundantly in massive quantities in the soils [77]. These mycelia or hyphae have reasons for being able to form stable elements within the structure of the soil. Mycorrhizal fungi are long-term soil stabilizing agents, and the extra matrix mycelial structures produce a mineral-adsorbing glycoprotein known as glomalin [78]. This glomalin is a hydrophobic protein that is thermo-tolerant, which implies that the protein is able to withstand the hot temperature of the soil. The water-repellency of the glomelin causes the stability of the water in soil aggregations, whose synthesis reaches its maximum in senescent mycelium. The glycoprotein is slightly more biodegradable by bacteria and fungi present in the soil, and such degradation is found to occur slowly. The basic goal of glomalin is to cement the compartments of the soil [79,80], to act as a cement that holds smaller maltese-cross micro-aggregations (diameter < 250 μm) as macro-aggregations [81]. These soil macro-aggregations enhance better water infiltration into the soil, reduce surface run-off, minimize soil erosion and nutrient and organic matter losses, and increase gaseous exchange, improving water and mineral retention, especially potassium, therefore enhancing plant growth [82]. These mechanisms help in avoiding pressure on soils and ensuring soil fertility [83]. In the case of AMF, it can be stated that these particles are capable of controlling soil structure based on their chemical and biophysical potential as enmeshing and aligning agents [76].

• (e) Biogeochemical cycles and mycorrhiza

Boyno et al. [84] aimed to provide an overall perspective on the impact of AMF and various days between irrigation on CO₂ release, soil property, plant growth, and AMF features. We noted that the varying irrigation intervals influenced AM symbiosis, and the extent of this change heightened as the irrigation interval increased. It was suggested that this AM symbiosis formed with the plant in question cut down on CO₂ emissions. Moreover, it was established that it controls the structural stability of the soil and enhances the health and development of plants. From the standpoint of the impact on the global climate, it can be stated that AMF species help mitigate CO₂ emissions by conserving water [84].

9. Genomic Research in Glomeromycota

Glomeromycota are unique in their biotrophy, which is obligate, multinucleate in nature, with large genomes and no sexual reproduction reported. All of these aspects have, in the past, constituted difficulties in genomic identification and alteration. Nevertheless, due to enhanced methods of DNA sequencing techniques, little information is available on the nuclear and mitochondrial genomes, which exhibit higher plasticity and diversification, and their roles in these organisms [85]. For instance, techniques such as suppression subtractive hybridization have been employed to depict the mechanisms of sleep and the mitochondrial genome. As the symbiotic characteristics of the Glomeromycota can only form AM associations with plants, the genetic determination of their specificity remains closely associated with their capability of forming AM relationships with their plant partners. This mutualism entails the fungi’s ability to bring nutrients like phosphorus and nitrogen to the plant in exchange for carbon. Consequently, there are several genes that have been proposed as being involved in this work of nutrient exchange, including phosphate transporters and some enzymes that are involved in nitrogen trade [86].

Rosling et al. [87] accept three monophyletic linages (Glomeromycota, Mucoromycota, and Mortierellomycota) as phyla. They provide a balanced taxon sampling and broad taxonomic representation for phylogenomic analysis; they refute a hard polytomy and place Glomeromycota in the sister group of the Mucoromycota and Mortierellomycota. The genes involved in plant cell wall degradation that have low copies cannot be attributed to the shift to a plant symbiotic life cycle but are likely to be an outcome of their ancestral phylogeny. While both plant symbiotic lineages—Glomeromycota and Endogonales—are deficient in many genes involved in thiamine metabolism, the absence of genes for fatty acid synthesis directly affects only AM fungi. Some of these genes are absent in all the analyzed phyla, while others can actually be found in some of the analyzed AM fungal lineages. For instance, the high affinity phosphorus transporter Pho89 is missing in Glomeromycota but is also absent in some phyla [87].

It has been established that Glomeromycota is one of the oldest groups of fungi that have coevolved with land plants. New insights from the phylogenomic context provide additional evidence that Glomeromycota is a sister group to Mucoromycota and Mortierellomycota, indicating that there are two evolutionary shifts to arbuscular mycorrhiza. These transitions were associated with a genomic context that is not representative of modern ectomycorrhizal fungi in the phylum Dikarya. Features of obligate endosymbiosis in Glomeromycota include the following: a low number of genes involved in plant cell wall degradation as compared to other intracellular mycorrhizal fungi; this has been considered to be ancestral and not due to symbiosis. Furthermore, the absence of specific genes involved in the metabolism of thiamine has been reported in plant symbiotic groups, whereas the deficiency of the genes required for the synthesis of fatty acids is known only in AM fungi [87].

Other studies also show that some of the genes that Glomeromycota need to colonize their hosts appear to have genes deleted from them, which would have enabled them to survive without such hosts. This genomic reduction is characteristic of many symbiotic organisms, and it is a testimony to the mutual dependence of both partners. These fungi have developed unique structures that aid them in this process, resulting in effective and widespread mutualism that is vital for the dynamics of the terrestrial biomes.

10. Negative Effects of AMF

In research conducted by Wang et al. [35], it was observed that the growth of plant biomass showed a synergistic increase with elevated levels of both soil water and soil nutrients. Interestingly, the introduction of arbuscular mycorrhizal fungi (AMF) resulted in a surprising suppression of plant height, particularly evident under conditions of low water availability. Additionally, the presence of AMF also led to a reduction in plant biomass, specifically noticeable under circumstances of low water and nutrient levels. Moreover, the application of AMF was found to have a significant impact on decreasing leaf phosphorus concentrations, which were notably heightened under conditions of high nutrient availability, while showing minimal effects on leaf chlorophyll and proline levels. In conditions of low water and nutrient levels, there was an enhancement in the specific root length as a result of AMF inoculation, accompanied by a decrease in the average root diameter. The adverse effects of AMF on plant development under low water and nutrient levels may suggest that the inoculation of AMF does not substantially contribute to the uptake of nutrients and water under such conditions. Conversely, it is plausible that AMF may have hindered the direct route of water and nutrient absorption by the plant roots, despite the low levels of mycorrhizal colonization. The presence of AMF led to a decrease in the population of the foliar herbivore Chrysolina aeruginosa on plants cultivated in low-nutrient soil, with no significant impact on plants grown in high-nutrient soil. Interestingly, the fertilization of plants resulted in an increase in the abundance of this herbivore, but only in plants subjected to high water levels. The reduced presence of the herbivore on plants with AMF could be correlated with the diminished leaf phosphorus content. This study suggests that AMF exhibit a negative influence on the growth of Artemisia ordosica while simultaneously reducing their attractiveness to a prevalent herbivore [35].

A research study conducted by Wang et al. [88] utilized benomyl to diminish mycorrhizal colonization of maize roots to investigate the impact of arbuscular mycorrhizal fungi (AMF) on nitrogen (N) uptake by maize plants in both field and greenhouse settings. The greenhouse segment of the study also examined the repercussions of benomyl on plant N assimilation and growth in soils that were either sterilized or non-sterilized, as benomyl’s influences on plant performance extend beyond its effects on AMF. The findings indicated that maize treated with benomyl exhibited increased shoot N concentration and content, resulting in higher grain production under field conditions. Moreover, greenhouse experiments demonstrated that benomyl promoted maize growth, N concentration, and N content in non-sterilized soil; however, it had no impact on maize biomass or N content in sterilized soil with the addition of a microbial wash. This suggests that the enhanced plant performance is partially attributed to the direct effects of benomyl on AMF. The study concluded that AMF can impede N acquisition, consequently diminishing maize grain yield in N-deficient soils [88].

Arbuscular mycorrhizal fungi (AMF) may also influence the nutrient uptake pattern, where nutrient control from the soil may change a little, but this may not be healthy for the host plant. This suggestion also implies that the fungi might selectively incorporate specific nutrients, denying the plant a chance to uptake other nutrients that are essential to its growth [85]. In the mutualistic relationship that exists between the members of this family and fungi, the plant part is expected to supply carbohydrates to the fungi. Where the plant is under stress or where the benefits of the relationship are negligible, the parasitic plant may be all but a drain on the plant’s intercalary energy stores [65]. Some plants can lose more in competition with other plants when forming symbiotic relationships with AMF than others, hence competing for fewer resources. This could potentially precipitate disturbances in biodiversity and the ecosystem portfolio. AMF themselves have no direct known negative effect on plants; however, they can alter host soil microbial populations and compositions. They are capable of changing the soil conditions, which may have some impact on the number and types of other effective microorganisms within the soil [89].

Table 5. Negative effects of Rhizophagus intraradices on plant health and sustainability.

Negative Effects of AMF	Description
Plant Growth Suppression	The introduction of arbuscular mycorrhizal fungi (AMF) suppresses plant height, particularly under conditions of low water availability, as observed by Wang et al. [35]. AMF presence also leads to a reduction in plant biomass, specifically noticeable under circumstances of low water and nutrient levels [35].
Root Morphology Alteration	AMF inoculation enhances specific root length and decreases average root diameter, especially at low water and nutrient levels, according to research by Wang et al. [35].
Nutrient Alteration	Wang et al. [35] found that AMF application decreases leaf phosphorus concentrations, especially under conditions of high nutrient availability.
Herbivore Population Control	AMF presence decreases the population of the foliar herbivore Chrysolina aeruginosa on plants cultivated in low-nutrient soil, as observed by Wang et al. [35], possibly linked to diminished leaf phosphorus content. This contrasts with the increased abundance observed in fertilized plants with high water levels [35].
Impaired Nitrogen Acquisition	Arbuscular mycorrhizal fungi (AMF) impede nitrogen (N) acquisition, resulting in diminished maize grain yield in N-deficient soils, as demonstrated in field conditions by Wang et al. [88].

summarizes the negative effects of arbuscular mycorrhizal fungi (AMF) based on the conducted research.

11. Challenges and Future Perspectives

In the realm of conventional agrochemical-based agriculture, arbuscular mycorrhizal (AM) fungi are underutilized due to their obstruction of symbiosis and effectiveness within this context. The abundance of high levels of major fertilizers, specifically phosphate and nitrogen, in addition to fungicides, pesticides, extensive tillage, and crop rotations involving nonmycorrhizal crops, act as barriers to the association, diversity, and activity of AM. Consequently, in agricultural environments, the diversity and abundance of AM flora and root colonization experience significant modifications and reductions in comparison to the adjacent natural soil conditions [89]. A recent exploration by Rodriguez-Morelos et al. [90] scrutinized the impacts of four fungicides (azoxystrobin, pencycuron, flutolanil, and fenpropimorph) at concentrations of 0.02 and 2 mg L⁻¹, evaluated in vitro on the hyphal branching pattern of Gigaspora sp. MUCL 52331 and Rhizophagus intraradices MUCL 41833. Detailed observations of reparative occurrences were meticulously carried out under a dissecting bright-field light microscope. The findings of the investigation accentuated the exacerbated negative influence of Azoxystrobin on both AM fungi at 2 mg L⁻¹, with fenpropimorph particularly impacting R. intraradices (demonstrating stimulation at low concentrations and inhibition at high concentrations). Conversely, flutolanil and pencycuron did not exhibit any noteworthy effects on either of the two AM fungi.

Kuyper and Jansa [91] posit that there are prevailing generalizations concerning AM symbiosis that are robustly supported by numerous research initiatives. Nevertheless, they acknowledge the potential presence of a geographic bias in mycorrhizal studies, which has predominantly developed within temperate and boreal regions. They propose that investigations carried out in alternative ecological contexts may reveal a wider range of feasible mycorrhizal and non-mycorrhizal strategies than presently acknowledged. Additionally, there is a discernible tendency towards excessive data interpretation, which could potentially obstruct the progression of certain research fields by disregarding experimental frameworks aimed at elucidating the fundamental principles of processes in preference for accumulating descriptive observations and correlational evidence.

Zhang et al. [2] revealed several problems in the study of the AMF effects on plant interactions in the presence of arsenic-contaminated soil conditions. These problems include identifying the actual mechanisms of action of AMF that result in improved nutrition and tolerance of plants to arsenic stress, considering the distribution of plant species responses to inoculation, finding the most practical way to use phytoremediation and crop productivity, and sustaining agriculture in regions where arsenic toxicity is present. The frame of future perspectives is as follows: AMF serve as a biotechnological tool that improves plant performance in contaminated environments; the functions of AMF in enhancing plants’ resistance to various environmental stresses are investigated; the results of omics approaches are used for the understanding of molecular pathways involved in the interaction of AMF with plants; and lastly, stakeholders and policymakers cooperate to apply AMF strategies for environmental Considering AMF’s potential benefits, ongoing research and innovation must keep up with that to take advantage of this tool for sustainable agriculture and environmental protection in arsenic-contaminated territories. The study by Pons et al. [21] also unfolds one of the little-known sides of the world of fungi: the fungal synthesis of phytohormones, a process that was earlier either neglected or studied indirectly under “indirect assays”. The distinctiveness of the interaction makes it imperative to carry out the studies directly and comprehensively to properly quantify the extent of the fungus’s role in hormone production. Considering the situation, decoding the molecular language and signal routes of the seasonal, persistent symbiotic link between fungi and plants is a signal of an open road to search for answers. The complexity of hormone biosynthesis and perception ways in these fungi involves understanding the greater extent of the ongoing process that occurs over some time. Thus, the pathways are seen as they evolve into a shared language. Also, the detailed confirmation of the function of different stimulator hormones arising from the arbuscular mycorrhizal fungi in the plant-fungus interaction and promotion of plant growth could be a milestone for the newly developed mycorrhizal-assisted strategies to boost plant productivity using the symbiotic association with the friendly fungi. However, challenges in investigating the production of phytohormones through yeast research remain. Nevertheless, the potential of the future in terms of maximizing our understanding of plant-fungal interactions, as well as the possibility of exploiting these relationships for agricultural and crop enhancement, is something that researchers need to consider.

12. Conclusions

Rhizophagus intraradices and other AMF present possible alternatives for both sustainable agriculture production and soil ecological preservation. They have the potential to enhance the natural soil structure or the cycling of nutrients while also stimulating the growth of plants, and thus afford organic farming systems with the bi-fertilizers that they need. While chemical inputs and specific geographical limitations to relevant research take place, integrating AMF into agriculture practice provides for long-term soil fertility, better crop productivity, and food security. However, there is a need for additional study and implementation of AMF-driven conservancies to ensure that we take advantage of the full potential of these beneficial agents in our ecological agriculture.