Enhancing the Resilience of Agroecosystems through Improved Rhizosphere Processes: A Strategic Review

1. Introduction

The swift increase in the global population has markedly heightened the need for energy, food, and other essential goods, leading to the expansion of agricultural land use. However, poor farming techniques, urbanization, and inadequate soil management practices have had negative impacts on agricultural soil, such as reduced soil fertility, the loss of beneficial soil microbiota, and the migration of soil organisms [1]. The top layer of soil surrounding plant roots, known as the rhizosphere, is home to a diverse range of microbes that play vital roles in promoting plant growth, organic matter degradation, and maintain the soil sustainability. However, in the lack of proper soil management, coupled with inappropriate agricultural practices, the quality of rhizosphere soil deteriorates, and its microbial communities weaken [2,3].

The rhizosphere serves as a microbial hotspot owing to the exudates emitted by plant roots, which supply vital nutrients for microbial activities [4]. Dynamics for example root zones, plant growth phases, plant species, and environmental conditions change the diversity and composition of soil microbial communities (e.g., bacterial and fungi) in the rhizosphere [5]. Multiple species can compose microbial groups, demonstrating comparable mechanisms of action, yet differing in their tolerance to plant cultivars and various environmental stresses. The microorganisms found in the rhizosphere include fungi, bacteria, and nematodes [6]. Large numbers of this community have an impartial effect on soil and plants, but some microbes are directly or indirectly connected with the plant–soil systems and provide nutrients from the rhizosphere to the plant. Additionally, rhizosphere microbiota contains microorganisms with both positive and negative effects on plant growth and soil health. Harmful microbes include pathogenic fungi, nematodes, and bacteria, while beneficial microbes, such as plant growth-promoting microbes (PGPM), nitrogen-fixing bacteria, and mycorrhizal fungi, contribute to plant nutrition and soil health [6,7]. However, beneficial microbes provide essential plant nutrients and contribute to lowering greenhouse gas emissions, improving nutrient availability, suppressing soil-borne plant diseases, and balancing nutrient cycling [8].

Conversely, many authors have pointed out that use of various agricultural techniques, overuse of mineral fertilizers, agrochemicals and farming practices could reduce soil fertility and disturb the rhizosphere microbiota, resulting in decreased soil health and crop production [9,10]. In general, overuse of agrochemicals (i.e., fungicide, herbicides, nematicides, insecticides) is being used non-judiciously, which has a harmful effect on soil positive microbiota in the soil as well as the overall health and quality of the soil [11,12]. This impact is mostly related to changes in microbial parameters such as enzymatic activity and biomass, which are the most important features of soil health and are important tools in monitoring soil quality. Eighty to ninety percent of soil processes are controlled by soil microorganisms and are strongly linked with plant and soil health, in addition to the role of microorganisms in the suppression of soil-borne diseases, nutrient cycling, soil resilience, and maintenance of soil sustainability [13,14]. Nevertheless, several authors reported that green manure is an alternate way to sustain agriculture and maintain soil health. The integration of the entire plant, containing more nutrients than crop straw, into the soil enhances soil fertility by adding more organic matter. Green manure improved crop yield and growth; reduced pests insects, suppress plant diseases; and increased soil enzyme activities, which regulate nutrient fluxes and stimulate plant growth [15,16,17]. Therefore, a sustainable solution must be sought by utilizing all available resources to modulate the rhizospheric process for sustainably enhancing agroecosystems productivity.

It is important for long-term sustainability in agricultural systems to keep agroecosystems stable and improve rhizosphere processes that make soil more resilient. This includes keeping and expanding the diversity of microorganisms in the rhizosphere. The rhizosphere is crucial for facilitating nutrient cycling, enhancing soil structure, and promoting plant health. The primary goal of this review is to investigate several methods for improving agricultural ecosystem resilience through rhizosphere activity optimization. We can implement these practices by utilizing beneficial microbes, green manures, and intercropping. These strategies jointly enhance synergistic communications between soil microorganisms and plant roots, creating an environment favorable for soil health and plant growth. The findings of this review improve comprehension of sustainable agriculture techniques, highlighting the importance of natural and organic resources in boosting crop production while preserving ecological balance. Using these rhizosphere-driven processes, we could develop more sustainable and resilient agricultural systems that ensure food security and environmental preservation amidst changing climate situations.

2. The Rhizosphere: Its Mechanism and Roles

The rhizosphere refers to the area surrounding the root zone [18,19]. This zone is considered essential for biological activities because many exudates produced by plant roots provide nutrients for soil microorganisms. Thus, this region is vital for disease resistance, nutrient cycling, and plant growth [20]. The rhizosphere zone has a central role in the food chain of soil microorganisms. Microbial food chain mainly includes dead plant matter and living plant roots, which are the primary source of nutrients [21], and carbon from living plant tissues and root exudates. These are crucial for plant health and growth as these support disease suppression, protection, and nutrient uptake [22]. The activity of beneficial microorganisms in the rhizosphere not only provides essential nutrients to plants but also influences the quality and quantity of root exudates [22,23]. Furthermore, various metabolites exuded by plant roots into the soil primarily shape and attract the microbial community composition in the rhizosphere, facilitating interactions with both biotic and abiotic factors. Plants frequently adjust the diversity of these microbes according to the benefits they provide for growth and health [24]. In the rhizosphere, plants engage in a wide range of interactions with soil-dwelling organisms, including exploitation, competition, neutrality, mutualism, and commensalism. These diverse interactions are essential for plants to adapt to varying environmental conditions, which is crucial for their survival and agricultural productivity. In the rhizosphere, plants host a diverse collection of microbes, and they can inhabit the inner tissues (endosphere), and surface tissues (phylloplane and rhizoplane). Collectively, these microorganisms are referred to as the plant microbiome [25,26]. The plant and soil microbiome is critical for stimulating plant development, improving soil quality and fertility, and supporting agricultural sustainability by strengthening resilience to environmental stressors, nutrient cycling, and disease fighting [27,28]. The interplay between roots and their surrounding soil constitutes one of the most prolific and diverse ecosystems in nature. The rhizosphere, the tiny and thin soil layer around the roots, has a vast population of microbes, fueled by carbon-rich compounds exuded during photosynthesis, and provide essential nourishment for the recruited microorganisms [29]. Overall, the rhizosphere is a kind of microenvironment wherein plant root development and nutrient uptake, soil properties, and microbe activities interact in a corresponding manner (Figure 1).

2.1. Rhizosphere Processes: Nutrient Retention in Agroecosystems

The rhizosphere hosts diverse microbial groups that play critical roles in nutrient cycling, promoting plant growth, and protecting plants from pathogens, as well as from biotic and abiotic stresses [30]. Changes in rhizosphere processes directly contribute to nutrient retention in agroecosystems. Through plant-soil interactions, plants and their residues provide organic carbon (C) to the soil. The rate of soil carbon input depends primarily on the rate of plant growth, which is driven by photosynthesis. Root-derived carbon input, in particular, is a key regulatory factor in the plant-soil interaction within the rhizosphere, as it has a more direct impact on soil processes than carbon input from shoots [31]. This root-derived carbon plays a significant role in soil carbon sequestration. The amount of carbon that can be stored as soil organic matter (SOM) depends on the balance between carbon input and the rate at which plant materials decompose. Decomposition is the process by which microorganisms break down organic molecules into their inorganic components, such as nutrients and CO2. Carbon dioxide, produced during microbial respiration, is released from the soil back into the atmosphere. However, some decomposition products are protected from further breakdown, playing a critical role in forming stable SOM, which is essential for long-term carbon sequestration in agroecosystems [31]. As a result, the rhizosphere process is particularly crucial for the nutrients cycling, stabilizing SOM, making nutrients available for plant growth, and ultimately handling soil microorganisms. On the other hand, maintaining and increasing soil and it’s process through utilizing carbonized materials such as “Biochar” that have long-term stability [32]. Biochars can reduce the emission of N₂O and CH₄ from the soil [33]. Biochar comprises a stable C compound as a derivative of gasification and pyrolysis and is available either as a pelletized or powder form. Char is ubiquitous in natural soils, containing as much as 35% of total organic C (TOC) in fire-impacted soils. Laird [34] reported that the application of biochar in to the soil was found to enhance the soil fertility, significantly increase soil organic carbon (SOC) and nutrients, which leads to the improvement of soil health. SOC consists of a complex mix of partially decomposed substances, including polysaccharides, lignin, aliphatic biopolymers, tannins, lipids, proteins, and amino sugars derived from plant litter, as well as microbial and faunal biomass [35]. However, SOC has been classified into slow, active, and inert pools, depending upon the decomposition rate in soil [36]. Furthermore, biochar largely supports the SOC pool for stabilization while or green manure incorporation add to the more bio-accessible fraction of the soil C reserve. This is because the biochar decomposes typically slower than that of uncharred biomass, e.g., green manure incorporation, fresh crop residues [37]. However, green manure or fresh crop residues in agricultural fields, on the other hand, can be used as a SOC storage/sequestration strategy by supporting cover crops; conservation tillage provides benefits including nutrient cycling, control of surface run off of water, wind erosion, and crop production [38]. Yazdanpanah [39] reported that applying green manure or plat residues improved the stability and total porosity of soil aggregates and increased the soil C pool but depended on the type and application rate of soil amendments. Whereas Kenney, et al. [40] reported that removal of crop residues (e.g., corn stover, zea mays L.) decreased the soil C pool. Therefore, the following strategy should be considered to achieve higher soil C sequestration via soil amendments produced from green manure/crop residues or biochar. Indirect effects of using these amendments should be considered in the context of production/control of soil GHG, environmental health and economic cost benefits of their use. As per our knowledge, the combined effect of biochar and crop residues have rarely been investigated except one recently study Nguyen, et al. [41], and it should be considered in near future. Overall, biochar seems to have a greater positive impact on total soil SC while the incorporation of crop residues/green manures can increases the microbial biomass C of soil, enhances the rhizosphere process and reduce the carbon dioxide emission.

2.2. Rhizosphere Engineering: Turn into Sustainably Increases the Agroecosystem and Its Productivity

The rhizosphere is a hotspot of microbes because many exudates are produced by plant roots, which are the primary source of nutrients for essential microbial processes and sustain the agroecosystems and their functions. The rhizosphere contains diverse microbial groups that perform various functions and affect the nutrients cycling and plant growth promotion and this portion affected via different strategies such as crop rotation, green manuring, and sustainable use of PGPM and intercropping. However, addition of PGPM, Asghar and Kataoka [42] found that plant growth promoting fungi changed the fungal community composition, enhances the phosphatase and glycosidase enzymes activities in the soil and stimulated the lettuce and brassica plant growth. Further, Kataoka, et al. [43] reported that incorporating leguminous green manure (Hairy Vetch, Vicia villosa L.) enhances the soil fungal biomass and diversity and provides a healthier environment by producing soil phosphatase enzymes. Furthermore, these rhizosphere engineering and its processes are explained with different strategies. In short, these interventions improve the rhizospheric processes and sustainably increase the agroecosystem and its productivity. On the other side of the agroecosystems and maintaining the rhizosphere process, biochar has emerged as a crucial innovation in scientific research, offering multiple benefits for sustainable agriculture, rhizosphere management, and environmental health [44]. Biochar, a type of charcoal obtained after the combustion of feedstock under a minimal Biochar is a type of charcoal produced through the combustion of organic feedstock with limited oxygen. It is considered a valuable soil conditioner and an effective means of carbon sequestration, which helps mitigate global warming and climate change [45]. Biochar decomposes slowly, making it highly durable when applied to soil, where it can remain for the long term [46]. However, generally biochar is derived from waste materials such as animal manures, forest residues and agricultural byproducts [47]. Through scientific processes, these waste materials are transformed into valuable products that can directly or indirectly improve soil health and promote plant growth. Biochar enhances crop yield, improves soil quality, and maintains soil health by preserving biochemical properties [48]. In terms of soil biological properties, Uzoma, et al. [49] found that biochar positively influences soil microbes and their activity, leading to increased crop yields. However, the effect of biochar depends on the specific soil type and specific crops. Another study, Lu, et al. [50] highlighted that biochar porous structure creates a favorable niche for soil microbiota, boosting microbial populations. Conversely, biochar derived from rice straw has been shown to reduce certain microbial communities, such as Ascomycota fungi and Actinobacteria, though the abundance and diversity of soil microbes may vary with different types of biochar [51]. The application of biochar not only alters soil microbial communities but also affects nutrient cycling, which can have a direct impact on rhizospheric processes and agroecosystem productivity.

3. Role of Soil Microbes in the Rhizosphere Processes

The rhizosphere is home to various soil microbes, including fungi, bacteria, protozoa and nematodes, which play essential roles in nutrient cycling, plant growth, and maintaining agroecosystems. These microbes facilitate the breakdown of organic matter and nitrogen fixation, making nutrients available to plants [1]. In agriculture, two groups of soil microorganisms are particularly important—rhizosphere fungi and bacteria—due to their critical functions. Fungi and bacteria thrive in soil, adapting to a wide range of environments, including harsh and high-salt conditions [52,53]. Fungi in the rhizosphere include pathogenic, saprotrophic, and mutualistic species, with mycorrhizal and plant-growth-promoting fungi being especially important for increasing nutrient availability, promoting plant growth and stress tolerance, and improving soil structure and disease resistance [54]. In contrast, the main rhizosphere bacterial phyla are Firmicutes, Actinobacteria, Acidobacteria, and Proteobacteria [55]. Plant growth-promoting rhizobacteria (PGPR) are crucial for enhancing plant growth, improving disease resistance, responding to carbon inputs, nutrient uptake, and assisting in phytoremediation [56,57,58]. In recent decades, a substantial body of literature has emerged demonstrating the activities of microbial species in plant growth promotion, biocontrol of phytopathogens, and nutrient cycling, highlighting their potential for development as alternative or supplementary agrochemicals in sustainable agriculture.

3.1. The Role of Microbes in Agroecosystems

Rhizosphere microorganisms, such as fungi and bacteria, not only act as pathogens in agricultural plants but also facilitate plant growth, increase nutrient availability, and control plant diseases through their role as biocontrol agents [59]. Recent research has highlighted the utilization of rhizosphere microorganisms to enhance plant development and mitigate diseases, thereby reducing reliance on pesticides and herbicides [60]. These microorganisms establish symbiotic associations with plant roots, exemplified by mycorrhizal fungi, which augment water and nutrient absorption, especially phosphorus. Furthermore, specific bacterial and fungal species might inhibit detrimental infections, thereby reducing dependence on chemical pesticides. Furthermore, these microbes help in the degradation of pollutants, thereby improving soil quality and resilience [61,62]. In compare, the excessive application of chemical fertilizers and pesticides has detrimental environmental consequences, and growing reliance on these substances is concerning. Commercially available as biofertilizers and biocontrol agents, a wide range of microorganisms are utilized in agricultural production and the management of agroecosystems through rhizosphere processes those chemical fertilizers often disrupt. The diversity and activity of soil microbial communities are essential for preserving soil structure, enhancing plant growth, and sustaining ecosystem stability, rendering these microorganisms crucial for sustainable agricultural operations [63]. Therefore, enhancing the resilience of agroecosystems through rhizosphere microbes is crucial for promoting sustainable agriculture.

3.2. Plant Growth Promotion Via Microbes

The application of chemical fertilizers to meet the food demand for a growing human population has led to many unpredicted environmental concerns related to soil-plant health and agroecosystems [64]. To protect soil-plant health and the environment, there is a need to develop and adopt new biological techniques that are not harmful to agroecosystems, soil, and plant health. Many researchers and scientists have already reported that microbes related to biofertilizers are functional and could be an alternative to chemical fertilizers, provide maximum environmental benefits, and improve crop yield and soil microbial biomass. In this context, microbe-related biofertilizers are capable and could be used in an eco-friendly manner to enhance crop production and maintain agroecosystems [65]. Microbe-related biofertilizers are defined as biological inoculants of beneficial fungal and bacterial strains mobilizer that can increase crop productivity and sustain soil biodiversity [66]. Mazid and Khan [66] reported that these inoculants, applicable directly or indirectly to soil and plant roots, are cost-effective and supply important nutrients for plants, enhancing soil nutritional composition, structure, and fertility..

Moreover, biofertilizer-related microbes are commonly known as plant growth promoting microbes (PGPM). There are various fungal and bacterial strains that have already been reported and used commercially to improve plant growth, soil conditions, and the nutritional demand of plants. Such bacterial and fungal strains are Azotobacter, Pseudomonas, Azospirillum, Rhizobium, Streptomyces, Bacillus spp., Trichoderma, Penicillium, Phoma, Fusarium, and Aspergillus spp., and these strains have been gaining global attention due to their potential to control soil diseases, promote plant growth, and maintain agroecosystems [67,68,69]. The significant role and potential activities of PGPM are shown in Table 1.

3.3. Singling Between Plants and Microbes in the Rhizosphere

The rhizosphere contains four main components: soil, microorganisms, roots, and their interactions. These components collectively influence a range of physical, chemical, and biological processes that affect nutrient use, plant development, and overall plant health. The primary goal of rhizosphere signaling is the interaction between plants and the symbiotic microbes in their surrounding area, which promotes the growth of various rhizosphere microbial communities that have a beneficial impact on plant productivity [82]. A robust reciprocal influence marks the interaction between the plant and the rhizosphere microbiome (Figure 1), where they interact through the exchange of signaling molecules produced and recognized by both the plant and its related microbiosystem [19]. Disease-free and asymptomatic plants have complex relationships with their rhizosphere microbes, which improve plant performance and maintain the agroforestry system [23,83]. Plants change the pH level, the structure of the soil, the amount of oxygen that is available, and the energy source that comes from carbon-rich exudates. These changes have an effect on the microbiome around the plants’ roots. Many of the chemically varying primary and secondary metabolites found in plant root exudates have bioactive effects on microorganisms, influencing their composition and function [84]. The exudation of carbon from plant roots, which accounts for almost one-third of the carbon produced by photosynthesis, significantly influences the results of chemical interactions at both the individual and community levels [85]. Root exudates serve as a principal means of communication between plants and their living environment, enabling several reactions, including nutrient uptake, competition for resources, signaling across species, the attraction of microorganisms, and several other interactions [86]. Furthermore, sugars, amino acids, organic acids, phenolic compounds, and secondary metabolites like coumarins, glucosinolates, benzoxazinoids, camalexin, and triterpenes are the main organic parts that come from exudate [87,88]. Plant species cultivate a unique microbial community in their rhizosphere by creating a varied carbon-rich environment. This community provides many adaptive benefits to the plant host by influencing the composition of microorganisms and adjusting their advantageous characteristics [88]. Additionally, chemicals made from root exudates play a key role in creating a stress-resistant microbiome that helps plants deal with abiotic stresses like not getting enough food, being sick, and drought. The identification of stress-derived metabolomics and microbiota is a viable approach to addressing both abiotic and biotic limitations [89,90,91]. However, we have not thoroughly investigated the positive impacts of root-enriched microbial species, supported by specialized metabolites produced from root exudate [92]. This paragraph of the manuscript on a review of current research on the plant rhizosphere microbiota and the compounds produced by root exudates for nutrient acquisition as depicted in the conceptual (Figure 2).

4. The Role of Green Manures in Agroecosystems

Green manures represent a promising strategy to sustaining agroecosystems and improving the soil health and rhizosphere processes. Green manure can reduce chemical fertilizers in agroecosystems, ultimately improving soil health and quality [93]. Green manure provides various benefits to the agroecosystem and soil, such as soil covering, reducing soil temperature, organic matter improvement, increasing water infiltration, and reducing weed infestation [94]. Besides, green manure has environmental and economic benefits such as food production, maintaining biodiversity, soil carbon sequestration, and soil retention [95]. However, to enhance the resilience of agroecosystems and maintain soil health, planting the green manure is an essential and valuable practice and works to reduce soil-borne diseases through biofumigation. Green manure provides better soil health and biodiversity and promotes the beneficial fungal genera that break the soil-borne pathogen’s life cycle that is connected with the crop genotype [96]. Many types of green manures, including leguminous and non-leguminous, have multiple functions and benefits for soil and plant health such as incorporating leguminous green manure to enhance wheat yield and production due to the mineralization of inorganic nitrogen and stimulating biological fixation [97]. Furthermore, Kataoka, Nagasaka, Tanaka, Yamamura, Shinohara, Haramoto, Hayakawa and Sakamoto [43] also reported that incorporating leguminous green manure (Hairy Vetch, Vicia villosa L.) enhances the soil fungal biomass and diversity and provides a healthier environment by producing soil phosphatase enzymes. Therefore, it could be assumed that planting and incorporating different green manures could maintain the agroecosystems and rhizosphere processes by enhancing biological processes and increasing organic matter. Another point of view, green manure may alter the soil N and C availability such as hairy vetch (leguminous plant) fixes N₂ whereas barley (Non-leguminous plant) has high biomass productivity, thus adds more C, which influences ecosystems functioning and microbial groups in soil [98]. Chavarria, Verdenelli, Serri, Restovich, Andriulo, Meriles and Vargas-Gil [98] reported that the green manure incorporation can improves agroecosystems services by improving nutrient retention capacity, accelerating soil organic matter, and reducing greenhouse gases in agricultural soils. However, applying alternative management such as green manuring practices stimulates the improvement of soil diverse microbial communities, accelerating the specific enzyme activities related to P and C [99]. Thus the relationship between microbial community composition and their activity stimulate the plant growth and soil quality.

4.1. Green Manure and Their Beneficial Effects on the Rhizosphere Processes

The application of green manure is an additional practice for enhancing the resilience of agroecosystems and rhizosphere processes and increasing soil’s productive capacity through nutrient availability. This application is geared towards maintaining agroecosystems and long-term environmental sustainability by enhancing processes such as nutrient cycling and preserving and maintaining soil biodiversity and the physical and chemical stability of the soil. Incorporating green manure can positively affect soil microbial communities by directly adding nutrients after incorporation and indirectly by changing plant and soil properties [100,101]. At the same time, Sun, Zhang, Guo, Wang and Chu [54] reported that the plant could affect soil microbial diversity and community through releasing root exudates. The decomposing residues of brassica green manure release glucosinolates, which assist in controlling parasitic nematodes [102]. Furthermore, during this phase, they can induce chemical and physical alterations in the soil, promote root penetration of subsequent crops, and serve as a kind of buffer protecting the soil. Furthermore, the exclusive use of grass species may improve the soil nutrient profile compared to monoculture. The advantages of green manure designate it as a sustainable practice capable of providing various agro-ecological services; however, effective management of green manure is essential to substantially enhance soil carbon stocks and mitigate climate change, particularly in semi-arid Mediterranean regions, by decreasing greenhouse gas emissions [103,104]. Furthermore, many studies have proven that planting and incorporating green manure have multiple beneficial effects on soil health and the rhizosphere process [93,105]. The different types of green manure and their beneficial effects on the rhizosphere are shown in Table 2.

4.2. Green Manure and Their Effects on Soil Health

Soil health is a primary requirement for agriculture and plant growth, but most of the agricultural soils are poor in organic nutrients and organic matters due to the high applications of inorganic or chemical-based fertilizers to achieve high crop yields. Different agricultural techniques should be adopted; otherwise, it can become very hazardous and lead to a lack of organic matter. Improving soil health through chemical, physical, and biological properties is attributed to the integrated application of green manure and organic application due to better nutrient uptake and preservation of soil health [115]. A variety of green manures, including grains, root crops, legumes, and oil crops, can serve as vegetative covers, each offering different benefits for enhancing soil health. Therefore, growing and incorporating green manure in agricultural lands help maintain and preserve soil health and soil nutrient availability and ultimately increase soil organic matter content. Incorporation of green manure provides soil nutrients and organic matter to the soil, and organic matter plays an important role in soil biodiversity, soil microbiota, and the arrangement of soil aggregates to improve the soil structure [116,117]. Therefore, incorporating green manure leads to an increased organic matter content, which has an important role in soil health and quality. Furthermore, green manure suppresses soil-borne diseases through biofumigation. Soil-borne diseases also affect soil health, reduce crop productivity, and negatively affect soil biodiversity. Many soil-borne pathogens have negative effects on plant growth and crop production, such as Phytophthora spp., Fusarium spp., Verticillium spp., and Rhizoctonia spp. Soil-borne diseases reduce agricultural yield by as much as 50–70%, including those of wheat, vegetables, and cotton [118,119]. However, the practices of green manure in agricultural lands produces significant benefits such as increased soil nutrient availability, enhanced soil organic carbon, reduced soil compaction, improved particle aggregation and soil structure, as well as strengthened microbe activity, diversity, abundance, and suppression of soil-borne diseases.

To protect crops from soil-borne diseases, many fumigants and fungicides need to be used regularly. Later, it was noted that the use of fumigants and fungicides or any other chemical-based product causes ecological problems such as human health hazards and reduced beneficial microbes in the soil biodiversity, directly affecting soil health [120]. In this consequence, organically alternative strategies should be adopted to reduce soil-borne diseases, preserve soil health, and improve crop production. Alternatively, incorporation of green manure and cover crops are useful strategies for protecting soil health from soil-borne diseases and improving soil and plant health through biofumigation, providing nutrients and increasing beneficial microbial activity. Hao, et al. [121] reported that broccoli (B. oleracea) grown as green manure reduces the S. minor sclerotia in the rhizosphere. Whalen [122] also reported that Fusarium wilt is another soil-borne disease that reduces watermelon production in the southeastern United States. The soil-borne disease Fusarium wilts is due to Fusarium oxysporum that attacks the crop of watermelon and reduces the annual number of fruits, directly affecting the annual yield of watermelon production. For the management of Fusarium wilt disease, hairy vetch (Vicia villosa. L) green manure was incorporated. After incorporating hairy vetch, the occurrence of Fusarium wilt disease in the rhizosphere of the watermelon field was reduced, leading to an increased annual watermelon yield by 45% [123]. Papp, et al. [124] demonstrated that the cultivation of green manures influences soil microorganism environments, which are essential for sustaining soil functions and ecological system sustainability because they participate in nutrient cycling and organic matter turnover, providing multiple services. Researchers have observed that the incorporation of green manure modifies the composition and dynamics of soil fungus and bacterial communities, and encourage the beneficial microorganisms. Ntalli and Caboni [125] observed that certain cruciferous green manures, including canola (Brassica napus L.) and rape (Brassica rapa L.), upon termination, release isothiocyanates (ITCs) via the hydrolysis of glucosinolates (GSLs) during the decomposition of their tissues, serving as effective biofumigants against various soil-borne pathogens and pests. The utilization of cruciferous species as green manures may facilitate the natural management of possible soil-borne diseases. Furthermore, Waisen, et al. [126] demonstrated that brown mustard (Brassica juncea L.) and radish (Raphanus raphanistrum subsp. sativus) serve as excellent biofumigant crops that protect against plant-parasitic nematodes, while keeping the soil healthy and maintaining the strength of the nematode population structure strong. Aydınlı and Mennan [127] also found that planting arugula (Eruca sativa) and radish (R. sativus) as winter crops before planting plants that are easily damaged by the root-knot nematode Meloidogyne arenaria may lower the number of eggs laid, the gall index, and the damage that occurs, while also increasing crop yields. Leguminous green manure can substantially enrich the soil with nitrogen throughout its growth and can acidify the rhizosphere by enhancing the absorption of insoluble phosphorus into the soil [128,129]. Leguminous green manure can fix atmospheric nitrogen via symbiosis with rhizobia in root nodules [130]. Furthermore, the fixed nitrogen can be allocated to intercropped non-leguminous plants within mixed cropping systems, or it may succeed crops in rotational practices. Biological nitrogen-fixing (BNF) systems may decrease the reliance on commercial nitrogen fertilizers [131,132]. Further, Scavo, et al. [133] reported that the existence of Trifolium subterraneum for three straight years resulted in a significant rise in nitric nitrogen, ammoniacal nitrogen, and nitrogen cycle bacteria. Campiglia, et al. [134] observed similar wheat yields when they used underground clover as living mulch in intercropping systems. In addition, Guardia, et al. [135] showed that the mitigating effect of the legume green manure (vetch) mostly comes from less synthetic nitrogen being added to the next cash crop, less indirect N₂O emissions from NO₃^– leaching, and more carbon being stored because photosynthesis is higher. Therefore, green manure and cover crops should be adopted to protect soil health, reduce soil-borne diseases as well as refining water use efficiency and many more beneficial impacts as depicted in the conceptual (Figure 3).

5. Role of Cropping Systems in Agroecosystems

Understanding the value of agroecosystems requires knowledge of soil, its different properties, and the processes that maintain its health. Soil is a complex ecosystem and is one of our most important resources due to their many vital functions, such as providing food, fuel, and fibre; recycling of nutrients that turn into beneficial nutrients for crop and plant necessities; organic matter decomposition, including plants and animal residues; regulation of water supply and quality; and provision of soil microorganisms, which are important for soil health and play vital roles in agroecosystems [136]. Unfortunately, the soil is currently being degraded rapidly due to extensive application of chemical-based fertilizers, lack of agricultural techniques, and irregular cropping are rapidly degrading the soil, but what is most concerning is that soil is a non-renewable resource at a human temporal scale [96]. Therefore, scientists and researchers have been trying to adopt alternative strategies to protect soil health, ultimately enhancing agroecosystems and rhizosphere processes. Cropping systems, such as intercropping and crop rotation practices, could serve this purpose in agricultural practices, thereby positively influencing soil health and agroecosystems [137]. Cropping systems are adopted to maximize the crop yields of agroecosystems as well as to maintain agroecosystems through soil health and quality preservation. In contrast, minimization of chemical-based products directly or indirectly affect agroecosystems and rhizosphere processes [138]. With the primary goal of soil health maintenance to ensure long-term stability of agroecosysemts and high production of crops, we need to adopt agronomic practices such as intercropping or crop rotations. Intercropping practices can improve agroecosystems by reducing the use of chemical-based fertilizers, soil pollution, and preserving soil microbial diversity.

5.1. Intercropping and Their Effects on Rhizosphere Processes and Soil Health

Intercropping, which involves the cultivation of two or more crops in a field concurrently, is a useful strategy in agronomic practice. Different crops such as cover and cash crops grow at the same time. The practice has gained global attention due to their beneficial effects for the enhancement of agroecosystems and soil health. In brief, intercropping practices can maintain agroecosystems and soil health by the reduced use of chemical-based fertilizers [139], enhancing soil-plant functions [140], suppressing the occurrence of soil-borne diseases [137], increasing soil nutrient and organic matter contents [141], and promoting the beneficial soil microorganisms, which support the rhizosphere processes [142]. Cong, et al. [143] reported that intercropping systems, including that of faba beans, corn, and wheat, had about 11%, 4%, and 23% higher belowground plant biomass as well as increased organic carbon (C) and nitrogen (N) contents than those in plant species rotations found in Gansu, China. Furthermore, de Medeiros, et al. [144] reported that intercropping with beans and pigeon pea considerably minimize black root rot (Scytalidium lignicola) in cassava by up to 50% when matched with cassava in monoculture systems, as well as enhanced the rhizosphere process, that is, increasing the soil enzymes activities, microbial biomass, and soil nutrients related to organic C and N. Increasing the use of intercropping with different plant species have been typically interconnected with the enhancement of rhizosphere processes, providing environmental benefits [145]. For example, leguminous species are advantageous for soil through providing nitrogen-fixing microorganisms and enhancing soil enzymes activities. On the other hand, non-leguminous species usually provide soil cover and nitrogen availability; such intercropping self-regulates soil nitrogen levels to improve soil nutrient use and reduce the C footprint [146]. Furthermore, Graf, et al. [147] also reported that compared to sole cropping, intercropping practices on Dactylis glomerata and Medicago sativa have led to increased shoot biomass and nitrous oxide (N₂O) production rate, which suggests that understanding the intercropping strategies is helpful for the maintenance of agroecosystems and soil health. Intercropping is regaining agronomical and ecological importance because of its ability to self-regulate soil nutrients and preserve soil health. An overview of intercropping in agroecosystems and its beneficial interactions based on Brooker, et al. [148] and their outcomes are shown in Figure 4.

Furthermore, legume and cereal intercropping systems have been extensively employed to address limitations on natural resources, promote sustainable agricultural development, and guarantee food security due to their economic and ecological advantages [149]. Faba/wheat intercropping decreased nitrogen fertilizer application by 5–16% while simultaneously enhancing wheat production by 15–25% [150]. While, Luo, et al. [151] reported that a 40 percent reduction in synthetic nitrogen input, coupled with soybean intercropping, might sustain sugarcane productivity and promote sustainable soil management. Many research studies have demonstrated that belowground facilitative interactions among species can improve nutrient availability and utilization. [152] revealed that the root interactions between maize and faba beans, along with the root exudates from maize, significantly improved the symbiotic N₂ fixation and nodulation in faba beans grown alongside maize. Intercropping can make crop roots release more organic acids and control the mineralization of organic phosphorus, the dissolution of inorganic phosphorus, or both. This makes more phosphorus available in the soil. Recent research shows that growing cereals and legumes together improves metabolic function and changes the structure of the soil’s microbial community through interactions between species [153]. According to Zhang, et al. [154], elevated carbon uptake by maize (Zea mays L.) promoted nutrient cycling by altering the abundance of functional groups in soil microbes and improving the stability and complexity of microbial networks in soybean/maize intercropping systems. Teshita, et al. [155] proposed that, particularly in low-nitrogen soils, intercropping maize with alfalfa (Medicago sativa L.) could enhance the structural complexity of the soil food web. Moreover, intercropping improves agricultural sustainability by utilizing crop diversity to exploit synergistic interactions across species [156]. This method improves crop yield and nitrogen utilization efficiency through similar and beneficial interactions. The rhizosphere of leguminous plants cultivates distinct microbial communities, including nitrogen-fixing bacterium (nifh) populations, via root exudates in legume-based intercropping systems, enhancing ecological benefits such as nitrogen fixation and phosphorus mobilization [157,158]. Within these approaches, maize/soybean intercropping is notable for its effective transfer of fixed nitrogen from soybean to maize, hence improving nitrogen efficiency and yields [159]. Multiple factors, such as cropping configurations and fertilization methods, affect how well maize and soybean intercropping systems work. Improving microbes is crucial for nutrient absorption and yield maximization [160,161]. Understanding how rhizosphere microbial communities react, especially in terms of their ability to fix nitrogen, would help improve intercropping patterns and fertilizer management, which would lead to more sustainable farming and food security.

5.2. Crop Rotation and Their Effects on Rhizosphere Processes and Soil

Crop rotation is a conventional and effective method for maintaining agroecosystems, managing biodiversity by improving soil health, suppressing disease and pest occurrences, and hence enhancing crop yields [162]. The efficiency and value of crop rotation are dependent upon various elements, including the types of crops utilized in the rotation, the sequence and frequency of specific crops, the duration of rotation, the agronomic history of the agricultural land, and the properties of the soil [163,164]. Recent studies reported that farmers had used crop rotation through traditional methods to manage crop pests and diseases and manage soil productivity [165,166]. Usually, these crop rotations involve growing three or four different types of crops in a sequence. However, with increasing food demand and agricultural production in recent years, many farmers grow just one or two crop species, with pesticides and mineral fertilizers contributing to compensate for the lack of crop rotations [167]. The crop rotations are not always helpful and also decline the soil quality and crop production have been reported with the number of crops grown linked with short rotation or continuous cropping, including soybean, sugarcane, maize, wheat and oilseed rape [168]. Interestingly in crop rotation, oilseed rape is very important for the rotation and even highly profitable when grown as a break crop for cereals. Crop rotations with oilseed rape and maize affect the dynamics and structure of soil plant-associated microbial communities, are known beneficial for soil health via suppression of soil-borne diseases and plant growth promotion [169]. Microbial species living nearby or associated with plants are directly influenced by the root’s architecture and the chemical characteristics of root exudates when we rotate with maize or oilseed rape crops [170]. The direct influence of plant roots around soil is known as the rhizosphere. The rhizosphere is the habitat of plant beneficial microorganisms and plants pathogens [171]. With the research evidence of Benitez, Osborne and Lehman [169], crop rotations promote beneficial plant growth-promoting microbes and affect the soil microbial community in the rhizosphere, and influences maize seedling growth characteristics.

Furthermore, rotating crops with grain legumes can significantly improve the yield and protein content of subsequent wheat crops, owing to the increased nitrogen availability in the soil from legume biological fixation [97]. Leguminous crops (such as peas and chickpeas) and various chickpea genotypes (cultivars) in rotation can alter soil functional microbial populations and affect the productivity of pulse crops and subsequent wheat crops. Different crops can produce root exudates and distinct residues that enhance soil microbial diversity and activity, as well as microbial biomass, nitrogen and carbon cycling [164,172,173]. Modifications in crop rotation duration and frequency of identical crops throughout time might influence the prevalence of root rot diseases and improve crop production and soil health. Short series rotations exhibit heightened sensitivity to host-specific diseases, resulting in poorer yields compared to lengthier series rotations [167,174]. While, Lupwayi, et al. [175] found that wheat phase of a five-year rotation exhibited greater microbial biomass in both rhizosphere and bulk soil compared to three-year rotation of wheat phase, likely due to increased carbon inputs from crop residues. In Canada particularly western part, two phases of pea in a four-year rotation increased soil nitrogen levels, whereas three legume phases markedly altered the function and composition of the rhizosphere bacterial community in comparison to continuous wheat cultivation and growth [176]. Increasing the rate of one crop in rotation can be detrimental for soil health. For example, Bainard, et al. [177] observed that a higher pulse phase in rotation caused host-specific fungal pathogens to build up in the soil, which could make rotation less beneficial for crop yield and soil health. Meanwhile, an additional crucial factor in crop rotation design is the ability of soil-borne diseases to utilize alternate crops as hosts or to remain dormant in the soil for extended periods, as well as the response of these crops to disease. Utilizing non-host plants in crop rotations to manage diseases transmitted by the soil is critical for mitigating yield losses, particularly given that many pathogens can persist in the soil for extended periods as spores or other latent forms in the absence of their preferred host plants [167,178]. For example, Nayyar, et al. [179] reported that Fusarium root rot in peas cultivated in rotation on the Canadian prairie was associated with a restricted soil microbial community and reduced populations of arbuscular mycorrhizal fungi and beneficial bacteria. In certain instances, continuous cropping with enhanced crop diversification elevated the population of antagonistic soil microorganisms, hence lowering the populations of soil pathogens and reducing the “take-all” effect in wheat. Typically, incorporating three or more crops within a cropping system can improves soil health and optimizes the productivity of crops [166,167]. However, the benefits of crop rotation are practical; understanding the specific effects of crop systems and how they affect subsequent crops will encourage and adopt a worthy crop rotation, which will promote soil health and increase crop productivity. These findings make it easier to create customized interventions that use microbial populations to maintain soil health, decrease the emissions of greenhouse gases (GHGs) and crop production, and the efficient use of resources in intercropping systems. According to references, we propose intercropping in agroecosystems, as depicted in the conceptual (Figure 5).

6. Indicators for Assessing Soil Health in Agroecosystems

Soil is a highly intricate and complex, multifunctional system including gaseous, liquid, and solid elements that interact through various chemical, physical, and biological processes. A healthy soil sustains agroecosystems and facilitates the provision of essential services to ecosystem [180]. Moreover, soil health typically refers to the capacity of soil to operate as a crucial living system that supports biological productivity, preserves both soil and plant health, enhances environmental quality, and maintains an agroecosystem [181]. In order to evaluate and sustain agroecosystems, it is essential to consider the biological, physical, and chemical functions and traits of the soil, particularly the biological ones that serve as sensitive indicators of soil health and quality [182]. Microbiological and biochemical markers show that the variety and activity of soil microbes are important for the long-term health of agroecosystems because they keep soil health functions going, like cycling carbon and nutrients [183]. Microbial indicators exhibit more sensitivity than physical traits to environmental alterations such as soil usage and management; hence, they enable early detection and forecasting of changes and disturbances in environmental sustainability [184]. Related studies recognize soil microbial biomass, which includes fungi, bacteria, and algae, as a primary biological indicator of soil health and as a crucial source of nutrient cycling and delivery relative to plant demand [185]. Additionally, through photosynthesis, plants fix and transfer carbon as carbohydrates into the food web, making it one of the most critical biological processes on Earth [183]. Both agricultural and forestry soils widely use soil respiration and microbial biomass as bio-indicators of soil health.

We expect biochemical indicators to effectively integrate the combined impact on soil’s chemical, physical, and biological processes and characteristics, making them suitable for diverse management and environmental conditions. This review aims to elucidate and augment our focus on soil quality and related research, particularly with biochemical soil quality indicators such as enzymatic and microbial activity [186]. Due to their role in nutrient cycling through microbial processes, soil enzyme activities frequently serve as sensitive indicators of soil biochemical quality and as measures of ecological quality. They can effectively respond to both anthropogenic and natural alterations in soil and are easily quantifiable [187]. However, soil enzymes are important in functioning of soil ecosystems, including nutrient and carbon cycling, and maintenance [188]. For example soil enzymes have an important role in C (β-glucosidase and galactosidase), N (urease), P (acid phosphatases and alkaline) cycling, and these enzymes play crucial roles in breakdown of OM and release nutrient, which are important for soil health and plant growth promotion. Dick and Tabatabai [189] reported that soil enzymes serve as reliable indicators of soil quality because of their close association with soil biological processes, their ease of measurement, and their swift response to alterations in soil management. In summary, soil enzymes are valuable tools for assessing both long and short-term changes in soil quality and management practices.

Furthermore, indicators of soil health for sustaining agroecosystems need to be associated with soil processes and responsive to alterations in management and environmental conditions. Soil biological traits, such as microbial biomass and its activities, serve as sensitive and rapid indicators that capture responses and data from diverse environmental conditions [190,191]. We use soil biological metrics, such as microbial density, activity, and biomass, as indicators of soil health [192]. Furthermore, a specific drawback of employing soil microbial characteristics as soil health indicators is the technological limitations encountered in the research of soil microbial populations. Molecular techniques that are more advanced, especially next-generation sequencing (NGS) methods (such as shotgun sequencing for structural and amplicon sequencing and functional microbial diversity investigations), have made it possible to study the part of soil microbial communities that can’t be grown in a lab. This is because most soil microorganisms don’t grow on media or in a lab setting. However, while analyzing the data, we must acknowledge the limitations of these novel methodologies. In conclusion, we can use soil to focus on agroecosystem maintenance and enhance rhizosphere processes; soil health indicators are used to inform management techniques, optimize fertilizer application, and promote sustainable crop productivity.

7. Integrated Agricultural Practices for Improving Rhizospheric Processes

Integrated agricultural management established soil properties (biological, chemical, and physical properties) that influence nutrients cycling, soil microbial community composition and structure, and enhance the rhizospheric process [193]. The disturbance of rhizosphere processes and depletion of organic matter are restraining agricultural productivity around the globe via improper agricultural practices. To reduce adverse effects, integrative biofertilizers, crop rotation, green manuring, intercropping, and mulching practices should be promoted and tested worldwide to improve the rhizosphere processes and agroecosystems resilience. In short about integrated agricultural practices (IAP), are based on the integration of different crops, livestock wastes, and fertilizers into production systems that, through valuable management practices, maintain a high level of soil fertility, productivity, and quality and pursue to reduce external inputs of agrochemical and fertilizers, and enhance the functions of soil inside biological cycles and its processes. Mixed crop-livestock and other available resources such as seed primed, the basis of integrated agricultural practices, allow the most efficient and effective use of natural resources and biological cycles to improve belowground activities [194]. Sarkar, et al. [195] reported that microbial-assisted nutrient management is a sustainable, eco-friendly, and cost-effective option under integrated agricultural systems. The usage of less amount of agrochemicals but provides support organically or naturally to protect the environment from nutrients denitrification or runoff, land degradation, and soil pollution. Duarah, et al. [196] stated that reducing the amount of synthetic NPK fertilizer application and seed priming (with bacteria) can significantly improve the nitrogen use efficiency. While, Entesari, et al. [197] witnessed that bio-priming seeds of soybean with Trichoderma sp., prior to planting enhanced the nutrient status of crop and improve the crop yield. Phosphorus (P), an essential nutrient, is often fixed in the soil and forms complexes with metals, limiting its availability to plants. However, certain fungal and bacterial communities have a trait called P solubilization, which allows them to convert unavailable or fixed phosphorus into forms that plants can absorb. Kim, et al. [198] reported that incorporating green manure can help re- mobilize phosphorus and make non-exchangeable potassium available, circulating nutrients more efficiently. This integrated approach also enhances phosphorus availability, which is crucial for both plant growth and the activity of soil microorganisms. However, advantages of IAP are the selection of crops and available resources into creative integrated agricultural systems that can effectively achieve following points: minimize the disease and insect problems, minimize the outputs and reduces the energy requirements, reduces the need for agrochemical and pesticides, and also reduces the climate and economic fluctuations risks. Improved rhizosphere processes promote healthy soil, allowing agroecosystems to continue providing ecosystem services that benefit humans and animals. Thus, optimizing the rhizosphere is essential for the agroecosystem’s resilience and future food and fiber production. To achieve these benefits are significant for the improvement of the rhizospheric processes and agricultural systems.

8. Concluding Remarks and Future Directions

Understanding the significance of the rhizosphere and its interactions with microorganisms holds tremendous potential for fostering sustainable agroecosystems. The rhizosphere provides an ideal environment for a variety of microbes that enhance plant growth by improving nutrient availability, controlling pathogens, facilitating hormone signaling, and altering soil structure. Exudates from plant roots, green manure cultivation, and intercropping of various plant species are key drivers influencing microbial community dynamics in the rhizosphere. Emerging research underscores the importance of rhizosphere engineering, coupled with green manures and intercropping, in delivering essential life-support functions for host plants, including nutrient uptake, growth promotion, tolerance to abiotic stress, disease resistance, and the overall maintenance of agroecosystems. The cultivation of green manures offers multifaceted benefits: improving soil health, enhancing nutrient cycling, increasing carbon sequestration, reducing greenhouse gas emissions, decreasing reliance on synthetic fertilizers, and rebuilding rhizosphere microbial communities. These practices also contribute to economic advantages by stabilizing crop yields and enhancing soil fertility through organic matter accumulation. Additionally, green manures improve water conservation, soil structure, and pest and weed management, all of which are critical for supporting rhizosphere functions and maintaining agroecosystem stability.

A thriving agroecosystem upholds soil fertility, prompting the production of food and fiber, which is crucial for both human and animal health. Optimizing rhizosphere activities such as nutrient cycling and beneficial microbial interactions improves soil structure, nutrient availability, and plant growth. These enhancements increase tolerance to environmental impacts and reduce synthetic inputs, ensuring agricultural system sustainability. Improved rhizosphere processes promote healthy soil, allowing agroecosystems to continue providing ecosystem services that benefit humans and animals. Thus, optimizing the rhizosphere is essential for the agroecosystem’s resilience and future food and fiber production.

There is growing interest in utilizing microbial inoculants, microbial-derived products, green manures, and intercropping systems to bolster rhizosphere activity, enhance crop productivity, and sustain soil quality. These methods have the potential to enhance the long-term sustainability of low-input agroecosystems, contributing to food security and environmental resilience. The findings from this review provide valuable insights to agronomists, soil scientists, and crop managers on optimizing rhizosphere processes to improve agroecosystem resilience. In closing, the rhizosphere will be central to future ecological innovations in agriculture, driving both resilience and sustainability. However, further experimental research is required to fully unlock the prospective of the rhizosphere. Future studies should focus on integrating advanced technologies, such as microbial genomics and precision agriculture, to optimize rhizosphere management for more resilient and sustainable agroecosystems. The development of smart agricultural strategies, coupled with policy support, will be vital for addressing the growing challenges posed by climate change and soil degradation.