Diversity in Soil Microbes: An Essential Factor in Food Security and Human Health-A Review

Introduction

By 2050, it is expected that there will be 9.7 billion people on the planet, greatly increasing the demand for both water and food 1. By then, food production will have to increase by 70% in order to satisfy this demand. Historically, intensive agricultural techniques, such as the heavy use of water, agrochemicals, and fertilizers based on minerals, have been used to achieve this rise. Nevertheless, these practices have aided in resource depletion, contamination of the environment, and destruction of land. n. A wide variety of microorganisms are hosted by plants in the rhizosphere (root zone), phyllosphere (surface tissue), and endosphere (interior tissue), resulting in an elaborate ecosystem with multiple niches for life. These microbes engage in a variety of ways that may be advantageous, neutral, or dangerous.

In addition to being an essential resource for food, fibre, and biodiversity, soil is also important for agriculture, human health, and the environment 2 as healthy soil gives plants access to clean water and key nutrients. Even though the land produces 95% of our food, we frequently underestimate the role that healthy soil plays in the food chain. The resilience of ecological systems, plant development, and soil health are all dependent on the soil microbiome 2. It is made up of a variety of microbes, including algae (e.g., Chlorella), fungus (e.g., Mycorrhizae, Trichoderma), and bacteria (e.g., Rhizobium, Bacillus). By fixing nitrogen and breaking down organic materials, bacteria improve the nutrients in soil. Through symbiotic connections, fungi enhance plants' ability to absorb nutrients, and through the process of photosynthesis, algae provide organic matter.

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When these organisms work together, they improve resistance towards diseases, soil structure, and water retention capacity that support a sustainable agricultural system 3. Additionally, the production of secondary metabolites by various microbes, many of which act as antibiotics, fungicides, and other medications, is influenced by the soil microbiome [Fig.1] . Antibiotics like streptomycin are produced by bacteria like Streptomyces, whilst antifungal substances are secreted by Bacillus species. Penicillin is a renowned antibiotic that is produced by fungi, such as Penicillium 4. Algae, including Cyanobacteria, produce bioactive substances that may have medical applications. These chemical compounds offer plants pathogen defence as well as a wealth of information for the development of new drugs for human use 5. Thus, this review focus on the importance of soil microbiome across medicine, agriculture, and the environment.

Soil Microbiota for Human health as therapeutic agent

In order to promote knowledge transfer for sustainable agriculture, agricultural microbiology is essential to the integration of biotechnology, microbiology, and microbial ecology. There are several approaches focused for human health improvement which have been discussed in previous literature by the use of computational methods, protein targeting, and exploration of natural products. Natural products are the chemicals that are useful in the treatment and management of a wide range of infectious and non-communicable disorders 6-15. they are believed to be affordable, safe, and have substantial bioactive potential in the treatment of a wide range of illnesses that are resistant to several medications, such as metabolites originating from fungus, bacteria, and plants. Plants and microbes are a rich source of naturally occurring chemical substances that possess potent antioxidant properties. These compounds have potential use in the treatment of hepatic, neurological, and cardiovascular illnesses, diseases associated with oxidative stress 16-24. In order to restore microbiota in agricultural and natural ecosystems, it is crucial to comprehend the microbial flux between soil, plants, and animals 25. Due to its distinct bioactive chemicals and ecological roles 13 soil microbiota, which is made up of a wide variety of microorganisms such as fungi, bacteria, and archaea, has great promise as therapeutic agents 26 [Fig. 2]. Using soil microbiota for medicinal purposes involves the following major uses.

Figure 2: Utility of Soil Microbes as therapeutic agent

1. Antibiotics Production: A variety of microbes, including those in the genera Bacillus and Streptomyces, are capable of producing antibiotics, which are useful against infections 27. Certain bacteria isolated from natural sources play a crucial role in treating human diseases. For example, Streptomyces species produce antibiotics like streptomycin, which inhibits protein synthesis in harmful bacteria, treating infections such as tuberculosis. Lactobacillus species, commonly found in probiotics, help restore gut flora balance and treat gastrointestinal disorders. Another example is Escherichia coli, genetically modified to produce insulin for managing diabetes, where it synthesizes the hormone used in insulin therapies. These bacteria work by either directly attacking pathogens or producing vital compounds for human health. Penicillin and streptomycin act as a natural antibiotic produced by microbes. Among microbes, one of the most common microorganisms, Actinomycetes, can be found in a variety of locations including both soil and water. They are well-known for their inherent capacity for yielding antibiotics, which include tetracycline, macrolides, chloramphenicol, nucleosides, and polyenes 28, erythromycin, gentamycin, rifamycin, and streptomycin, etc. 29, 30. These microbial compounds are essential for treating a wide range of diseases, but despite their enormous potential to produce secondary metabolites, difficulties persist in streamlining identification and production procedures 31, 32. Moreover, the emergence of microbial immune towards antibiotics highlights the pressing need to investigate alternative sources of antibiotics 33. A number of fungi are recognized for releasing antibiotics which help manage diseases. Penicillium chrysogenum generates penicillin, used to deal with bacterial infections such as strep throat and syphilis. Cephalosporium acremonium produces cephalosporins, which are efficient against skin infections, respiratory illnesses, and urinary tract infections. Aspergillus terreus yields lovastatin, primarily utilized to lower cholesterol but also displaying antimicrobial effects. Fusidium coccineum produces fusidic acid, utilized in treating skin infections including impetigo and infected wounds 34. These fungal antibiotics or fungal mediated nanoparticles have been essential in medical treatments 30, 35, 36

1. Probiotic Applications: The probiotic potential of some soil-derived microorganisms is being investigated. Through fostering advantageous microbial communities, improving digestion, and bolstering the immune system, these microbes help improve gut health 37. As probiotics, for example, many bacteria found in soil have been demonstrated to possess antibacterial qualities and may be able to stabilize the gut microbiota. Probiotics originating from microorganisms found in soil are crucial for improving immunological performance. These helpful microbes, which are frequently discovered in soil, influence the gut microbiota, which is closely related to the immune system. Soil-based probiotics, such as some species of Bacillus and Lactobacillus, can boost the development of immune cells, including T cells and macrophages, by maintaining a healthy balance of gut bacteria 38. By strengthening the gut barrier and lowering inflammation, they help improve the body's defences against infections. Thus, general immunity is bolstered and potential defences against infections, autoimmune disorders, and allergies may be strengthened.

1. Immune modulation: Soil microbes play an important role in immune modulation by interacting with the human immune system and influencing its response to pathogens 39. Bacteria such as Lactobacillus, Bifidobacterium, and Bacillus subtilis found in soil and the environment can promote immune tolerance and anti-inflammatory responses. These microbes interact with immune cells like macrophages, dendritic cells, and T-cells through the release of metabolites such as short-chain fatty acids (SCFAs), which help regulate immune function 40. Certain soil-derived mycobacteria, such as Mycobacterium vaccae, have been shown to trigger anti-inflammatory pathways by stimulating the production of anti-inflammatory cytokines like IL-10. They also influence the gut microbiota, which plays a key role in shaping immune responses through the gut-associated lymphoid tissue (GALT). Additionally, these microbes can help prime the immune system by promoting a balanced Th1/Th2 response, enhancing resistance to autoimmune diseases and allergies. Through their effects on both innate and adaptive immunity, soil microbes contribute to a healthier, more regulated immune system.

Soil-Microbiota in Sustainable Agriculture

One prospective long-term answer to concerns with food security, human health, and environmental pollution is the employing of soil bacteria in agriculture. It is anticipated that important agricultural microorganisms would be crucial to a number of approaches meant to lessen the need for agrochemicals while preserving crop yield. This is particularly valid for strategies like integrated control of diseases and pests and the control of nutrients. Microbes are used in agriculture as bio stimulants, which help plants absorb nutrients41, biocontrol agents, which help manage pests and diseases, and biofertilizers 42. There is no need for repeated applications because these organisms are self-sustaining and self-replicating 43. A variety of environmental circumstances, plant species, and the makeup of the microbial community influence how well these microbes work to improve soil health and encourage plant development. 6 These microorganisms generate substances that inhibit pathogenic organisms and regulate phytopathogens, such as auxins, gibberellins, and antibiotics. Additionally, they are essential to crop biofortification, raising the concentrations of micronutrients like zinc, iron, and selenium in staple crops. These helpful bacteria can lessen the negative effects of conventional farming methods by encouraging plant growth, nutrient cycling, cutting waste, and decomposing pollutants and pesticides 44. Multiple benefits of sustainable agriculture comprise improved social welfare, economic prosperity, and environmental protection. Communities with greater diversity are more durable and robust to environmental stress. Sustainable agriculture lowers input costs financially by reducing the demand for synthetic pesticides and fertilizers [Fig. 3]. Furthermore, it creates new markets for products made organically and sustainably, giving farmers more chances to make money. Sustainable agriculture benefits both farmers and consumers by lowering environmental damage and enhancing soil health, which results in a more dependable food system 44. Improved nutritional value, greater farmworker safety, and community-focused methods that promote long-term agricultural sustainability are examples of social advantages.

Figure 3: Advantages of Sustainable Agriculture

1. Biofertilizers: Now a days, maintaining food security and sustainability at the same time is getting more and harder. To enhancing the crop yields and agroecosystem health while reducing the effects of climate change is the goal of sustainable agriculture. It entails combining ecological, chemical, physical, and biological aspects. Thus, by using microorganisms in the form of biofertilizers, biodiversity is preserved through improved root growth, nitrogen cycling, water retention, carbon storage, pollution filtration, and nutrient cycling 45 as conventional agricultural activities, nevertheless, has the potential to deteriorate soil health, underscoring the necessity of methods to enhance it. Biofertilizers are natural fertilizers containing living microorganisms that enhance plant growth by increasing the availability of essential nutrients. These microorganisms, including bacteria, fungi, and cyanobacteria, form symbiotic relationships with plants, improving soil health and reducing the need for chemical fertilizers. Types of biofertilizers include nitrogen-fixers like Rhizobium and Azotobacter, phosphate-solubilizers like Pseudomonas, potassium-solubilizers like Frateuria aurantia, and mycorrhizal fungi that enhance nutrient absorption. The mechanism involves these microbes converting atmospheric nitrogen into usable forms, solubilizing phosphorus and potassium, or extending the plant's root system for better nutrient uptake. Examples include Rhizobium for legumes, Azospirillum for cereals, and mycorrhiza for various crops. Overall, biofertilizers promote sustainable agriculture by boosting crop productivity, improving soil structure, and reducing dependency on chemical inputs. Biofertilizers are eco-friendly, improve soil health, and provide a sustainable nutrient supply, unlike chemical fertilizers which can harm the environment. They are cost-effective and enhance beneficial soil microbes, promoting long-term plant growth.

In current agriculture, integrated pest management (IPM) is a useful strategy that tries to keep insect populations under controlled at reasonable levels without endangering the environment or public health. Integrated Pest Management (IPM) integrates diverse techniques to avert pest infestations and employs plant protection chemicals in a cost-effective and ecologically conscious manner. Natural pesticides include substances like limonene, pyrethrins, rotenone, and sabadilla and are produced from plants including neem, custard apple, tobacco, and pyrethrum 46. Pests like fleas, aphids, ants, beetles, and caterpillars are managed using these all over the world. Effective pest management while lowering hazards to the environment and public health is the aim of integrated pest management (IPM).

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1. Intercropping: In intercropping, multiple crop species are grown together in the same field to maximize resource use, increase biodiversity, and promote sustainable agriculture 57. Common plant combinations include cereals (e.g., maize, wheat) with legumes (e.g., beans, peas), as legumes fix atmospheric nitrogen, enriching the soil for the cereals. Other combinations include root crops (e.g., carrots, onions) with leafy crops (e.g., lettuce), and tall plants (e.g., corn) with shade-tolerant crops (e.g., squash). Intercropping can be practiced in various seasons depending on the crop species involved, typically based on complementary growing patterns—warm-season crops (e.g., corn) are often paired with cool-season crops (e.g., peas or spinach) 58. Mechanistically, intercropping enhances sustainable agriculture by optimizing light, water, and nutrient use. Tall plants provide shade for smaller ones, while deep-rooted crops bring up nutrients from lower soil layers, benefiting shallow-rooted plants 59. The combination of different plants breaks pest and disease cycles, reducing the need for pesticides. Microbial activity is also stimulated by intercropping. The diversity of plant roots supports a wider range of beneficial soil microbes, such as nitrogen-fixing bacteria in legume roots and mycorrhizal fungi, which improve nutrient uptakes for all plants. Increased organic matter from diverse crops supports microbial populations, boosting soil health, nutrient cycling, and long-term agricultural sustainability.

1. Conservation Tillage: Using a Plow and leaving at least 30% of crop residue on the soil's surface following harvest is known as conventional tillage (CT). To counteract the detrimental consequences of traditional farming, sustainable agriculture supports conservation tillage (CT) techniques including reduced tillage (RT) and no tillage (NT) 60. NT modifies the dispersion of soil microorganisms and raises the carbon and nitrogen content in the surface soil, improving moisture, microbial activity, and enzyme function. Although they may result in decreased crop yields, these techniques minimize the danger of erosion, increase soil stability, variety, and fungal networks, and cut tillage expenses. Furthermore, the amount of organic matter in surface soil influences gas exchange, rainfall, fertilizer efficiency, and organic material performance 61.

1. Green Manuring: Green manure crops such as sunn hemp and dhaincha improve soil fertility, promote microbial development, and improve soil framework through root secretions and polysaccharide gums 62 .Breaking down more gradually than traditional nitrogen fertilizers, GM crops result in greater crop yields, more effectively soil health, and minimized nitrogen loss. Green manuring (GM) is the feasible practice of adding green plants to the soil prior they bloom to boost soil nutrients and organic material 63.

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1. Vermicomposting: Often referred to as "the farmer's friend," earthworms are important for improving the chemical, microbiological, and physical characteristics of soil. They release more organic materials for microbial breakdown by dissolving big soil particles and leaf litter. Earthworms use both aerobic and anaerobic bacteria to break down organic waste into vermicompost, which is a rich source of micro- and macronutrients that are vital for human health as well as microbial enzymes 66. Their actions enhance the availability of nutrients and inhibit pathogenic microorganisms while fostering healthy microflora. Earthworms increase soil aeration through their digging, which promotes microbiological activity. Beneficial soil microbes such as rhizospheric bacteria like Pseudomonas, Rhizobium, Bacillus, Azospirillum, and Azotobacter, which all assist plant growth, proliferate more in this improved habitat 67. Earthworm-soil microbe interaction improves overall soil health and nutrient cycling by indirectly influencing soil chemical processes. In order to preserve productive, healthy soils for sustainable agriculture, worms that live are essential for their contributions to soil structure, aeration, and diversity of microbial species.

1. Table 1 offers a succinct summary of some important microbes and the beneficial substances they generate, emphasizing the wide range of uses they have in environmental management, the agricultural sector, and medicine.

Table 1: Important microbial strains and the beneficial metabolites

Microbe	Released Compounds	Utility	References
Streptomyces	Antibiotics (e.g., Streptomycin, Erythromycin)	Treatment of bacterial infections, including tuberculosis and other serious infections	68
Bacillus	Bacitracin, Polymyxin, Lipopeptides	Antibiotic use and pest control; some strains used as biopesticides in agriculture	69
Penicillium	Penicillin, Griseofulvin	Antibiotic for treating bacterial infections and fungal infections	70
Actinomyces	Actinomycin, Streptothricin	Antibiotic and anti-tumour agents; useful in cancer treatment and bacterial infections	71
Pseudomonas	Pyocyanin, Phenazines, Antibiotics	Antimicrobial properties, plant growth promotion, bioremediation of pollutants	72
Trichoderma	Enzymes (e.g., chitinase, cellulase)	Biological control of soil-borne plant pathogens, promoting plant growth	73
Bacillus thuringiensis	Cry proteins	Biopesticides for controlling insect pests in agriculture	74
Clostridium	Acetone, Butanol	Used in industrial fermentation processes; potential for biofuel production	75

Sustainable Agriculture for Environmental Health

The excessive application of fertilizers and agrochemicals throws off the nutrient cycles of the soil, and pesticide runoff contaminates water systems, damaging insects that are beneficial, plants, and soil microbes 76. In addition to creating temperature changes and inconsistent rainfall, these farming methods also contribute to climate change. This damages the soil's composition and productivity by reducing soil moisture levels. In sustainable agriculture, soil microbiota is essential for fertility of the soil, plant growth, stress resistance, and the recycling of nutrients. Through rhizospheric, endophytic, and phyllospheric interactions, different microbial communities assist plants in accessing nutrients either symbiotically or autonomously 77. To further safeguard crops, bio fungicides and biopesticides are applied. Conserving natural resources like soil and water is essential for ensuring nutrient availability, agricultural productivity, human health, and environmental safety. Sustainable farming practices focus on protecting these resources, preventing degradation, and maintaining soil health and biodiversity. Farmyard manure (FYM) and crop residues are examples of how renewable and non-renewable resources are effectively used in sustainable agriculture to meet food and fibre demands, improve farmers' livelihoods, and protect environmental quality 78. Other sustainable farming practices include agroforestry, growing cover crops, conservation agriculture, green manuring, intercropping, crop rotation, and the use of biofertilizers.

In terms of environmental health, microbes such as Alcaligenes and Sphingomonas degrade organic pollutants and detoxify heavy metals through bioremediation 79. By metabolizing toxic compounds and converting them into less harmful forms, these microbes reduce pollution and restore soil ecosystems. Overall, soil microbes sustain plant growth, improve soil aeration and water retention, and mitigate environmental contamination, making them crucial for both soil health and environmental restoration.

Bioremediation

To remove environmental pollutants like pesticides, heavy metals, and hydrocarbons, soil microorganisms are used in bioremediation procedures. By breaking down or changing dangerous compounds into less toxic forms, these bacteria help restore damaged habitats and improve the quality of soil and water. Soil microbes play a crucial role in bioremediation by breaking down or neutralizing pollutants in contaminated environments. Bacteria such as Pseudomonas, Bacillus, and Mycobacterium degrade hydrocarbons and organic pollutants through enzymatic reactions, transforming them into less harmful substances 80. Fungi like Trichoderma and Aspergillus break down complex pollutants like heavy metals and pesticides by secreting extracellular enzymes and organic acids. Actinomycetes, like Streptomyces, contribute to the degradation of aromatic compounds in soil. In the case of heavy metals, microbes can employ biosorption, bioaccumulation, and biomineralization to immobilize or detoxify metals. Some microbes, like Thiobacillus, oxidize harmful substances like sulfur compounds into less toxic forms 81. These microbial processes improve soil health and reduce pollution in a sustainable way, making bioremediation a valuable tool for environmental restoration

Factors affecting microbial diversity

The impact of alterations and disruptions to the environment on soil bacterial communities has been investigated in recent research. The makeup of the microbial community is shaped locally by variables such crop rotation, carbon and nitrogen availability, and type of vegetation 82. Soil pH is a more significant predictor of microbial structure on a broader continental scale. Redox potential (Eh), which is crucial for sustaining life through oxidation-reduction reactions, has not gotten as much attention as pH. According to research, vegetation type has a major impact on the organization of microbial communities, and soil parameters, rather than land-use practices, are the main determinants of bacterial diversity in soil 83.

Role of Biotechnology in Agriculture

While the mid-1900s Green Revolution increased food production, it also had unfavourable ecological effects such pollution, climate change, and decreased biodiversity. Through the use of transgenic crops and genetically modified organisms (GMOs), biotechnology and microbiology provide a sustainable substitute while increasing agricultural 84. Sustainable agriculture depends on microbial biotechnology because it creates biopesticides, bioherbicides, and fertilizers that solve biotic and abiotic problems and encourage environmentally friendly farming methods [Fig. 4]. This depends on genetically modifying microbial organisms to lower the virulence of diseases, enhance biocontrol, and facilitate bioremediation. The accomplishment of microbial biotechnology depends on soil microbiomes, which offer a variety of rhizosphere homes for a broad spectrum of microbes. Microbiome research has been transformed by advances in genetic sequencing and computation, such as metagenomics and Next-Generation Sequencing (NGS), which allow for quick gene annotation and high-throughput analysis. By revealing the diversity, composition, and interactions of microbes, these technologies aid in the development of methods to enhance nutrient absorption and stress tolerance 85. Microbiomes need to be carefully controlled and altered in order to enhance agricultural output and reduce environmental impact. Among the many advantages of biotechnological interventions are less chemical consumption and improved environmental stewardship. More environmentally friendly agriculture is supported by genetically modified crops that have longer shelf lives, are resistant to fungi and insects, and can withstand herbicides. In order to promote knowledge transfer for sustainable agriculture, agricultural microbiology is essential to the integration of biotechnology, microbiology, and microbial ecology 86. In order to restore microbiota in agricultural and natural ecosystems, it is crucial to comprehend the microbial flux between soil, plants, and animals.

Figure 4: The utilization of microbial technology in numerous applications

Future Prospects

One of the biggest scientific challenges in agricultural soils is maintaining rhizosphere biodiversity 87. While microbial inoculants have shown promise in treating specific agronomic problems, their limited applicability in many environmental settings stems from their variable effectiveness. Global interest in sustainable agriculture and the microbiome is rising as worries about food safety and technological breakthroughs grow 88. It is essential to comprehend the effects of climate change and agronomic practices on the composition and activity of soil microbes. Because of its ability to lessen soil degradation brought on by the widespread use of agrochemicals and mineral fertilizers, sustainable agriculture is becoming more and more important in a variety of areas.

The variety and abundance of organisms in the soil rhizosphere play a major role in determining the health of the soil, which is essential for human well-being and sustainable agriculture. The microbiome provides a non-transgenic way to increase agricultural yields and improve soil health 89. It is important for plant productivity and soil quality. Examining the effects of various production methods on the rhizosphere, plant systems, and soil will help us evaluate soil health markers more accurately and advance sustainability in the short- and long-term.

A number of the Sustainable Development Goals (SDGs) centre on soil, emphasizing the significance of sustainable land management 90. An essential component of maintaining agroecosystems is soil health, which is characterized by its ability to sustain biological productivity and improve environmental quality. Resources like fuel, water, and soil become scarcer as the world's population rises, underscoring the necessity of efficient and sustainable management 91. Even if conventional agriculture can feed a burgeoning population, the environment may suffer from its intensive methods. In general, organic farming techniques are superior to conventional approaches when it comes to fostering soil health.

Conclusion

Sustainable agriculture and human well-being depend heavily on healthy soil, which is mostly determined by the variety and quantity of microorganisms in the rhizosphere. The microbiome provides a natural way to raise agricultural yields and improve soil health by improving plant production and soil quality. An understanding of the effects that various agricultural techniques have on plant and soil systems can aid in advancing long-term sustainability. A number of the Sustainable Development Goals (SDGs) depend on healthy soil, which emphasizes the necessity of sustainable land management. An increasing number of people means that there are less resources available globally, making proper soil management even more crucial. Although productive, traditional agriculture can have negative environmental effects; in contrast, organic farming practices typically improve soil health. Due to conventional pesticides' 10% efficacy and decline in biodiversity, human activities pose a threat to microbial diversity. Enhancing soil health and biodiversity can be accomplished through integrated pest management and intercropping. The need for sustainable farming methods that guarantee food security and reduce environmental damage is growing as the population increases.

Conflict of Interest

Author declares that there is no conflict of interest.

Institutional Review Board Statement

Not applicable because human, animal, and cell lines samples and their data are not used in this study.

Informed Consent Statement

Not applicable.

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