Keywords

1.1 Introduction

Over the last decades, the global demand for food products has increased dramatically (Elferink and Schierhorn 2016). Global food demand is projected to enhance by 59–98% by 2050. In developing nations, food demand is also increasing, where the expansion of croplands resources is limited. In this scenario, for enhancing food production from existing land is hard to contribute to meet such an essential requirement (Bargaz et al. 2018). In order to address this problem, there is a need to enhance agricultural production sustainably through the use of efficient agro-bioresources, whereas soil microbial diversity can play an important role and also help to mitigate many problems associated with soil fertility, abiotic stress, insect pests, and diseases (Tilman et al. 2011; Utuk and Daniel 2015; Timmusk et al. 2017).

Soil serves as a plant growth medium and a major source of plant nutrients for quality food production. Nitrogen (N), phosphorus (P), potassium (K), and iron (Fe) are essential nutrients in crop production. Since most of the world’s soils are known to lack in these nutrients, and there would be a high demand for chemical fertilizers to meet the deficiency of nutrients. Hence, there is an urgent need to explore the potential of soil microbes for proper nutrient recycling and to recognize alternative, sustainable, environment-friendly options for reducing the use and impacts of synthetic fertilizers (Malav et al. 2015). In this scenario, maintaining soil fertility and crop productivity through the use of natural microbial diversity could be a well-off approach for enhancing the bioavailability of nutrients and increasing soil health (Singh et al. 2015; Timmusk et al. 2017; Bargaz et al. 2018; Rana et al. 2020a, b).

Soils are regarded as home to a wide range of macro- and microorganisms of rhizospheric nature. Soil microbe diversity is the fundamental key component in regulating biogeochemical cycles (e.g., C, N, P, and many more). Biogeochemical cycling affects soil ecosystems, composition, and functions as well as the capacity of soils to provide readily available nutrients to plants and animals by converting dead organic matter into various nutrient forms and many auxiliary services to living beings (Aislabie et al. 2013). Biofertilizers and organic manure could be regarded as a better choice in the crop integrated nutrient management approach (Chaer et al. 2011; Kour et al. 2020b).

In this integration, soil microbes such as bacteria, archaea, and fungi play various crucial roles. Though very little is acknowledged about the small creature that is accountable for countless soil mechanisms in natural and managed agro-ecosystems (Yadav and Sidhu 2016; Sahu et al. 2017). Soil microbes have an immense impact on relations between soil and plant and microbe and play a vital role in sustaining soil fertility (Yadav et al. 2020c). Nutrient cycling is the most significant of these relationships. This chapter explains the potential of soil microbes for proper nutrient recycling, including diversity, abundance, and distribution, and their role in nutrient cycling of soil microbe organisms.

1.2 Soil Health and Sustainability

Soil health is defined as functional ability within agro-ecosystem boundaries that support biological productivity, promote plant and animal fitness, and sustain environmental quality (Doran and Parkin 1994). Healthy soil functions are to resist erosion, support water, and nutrient cycling, inactivate toxic pollutants, suppress pathogens, maintain soil organic matter, and enhance overall system productivity and sustainability (Singh et al. 2015; Dubey 2016; Sahu et al. 2017). The soil health directly or indirectly impact plant health, environmental health, and food safety and quality (Singh et al. 2020a; Takoutsing et al. 2016). The soil serves as a biological filter for removing unwanted solids and gaseous constituents from air and water (Singer and Ewing 2000; Sahu et al. 2017). Healthy soils produce nutritious crops that, in turn, nourish humans and animals. Certainly, soil quality is directly linked with food quality and quantity. Maintaining healthy soil implies managing land sustainably (FAO 2015). Managing soil health is not only necessary for agricultural sustainability but also for ecosystem function. However, erosion, deforestation, and intensive agriculture have led to the degradation of many soils. As we know, soils constitute the foundation for sustainable agricultural development. Therefore, keeping healthy is essential to maintain food production for future generations.

1.3 Soil Quality

Soil quality is the capability of the soil to perform functions that are crucial to agriculture and the environment. Soil Science Society of America established soil quality as the ability of particular kind of soil to function, within a natural or managed ecosystem, to support plants and animals productivity, maintain or improve quality of water and air, and promote human health and habitation (Carter et al. 1997). Soil quality is not limited to agricultural lands although most soil quality work has been done in agrarian systems. It is a blend of inherent and dynamic soil properties. Soil properties include soil organic matter, nutrient, soil structure, water infiltration rate, bulk density, and water holding capacity. Soil properties can change over months and years in response to land use.

Soil properties are dynamic and changed, depending on land management practices and the inherent properties of parental material (rocks). The soil quality is necessary for the integrity of ecosystems and sustainably supports human and animal health, plant growth (Pankhurst and Doube 1997). Declining soil quality is a vital concern worldwide (Singer and Ewing 2000). Healthy soils improve crop yields, drought and flood tolerance, and air and water quality and balance a range of other functions to satisfy the demands of both farmers and the community. Soil quality is a critical part and basic features of sustainable agro-ecosystem management, similar to water and air quality. The relationship between soil quality, environmental quality, and agricultural sustainability is shown in Fig. 1.1.

Fig. 1.1
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Relationship between soil quality, environmental quality, and agricultural sustainability

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1.4 Soil Quality Indicators

Soil quality indicators are used to assess and identify soil properties that are responsive to management, affect, or associated with environmental consequences. There are three primary levels of soil indicators: chemical, physical, and biological. Soil quality integrates all of these indicators. Table 1.1 below shows the relationship between indicator type and soil function. Organic matter or soil carbon is itself an indicator of soil quality (Doran and Parkin 1996). It further affects other indicators like soil aggregate-stability (physical), nutrient availability (chemical), and nutrient cycling (biological). Chemical indicators give knowledge about equilibrium within soil solution (water and nutrients) and exchange sites (clay particles, soil organic matter), plant health, nutritional demands of plant and soil communities, levels of soil contaminants, and their availability for uptake by plants and animals.

Table 1.1 Indicator type and soil function relationship
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Physical indicators give knowledge about soil hydrologic properties, such as water retention, that affects the availability of water to plants. Some indicators are related to nutrient availability by their impact on rooting volume and aeration status. Other measures tell us about the erosional situation. Biological indicators provide information regarding the organisms that form the soil food web that is responsible for organic matter decomposition and cycling of nutrients. Soil microbial respiration indicates the soil’s ability to sustain plant growth (Doran and Parkin 1996).

1.5 Potential Role of Microbes for Soil Health

Soil microorganisms are responsible for making nutrient and organic matter cycling, in improving soil fertility, and leading to ecosystem productivity. Soil microbes form symbiotic relationships with plant roots (rhizobia, actinomycetes, mycorrhizal fungi, diazotrophic bacteria). They have the potential to improve nutrient mineralization and availability, produce plant growth hormones, and are antagonists of plant pests, fungi, or diseases (biocontrol agents). These organisms typically live in the soil, although, in some situations, they may help increase their communities by either inoculation or using several farm management techniques that improve their abundance and activity.

1.5.1 Soil as a Microbial Habitat

Soil represents a hospitable and dynamic habitat for microorganisms and is occupied by a wide range of microbial species. Microbes hold a fraction (<0.5%) of the total soil volume of topsoil. Usually, per gram of soil between one and ten million with a dominant number of bacteria and fungi is present (Fig. 1.2). The decomposition of organic residues and the cycling of nutrients is the significant role played by microbial species in soil (Pankhurst and Doube 1997). However, the soil also contains countless microorganisms capable of causing human disease (Rastegari et al. 2020b). Microbes are connected with the decay, and the nutrient cycling process is capable of sustaining and responding to quick changes in the environment. Hence, they rapidly adapt to environmental conditions, changes in microbial populations, and activities. Therefore, it can be considered as an excellent indicator of change in soil health (Singh et al. 2015; Sahu et al. 2017).

Fig. 1.2
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A soil aggregate or ped is a naturally formed assemblage of sand, silt, clay, organic matter, root hairs, microorganisms, and their secretions, and resulting pores. (Source: Fortuna 2012)

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Soil microbes are classified as bacteria, actinomycetes, fungi, algae, and protozoa. The interactions of gases, water, organisms, and organic and inorganic constituents can be visualized in a per gram of soil (Fig. 1.3). Up to ten billion bacterial cells survive each gram of soil in and nearby plant roots, a sphere is known as the rhizosphere. Rhizobacteria are the most abundant group of soil microbes, both in absolute number and in diversity. They perform a vital role in nutrient cycling and decomposition of organic residues (Pankhurst and Doube 1997).

Fig. 1.3
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Distribution of soil microorganisms with depth

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1.5.2 Soil Microbes and Agro-Ecosystem Stability

Ecosystem stability is an essential part of sustainability, where microbes play a critical role. Stability of equilibrium of any system has two components: (i) Resistance—the ability of the ecosystem to continue to function without any change when stressed by disturbance (ii) Resilience—the strength of the ecosystem to recover after disturbance (Odum 1989; Seybold et al. 1999). Soil is the junction between the air, water, minerals, and organisms and is performing various functions in the natural and agro-ecosystem that we call ecosystem services. Soils play an essential role in the entire natural ecological cycles—C, N, oxygen, water, and nutrient, and also provide benefits through their contribution in several unique processes called ecosystem services. Suggested practices to increase agro-ecosystem stability and function are given in Table 1.2. Soil microbial biodiversity reflects the variability among living microorganisms extending from the countless of invisible microbes to more familiar macro-fauna like earthworms and termites. Soil microbes play an essential role in agro-ecosystem stability, including rich biodiversity, healthy biological cycles, and soil microbial activity; consequently, they are contributing to the build-up of stable soil agro-ecosystem (Doran and Parkin 1996; Pankhurst and Doube 1997; Madsen 2005; Fortuna 2012; Yadav et al. 2020a, b).

Table 1.2 Suggested practices to increase agroecosystem stability and function
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1.5.3 Microorganisms and Soil Functions

Soil functions provide many benefits, such as cycling of nutrients, maintaining biodiversity and habitat, water relations, and maintaining water quality, acting as a biofilter and buffering providing physical stability and support crop production, and carbon sequestration. The summary of soil functions and its advantages for humans is given in Table 1.3. It is vital to maintain or improve soil quality over time and provide essential services in the face of disturbance, whether it is natural or human-induced. Typically, soil is not considered healthy if it is managed for short-term productivity at the cost of future degeneration (Doran and Parkin 1994).

Table 1.3 Summary of soil functions and advantages for humans
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The soil can store, govern the discharge and cycling of nutrients and elements. During these biogeochemical processes, similar to the water cycle, nutrients can be transformed into plant-available forms, contained in the soil, or even lost to air or water. Soil promotes the growth of a variety of plants, animals, and soil microorganisms, regularly by giving a different physical, chemical, and biological habitat. Soil acts as a filter to maintain water and air quality. Excess nutrients and toxic compounds can be degraded or otherwise made unavailable to plants and animals. Soil can maintain its porous structure to allow passage of air and water, resist erosive forces, and give a mechanism for plant roots. Soils also provide anchoring support for social structures (Doran and Parkin 1994).

Nutrient cycling and water regulation functions are natural soil processes occurring in each ecosystem. These functions provide various opportunities to humans for betterment of quality life, achieve sufficient food, quality water, flood control, and several more. Soil pollution can happen either because of anthropogenic activities or because of the natural process. However, it is mostly due to anthropogenic activities. A human can enhance the value of soil and take its maximum benefits because land management choices affect soil functions. Thus, it is necessary to realize what benefits we obtain from the earth. So we can have the greatness of achieving land management in a way that maintains essential soil functions. Several main benefits are long term or go beyond if the land is being managed properly. The community should respect the value of many off-site services and profits and the extent to which the landowner or community should pay to maintain these soil functions.

1.6 Role of Microorganisms in Nutrient Cycling

Soil microbes perform various functions in the pedosphere. They are essential in controlling biogeochemical processes (Table 1.4). The critical soil microbes regulated roles are: (i) soil organic matter formation and turnover which includes mineralization and carbon sequestration, (ii) nutrient cycling, (iii) disease dissemination and prevention, (iv) contaminant depletion, and (v) soil structure improvement (GHGs) (CO2, CH4, and N2O, etc.) are the by-products of metabolic redox reactions of carbon and nitrogen compounds in soils (Madsen 2008). Nitrogen fertilizer application and cultural practices in soil management can stimulate microbial processes such as nitrification, denitrification, and mineralization that play a major role in the emission of GHG (Pathak et al. 2003; Rastegari et al. 2020a).

Table 1.4 Examples of essential biogeochemical processes catalyzed by microorganisms in biosphere habitats
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The quantity and composition of the microbial biomass depend on soil characteristics and the abundance of carbon (C) for energy and cell metabolism. Soil carbon inputs varied in chemical composition and nutrient content. Carbon recycling, degradation, and microbial function frequently contribute to an increased organic matter, which leads to soil aggregation. Various ecosystems have different types of potential to support biota and sequestration of soils C in organic matter. Soil organic carbon (SOC) is the backbone of organic matter, which is the source of energy for most of the soil biota. Microbiological decomposition of crop residues and organic matter provides access to carbon and the nutrients needed by most living species. Mineralization of organic-nitrogen into ammonium and the use of nitrogenous chemical fertilizers containing ammonium promote nitrification with the help of nitrifying bacteria and archaea that turn ammonium into nitrate. Therefore, nitrate undergoes a further microbially induced stage, denitrification (Maier et al. 2009; Fortuna 2012).

The food web present in the soil consists of various groups of microbes and helps for nutrients transfers and flow between the biotic and abiotic components (Sylvia et al. 2005). Mesofauna (collembolan and mites) perform a prominent role in nutrient cycling by slicing stocks into smaller pieces and directly helping to enhance the surface area. It has greater exposure to microbes that are key to carbon cycling. All food webs include many trophic levels in a food chain. If organic carbon is derived from living animals, the term grazing is used. Soil microbes form an essential part of the detrital type of food chain because they obtain their organic carbon from dead substances. Elemental ratios of C:N:P:S relatively are constant in the biological systems and organisms. Those ratios and mass balance allow researchers to establish biochemical changes between species.

Most soil microbe members are chemo-heterotrophs, suggesting they receive carbon and energy by the oxidation of organic materials (Kumar et al. 2019b; Singh et al. 2020b). C-sequestration restricts the mineralization mechanism mediated by the CO2 producing chemo-heterotrophs. Mineralization process by-products are metabolites, heat, and CO2. CO2 production can minimize concentrations of O2 producing anoxic sites within micro-aggregates resulting in variation of micro-environments (Van Elsas et al. 2007; Sylvia et al. 2005). These microsites are habitats in which CO2 is converted by archaea known as methanogens into CH4 a GHG by anaerobic respiration. In neighboring microsites, methane can undergo oxidation into CO2 with the help of a group of bacteria known as methanotrophs.

Microbes play a vital role in nutrient cycling and organic substances decomposition. This transforms the natural materials into biomass or mineralizes them to CO2, water, and nutrients (Bloem et al. 1997; Pankhurst and Doube 1997; Malyan et al. 2019). Such effective microbes are also concerned with the production and oxidation of waste products, including organic industrial substances (Singh et al. 2016; Kumar et al. 2019a). The functions of these productive rhizospheric organisms own the potential to have a useful test of soil sustainability. This attribute cannot be obtained with higher organism diversity analysis and physical/chemical tests. Microorganisms respond quickly to environmental changes; hence, they adapt quickly to ambient conditions. This adaptation makes it possible for microbial studies to differentiate in the assessment of soil health. Thus, improvements in soil biota communities and activities can be an excellent predictor of soil health (Singh et al. 2015; Sindhu et al. 2016).

Soil is a diverse environment for several life forms and provides vegetation with mechanical assistance from which nutrients are derived. Soil microbes regularly interact with each other; at times, these relationships are beneficial to both parties (mutualism), symbiotic, and competitive. It increases soil health because the “healthy” soil biota may fight against the “poor” ones and also contribute significantly by degrading organic compounds to make nutrients available. Thus, the similar basic soil structure in the different geographical regions is found to support different biocommunities. Soils have different texture due to the percentage contribution of sand, silt, and clay, and that includes a diversity of microhabitats that sustain a wide variety of microbes. The atmosphere within soil shows less oxygen content from the above-ground due to the utilization of the available O2 by soil biota and other metabolisms. Similarly, the concentration of CO2 in the soil is higher than the level at the above-ground due to the generation of it as a by-product of microbial reactions (Sarkar et al. 2017; Kumar et al. 2017).

Microbes’ reaction to environmental changes/stress is rapid relative to higher species, owing to their top surface to volume ratio. Those productive microbial communities may be regarded as soil architects (Rajendhran and Gunasekaran 2008). Several environmental functions, including plant growth, drinking water protection, or carbon sequestration, are strictly related to microbial service and its functional characteristics (Torsvik and Ovreas 2002; Lombard et al. 2011). A study on the development of abiotic and biotic interactions is very complex microbes function on a 3 μm scale and form biogeochemical soil interfaces (Totsche et al. 2010; Monier et al. 2011). Furthermore, most functional features, such as plant litter depletion or the formation of food web systems and nutrient cycling, are not the function of a single organism, but of closely associated microbial communities (Aneja et al. 2006; Sharma et al. 2012).

1.6.1 Organic Matter Decomposition

The decomposition of various forms of soil organic matter is one of the essential functions of soil biota. To make these organic compounds accessible to the autotrophic organisms, they must be processed into simple inorganic forms. Mineralization is the process of organic matter conversion into simpler inorganic forms, which is rendered primarily soil microbes, mostly fungus and bacteria (Gupta and Germida 1988; Xu et al. 2015). The organic substances that are brought into the soil are divided into three groups: the easily decomposable, moderately decomposable, and difficult to degrade, distinctly attached by various microbiota types. The consequence of microbial mineralization is, on the one hand, the release of energy, water, gases, etc., and, on the other, the creation of complex amorphous material humus through the process of humification.

1.6.2 Carbon Cycling

The balance between respiration and photosynthesis dominates terrestrial carbon cycling. Carbon is transferred into the soil from the atmosphere by autotrophic carbon-fixing species, primarily photosynthetic crop/plants and also photo- and chemoautotrophic microorganisms, which synthesize carbon dioxide (CO2) in organic matter. Respiration is the primary process behind the transfer of carbon back to the atmosphere with the help of both autotrophic and heterotrophic organisms. The reverse pathway involves the decomposition of organic matter by heterotrophic carbon consuming bacteria, which use plant, animal, or microbial origin carbon as a metabolism base, retaining part of few carbons in their biomass and adding the remainder back into the environment as metabolites or as CO2 (Gougoulias et al. 2014).

1.6.3 Nitrogen Cycle

All organisms require nitrogen because the protein and nucleic acids are essential elements. Animals derive nitrogen from organic sources, whereas plants derive inorganic nitrogen sources like NH4+ and NO3− (Schimel and Bennett 2004). Nitrogen fixation is the reduction of atmospheric N2 gas to NH4+. Nitrogen fixation is the only natural mechanism by which new nitrogen reaches the biosphere, and is thus necessary for the ecosystem’s functioning. The enzyme nitrogenase catalyzes N-fixation. The ammonium generated by N-fixation is assimilated into amino acids and then converted into proteins. Under nitrogen-scarce conditions, N-fixing microorganisms have an advantage. Nitrogen fixation is carried out by free-living microorganisms such as Azotobacter, Burkholderia, Clostridium, and few methanogens, some of which may be kept associated with the rhizosphere of crops plants, and bacteria that shows symbiotic relationships with plants like Rhizobium, Mesorhizobium, and Frankia (Maier et al. 2009; Fortuna 2012; Santi et al. 2013). The nitrogen-fixing microbes have been reported from different habitats and host worldwide belonging to different genera of Arthrobacter, Azoarcus, Azospirillum, Azotobacter, Bacillus, Enterobacter, Gluconoacetobacter, Herbaspirillum, Klebsiella, Pseudomonas, and Serratia (Subrahmanyam et al. 2020; Suman et al. 2016; Yadav 2020).

Exudates from crop plants provide some of the energy needed to fasten nitrogen fixation. In agricultural soils, a significant source of N is rhizobia, which forms root nodules in symbiotic relationships with introduced legumes such as clover, lucerne, or lotus. Symbiotic interaction N-fixation levels are sometimes two to three orders of magnitude higher than free-living bacteria in the soil. Ammonia or ammonium ions are oxidized to nitrite and then to nitrate during nitrification. The two steps in nitrification—first are the formation of nitrite and then nitrate—are carried out by two distinct microbes. In soils, ammonia oxidation to nitrite is conducted by bacteria such as Nitrosospira and Nitrosomonas, while bacteria such as Nitrobacter and Nitrospira oxidize nitrite to nitrate. Nitrifying microbes utilize the energy derived from nitrification to assimilate CO2. Nitrification is especially vital in soils as the degradation of nitrite and nitrate ions from ammonium to nitrite shifts their charge from positive into negative.

1.6.4 Siderophores Production

Iron is a vital nutrient, and part of many compounds that regulate and promote plant growth and development. In the soil, naturally, iron is present as a ferric ion (Fe3+), which is too low to promote and facilitate soil microbial growth. It has been reported that some bacteria possess the ability to assimilate unavailable iron to overcome iron stress by producing ferric-specific ligands, referred to as siderophores, which are usually of low molecular weight (400–10,000) (Neiland and Nakamura 1997). Such microorganisms or bacteria are real iron scavengers as they have a high affinity for iron (Fe3+) chelators that transfer iron to bacterial cells (Leong 1986). Soil microorganisms, especially rhizobacteria, are of great interest for siderophore production. Under iron stress conditions, these bacteria have a high chelating affinity for Fe3+ than Fe2+ ions, and Fe3+ions are transferred to bacterial cells (Neiland 1995). Recent studies have indicated that biological control of different phytopathogenic organisms could be achieved using siderophore producing microorganism such as Alcaligenes, Bacillus, Clavibacter, Curtobacterium, Flavobacterium, Kluyvera, Microbacterium, and Pseudomonas (Verma et al. 2016, 2017; Yadav et al. 2017a).

1.6.5 Hormones Production

Microbial synthesis of the phytohormone has been known for a long time. Plant growth-promoting rhizobacteria (PGPR) is a group of microorganisms that colonize several plant species’ rhizosphere and roots. They confer beneficial effects to plants by a variety of mechanisms, including indole-3-acetic acid synthesis of phytohormone auxin (IAA), which is essential for plant growth (Patten and Glick 1996; Kour et al. 2020a; Rana et al. 2020a, b). Eighty percent of microorganisms isolated from the rhizosphere of various crops have the potential to synthesize and release IAA as secondary metabolites (Patten and Glick 1996; Yadav et al. 2017b). The most common phytohormone produced by PGPR is indole-3-acetic acid, which participates in root growth and increases root surface area, thereby enabling plants to absorb more nutrients from the soil. Gibberellins associated with plant extension, mainly stem tissue, have been reported to be produced by Bacillus pumilus and B. licheniformis in the form of gibberellic acid. The phytohormone-producing rhizospheric microbes, when inoculated to crops, help plant growth promotion, enhance yield, and increase soil fertility for sustainable agriculture (Kumar et al. 2016; Singh and Yadav 2020; Yadav et al. 2018b).

1.6.6 Phosphate Solubilization

Phosphorus, after nitrogen, holds a second essential role in various critical processes in plant growth and development, including the division of cells, photosynthesis, and decomposition of sugar, energy, and nutrient conversion in a crop plant. Plants utilize phosphate ion the form of phosphate anions, but phosphate anions are incredibly reactive and get immobilized through precipitation with cations present in the soil such as Ca2+, Mg2+, Fe3+, and Al3+. Rhizobacteria help in the decomposition of organic compounds and make phosphorus available by the action of minerals and acids released by soil bacteria. Phosphorus mineralization is greatly affected by the microbial community, and phosphate-solubilizing bacteria such as species of Bacillus and Paenibacillus have been applied to soils to enhance the phosphorus status of plants specifically. Pseudomonas, Bacillus, and Rhizobium are the most potent phosphate solubilizers in the cropping system (Rodríguez and Fraga 1999; Kour et al. 2019).

Possible mechanisms for solubilization from organically bound phosphate involve either enzymes, namely C-P lyase, nonspecific phosphatases, and phytases. However, most of the bacterial genera solubilize phosphate through the production of organic acids such as gluconate, ketogluconate, acetate, lactate, oxalate, tartrate, succinate, citrate, and glycolate (Yadav et al. 2015). The rhizospheric phosphate utilizing bacteria could be a promising source for plant growth-promoting agent in agriculture (Rana et al. 2019; Yadav et al. 2018a). The rhizospheric phosphorus-solubilizing microbiomes may be used for mitigation of abiotic stress in plants such as high/low temperatures, alkaline/acidic, drought, and saline environments (Kour et al. 2018, 2019; Kumar et al. 2019c).

1.6.7 Manganese (Mn) Solubilizers

Redox condition and hydrogen ion concentration (pH) are two significant factors that influence the availability of Mn in the rhizosphere. Some rhizosphere bacteria such as Bacillus, Pseudomonas, and Geobacter can reduce oxidized Mn4+ to Mn2+ form, which is metabolically useful for crops (Wani et al. 2015). Consequently, Mn-reducer function in the rhizosphere is strongly favored. Products of organic matter can also help reduce Mn (Hue et al. 2014). Gaeumannomyces graminis is also an Mn oxidizer that impairs root lignification at infection sites. Effective rhizosphere Mn reducers like Pseudomonas sp. could have beneficial effects on plant nutrition and also help in biocontrol of pathogens. In comparison, Mn oxidization by rhizosphere bacteria supports plant growth in flooded soils where the abundance of Mn2+ can be high.

1.6.8 Iron Solubilizers

Iron dynamics in the rhizosphere is almost similar to that of manganese (Mn). Fe in the soil is a part of the structure of insoluble minerals Goethite (FeOOH) or hematite, in oxidized forms Fe3+. Rhizosphere bacteria, such as Bacillus, Pseudomonas, Geobacter, Alcaligenes, Clostridium, and Enterobacter, can reduce oxidized Fe3+ to reduced Fe2+ form required by crop plants. Electrons and hydrogen ions are available in the rhizosphere, and consequently, Fe is diminished. However, it can be reprecipitated (Kaur et al. 2020; Wani et al. 2015).

1.6.9 Soil Enzymes

Soil enzymes act as a booster in the redox reaction through which plant residues decompose and make nutrients available. The material on that soil enzyme that has worked is considered the substrate. The enzymatic reaction releases a product, which may be a substrate-containing nutrient. There are so many sources of enzymes in the soil, such as living and dead microorganisms, soil animals, plant roots, and plant residues. Enzymes that are stable in the soil matrix retained or form complexes with humus, clay, and humus-clay compounds, which are no longer associated with sustainable cells. Stabilized enzymes contribute 40–60% of the total enzyme activity. It is believed that 40–60% of enzyme activity can come from stabilized enzymes. Thus, behavior is not strongly associated with microbial biomass or respiration. Enzyme activity is then the combined effect of long-term microbial development and viable sampling population activity.

Enzymes respond to changes in soil management long before more changes in soil quality indicators can be identified. Soil enzymes play a crucial part in the decomposition of organic matter and nutrient cycling (Table 1.5). There is no substantial evidence, apart from phosphatase activity, that directly relates enzyme activity to nutrient availability or crop production. The relation may be indirect because nutrient mineralization is achieved with the contribution of enzyme activity to plant-available sources. Limited enzymatic activity (e.g., pesticide degrading enzymes) may contribute to dangerous chemical accumulation for the environment. Many of these toxic chemicals can also impede soil enzymatic activity.

Table 1.5 Role of soil enzymes
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Apart from these, as we know, plant growth and yield depend on the availability of nutrients and their efficient management. Therefore, it is essential to adopt the 4R Nutrient Stewardship concept of right nutrient application (i) Right source, (ii) Right rate, (iii) Right time, and (iv) Right place (Johnston and Bruulsema 2014). This concept integrates soil health with sustainable and precision farming practices. Right source means matching the source of the nutrient to the crop need and soil properties. A significant part of the source is balanced between the various nutrients, a considerable challenge globally in improving nutrient use efficiency. The right amount means balancing the nutrients added to the need for the seed as basic as that.

The applications of too much fertilizer contributes to excess soil nutrients and environmental degradation. Ultimately, striking a balance between the crop needs, environmental conditions, and the farmer’s economic situation is required. Here, microbial biofertilizers can play a vital role in such cases. The right timing ensures that fertilizer nutrients are made available for the crop when needed. Efficiency in nutrient usage can be significantly improved when its supply is matched with crop demand. The right position means attempting to preserve nutrients so crops can use them. This is a question that presents the most significant challenge in smallholder farming systems, where most fertilizers are distributed, and in many cases, without incorporation (Johnston and Bruulsema 2014). Adaptation of 4R Nutrient Stewardship concept of right nutrient application with the potential soil microbes helps to better nutrient recycling and long-term sustainability goal of our agriculture production system.

1.7 Conclusion and Future Perspectives

In soil processes, including nutrient cycling, soil organisms and their products play a crucial role. These mechanisms are essential for agriculture as well as water, air, and habitat quality protection. Agriculture is currently facing excessive pressure due to population development and related rises in urbanization, resource extraction, etc. However, cultural practices are influenced by the microbial activities. Therefore, it is necessary to consider the potential role of soil microbes for proper nutrient recycling and its impacts on soil health.

Furthermore, expanding our core knowledge regarding diversity and function of soil microbial component is a necessary task to alleviate the harmful effects of soil degradation. Research focusing more on the credentials of innovative microbial diversity in the soil remains essential practices. In the future, that would play a more critical role favorably for enhancing plant growth and yield as well as contribute towards a more environment-friendly alternative to support sustainable development.