Keywords

1 Introduction

The global human population is on a perpetual upsurge, however, at the declining rates. The human beings inhabiting this planet are now approaching 7.5 billion, which marks a 100% upturn as compared to that of the early 1960s. This increasing number of human beings, undoubtedly, requires more food resources to proliferate and thrive in the existing environments. Therefore, the major challenge for the agricultural systems is to enhance the food crop production in the upcoming era simultaneously addressing the hazards as well as inconsistency along with the eco-efficiency (Jeranyama et al. 2020). However, some different strategies are already being followed for increasing the food crop production, for instance, use of chemical fertilizers, introduction of genetically modified plants, employment of agrochemicals, as well as the usage of sophisticated machinery. The explicit application of chemical fertilizers has amplified dramatically from 0.5 tons to 23 million tons from 1960 to 2008 correspondingly (Pandey 2018; FAO 2019a, b). The increasing levels of environmental concerns are laying a pressure on the farming community to produce the food crops sustainably (Rani et al. 2019; Singh et al. 2019; Sharma et al. 2019, 2020; Kapoor et al. 2020).

Since the domestication of plants, several strategies have been followed for enhancing the yield of food crops. The advancements in scientific researches and innovation of newer technologies introduced the green revolution which proved to be a milestone in attaining an enhanced food crop production. However, it accounted for a significant enhancement in food crop production persistence of the global monster of hunger coupled with the environmental sustainability concerns requiring the intervention of novel technologies that can fulfill the demands of a higher production along with the preservation of environmental sustainability. The quest to fulfill both these demands puts forward the idea of engineering the rhizospheric portion of plants. The rhizosphere seems to be the most complex habitat of a vast array of microbial population encompassing an intermingled network of plant roots, diverse microbial communities, and soil (Ahkami et al. 2017). This narrow zone of plant-microbe interactions represents the first plant-prejudiced microbial habitat which affects the plant growth in a direct as well as indirect manner. The rhizospheric portion is a complex dynamic and compactly inhabited zone of soil that proves to be an incredible site for the multifaceted set of inter- as well as intraspecies interactions and food web communications which lay a strong effect on the carbon flow as well as transformation (Dessaux et al. 2016; Walker et al. 2011). The plant systems have evolved in a realm of microorganisms. The coevolution of plants with the rhizospheric microbiome has resulted in a state where both these components start affecting each other from the very first day of the dawn of plant life. The roots of plant systems are largely known for altering the physical characteristics of the soil. Plants harbor a vast microbial population by secreting carbon-rich compounds via roots, where such labile substrates are largely favored by the members of microbial communities and they swiftly blend them (Doornbos et al. 2012). The alteration of physical as well as chemical environs of the rhizosphere by the plant systems largely affects the suitability of diverse microbiological clusters and microbial connections and has also encouraged the evolution of novel microbial systems that fit themselves in the rhizospheric life. The gain of fitness sustained by the microbial systems must overshadow the price to the plants in diverted carbon and energy (Vandenkoornhuyse et al. 2015). These plants associated with microorganisms largely assist the plant systems under their plant growth promotion attributes. They not only facilitate the plant systems in the uptake of several key nutrients but also protect them from many biotic as well as abiotic stresses. They are found to enhance the plant productivity directly by fixing the nitrogen, solubilizing the phosphate, producing the siderophore, and indirectly increasing the organic carbon pool of the soil, conferring the plants with the ability to tolerate various biotic as well as abiotic stresses (Mohanram and Kumar 2019). Numerous indications display that plants engineer their rhizospheric microbiome. The most primaeval lines of plants also display a strong capability of altering the comparative richness of different microbial clusters in the soils neighboring their rhizosphere (Chaparro et al. 2014; Valverde et al. 2016) that assists the plant systems in their growth. Apart from this ability of plants to alter their rhizospheric communities, various human practices have also proven to be key drivers in engineering the microbial population of a rhizospheric portion which strongly favors the establishment of advantageous microbial systems on the plant roots which ultimately results in improved plant health and upsurged plant productivity. Therefore, the present chapters strongly target different approaches that are often employed to engineer the plant rhizosphere to bring a qualitative as well as a quantitative upsurge in the productivity of plant systems.

2 Rhizosphere and Root Exudates

The rhizosphere seems to be the most composite microbial territory on the earth, encompassing a cohesive system of plant roots, soil particles, as well as an assorted microbial conglomerate of archaea, bacteria, virus particles, as well as micro-eukaryotes. This fine region of contact amid the soil particles and the plant roots establishes the foremost plant-prompted habitation faced by soil microbiota. The rhizosphere represents an active and compactly inhabited zone of soil upholding a multifarious set of inter- as well as intraspecies communications. In addition to this, it also acts as an active site for the ongoing food web interactions that are known to have a significant influence on the carbon flow and transformation (Ahkami et al. 2017; Dessaux et al. 2016). Adding more to it, the classical description of rhizosphere has described it as a four-dimensional (4D) body: three dimensions for the volume and the fourth dimension representing the time for the rhizospheric functioning (Kuzyakov and Razavi 2019). The assessment of the rhizosphere divulges that it is a habitat for diverse classes of microorganisms. The total volume of microbes inhabited in this zone is represented by some good, by some bad, and by a few ugly microbes. These good, bad, and ugly microorganisms denote at this point the good microbes, plant pathogenic microbes, and opportunistic human pathogenic microbes correspondingly (Dutta and Bora 2019). The microbial dwellers of rhizosphere that have sparked the interest in studies targeting rhizosphere and rhizospheric engineering are the microbes having constructive effects on the plant systems which are largely represented by nitrogen-fixing microorganisms, mycorrhiza, plant growth-promoting rhizobacteria (PGPR), and the microbes possessing antagonistic activity toward plant pathogens. However, the rhizospheric inhabitants that are found to be harmful for the plants take account of the phytopathogenic fungi, oomycetes, bacteria, and nematodes (Mendes et al. 2013).

This natural environment allows different microbial strains to co-occur and to form multifarious microbial populations as well as communities. Therefore, the rhizospheric zone has further been divided into three distinct sub-zones: the endorhizosphere which represents the fragment of the root cortex along with the endodermis where the microorganisms, as well as the mineral ions, exist in the apoplastic space amid the plant cells; the rhizoplane, which denotes the middle zone after the epidermal root cells and mucilage; and the ectorhizosphere, which symbolizes the farthest zone extending from the rhizoplane out into the bulk soil (McNear 2013). The term rhizoplane was denoted the direct exterior surface of plant roots along with any tightly clinging soil particle or debris as well as microbiological populations. The existence of rhizosphere is not under a section of limited extent or shape but should rather be considered as an ascent of physical, chemical, as well as biological possessions alongside the plant root. Therefore, the plant rhizospheric portion is of supreme significance for several valuable ecosystem amenities, for instance, to maintain the nutrient as well as water cycle, seizure of vital nutrients, and the sequestration plus storage of carbon (Adl 2016).

The plant metabolism strongly affects the rhizospheric portion by releasing the carbon dioxide and by emancipating the photosynthates by way of diverse kinds of root exudates predominantly via rhizoplane and ectorhizosphere. The importance of root exudates for plant systems can be understood by the fact that plants discharge approximately 40% of its photosynthates unswervingly into the soil systems primarily as compounds of higher as well lower molecular masses (McNear 2013). The plethora of interactions taking place amid rhizosphere and rhizospheric microbiome governs the plant growth as well as yield in their natural environments. The molecular events taking place in the plant rhizosphere precisely shape the plant rhizospheric microbiome or rhizobiome (Sasse et al. 2018).

The plant roots are the main plant structures that are held accountable for the acquirement of both water and essential nutrients and the secretion of different primary and secondary metabolites called as root exudates. The plant’s primary metabolites oozed through roots are predominantly organic acids, carbohydrates, and amino acids. In addition to it, plants also exudate a vast range of secondary metabolites, currently also called plant natural products such as alkaloids, terpenoids, and phenolics. In addition to this, these exudates have also been categorized into two clusters, i.e., low-molecular-weight compounds, for instance, sugars, amino acids, volatile compounds (VOCs), phenolic compounds, organic acids, and other secondary metabolites, and high-molecular-weight compounds, like polysaccharides and proteins. It has also been established that the root exudation is largely responsible for shaping the plant rhizobiome, and these exudates find engrossment in numerous biotic as well as abiotic connections. Several different root exudates have also been found responsible for the initiation of quorum-sensing mechanisms in either the repression or stimulation of quorum-sensing rejoinders of correlated bacterial class. However, the rhizospheric portion has been largely ignored, for its different possible attributes that can enhance the crop yield, predominantly owing to the several confronts allied with the sampling within the rhizospheric soil (Oburger and Schmidt 2016; McCormack et al. 2017; Dutta and Bora 2019). Additionally, the role of plant-allied rhizospheric microbiome has already been unveiled for its different plant growth-promoting attributes. In addition to it, the root exudates, apart from harboring the rhizobiome, are also known for the maintenance of the rhizospheric environment by the possession of several key and unique attributes. The root exudates are also acknowledged for enhancing the accessibility of several key nutrients, for instance, phosphorus, because of the discharge of phosphatases and chelation by the oozed organic acids that are known to concentrate the available phosphorus for the plant uptake (Dakora and Phillips 2002). The exudates are also known for deleteriously affecting the adjoining plants, for instance, via fabrication of allelochemicals (Callaway and Aschehoug 2000) which provides an opportunity for engineering the trait of weed inhibition in the plant systems. The exudates are also known for their possession of root-insect communication trait. The root herbivory by numerous pests like aphids can result in noteworthy reductions in produce as well as the quality of important crops which are known to be inhibited by the root exudates, thereby demonstrating insecticidal activity. The root exudates are also known for altering biochemical and physical properties of the soils inevitably. The root exudates are known to stabilize the soil structure along with an enhancement in the water retention capacity of the soil, thereby indirectly improving the plant growth by managing the soil health. Moreover, they also play an imperative character in the elevation of positive interactions among microbes, for instance, by instigating the colonization with mycorrhizae via releasing strigolactones (Biate et al. 2015). Consequently, an explicit range of traits associated with the rhizosphere are potent enough to be targeted for the improvement in crop yields along with a concomitant reduction in the input of chemical fertilizers and other agrochemicals (Preece and Peñuelas 2020). Therefore, the highly dynamic and potent attitude of plant rhizosphere makes it a suitable area of interest for its manipulation in the quest to obtain improved plant health and enhanced crop productivity.

3 Rhizospheric Microbiome

The rhizosphere acts as a definite hotspot and provides a platform for numerous networks in the interior of the bulk soil. It represents an important biological hotspot where respiration, gaseous altercation, nutrient and moistness usage, and confined provisions of organic matter are deliberated to be most concerned. On the contrary, the bulk soil represents an oligotrophic environ, specifically on the stock of root-instigated organic material. Therefore, the rhizosphere, as affected by root exudation, may encompass up to 1011 microbiological cells per gram root and with 1012 functional genes per gram soil belonging to over and above 30,000 prokaryotic inhabitants (Mendes et al. 2011; Prosser 2015). The cumulative genome of this rhizospheric microbiome appears to be much greater than the plant genome, and it is, therefore, denoted as the second genome of the plant. The rhizospheric microbiome and its role can be considered similar to the human intestinal microbial populations as they also play a great role in human health maintenance (Berendsen et al. 2012; Bron et al. 2012). The rhizospheric microbiota control diverse biogeochemical cycles along with the various other soil processes by influencing the main rhizosphere progressions, for instance, respiration, nitrification, and denitrification (Breidenbach et al. 2016; Philippot et al. 2013). They are also known to conspicuously influence the iron cycle in soils and have also been demonstrated as the essential drivers of soil organic matter decomposition in the temperate grasslands (Li et al. 2019). Therefore, total characteristics of the agronomic rehearse demand a superior considerate of the different rhizospheric progressions that aid plant progression as well as disease suppression. Consequently, owing to the non-replaceable role of rhizospheric microbiome, the exploration of the complex connection amid crop, soil, and microorganisms in the plant rhizosphere has become the fundamental part for nourishing vigorous as well as high-yielding production structures (Uzoh and Babalola 2018). Therefore, the term rhizosphere diversity is often employed to decrypt a vast array of microorganisms residing in the zone of soil, bordering, and habitually stimulated by plant roots. The intimate interactions of plants with microbial communities in this special zone of soil have made the rhizosphere a place for extraordinary microbial accomplishments (Huang et al. 2014; Nicolitch et al. 2016).

The major proportion of the diverse microbiota harbored by the plant systems is picked up throughout their lifespan from the adjacent environs; thereby, it seems that a considerable part of the plant microbiome finds its origin from the seeds. The seed-allied microbiota is supposed to play an indispensable part in initial phases of the plant development, thereby upsetting the germination as well as the subsistence of the seedling (Pitzschke 2016; Truyens et al. 2015). The soil-based microbes come later into the play and have to contend alongside the previously established microbiota. The microbiota selected in the rhizospheric zone will move to other plant parts and later inhabit diverse plant tissues especially leaves which later represent a major part of the phyllosphere microbiome (Hardoim et al. 2015; Mitter et al. 2016; Sánchez-Cañizares et al. 2017). The plant-originated metabolites known as root exudates play an indispensable role in the root colonization of rhizospheric microbiome. These are usually of low molecular weight and accordingly are straightforwardly easily utilizable, consequently, fashioning an upsurge in the microbiological population thickness of rhizosphere as equated to the bulk soil. The most noticeable and earliest work on the “the rhizosphere effect” was done by Albert Rovira, the research provided detailed views of plant-driven microbial colonization of the rhizosphere at the microscopic scale (Burns 2010; White et al. 2017). This comparative increment in the integer of microbes in plant rhizosphere is usually articulated as the R/S ratio, where R denotes the numbers per gram of soil in the rhizosphere and S in the bulk soil. There is a great variation in these ratios which range between 5 and 50 which may cross 100 also, and this variation is governed by several factors like microbial members, stage of development of plant systems, plant species, as well as the nutritional eminence of plant systems. It should also be taken care of that only a definite percentage of the root surface is shielded by the microbes, for instance, of the total root surface area of maize, the bacteria cover only 4% in apical zones, 7% in the root hair zone, and up to 20% in basal zones. The inhabitation of a root by the rhizospheric microbiome is, however, not limited to rhizoplane only but can also happen in the apoplast of the cortex to varying degrees as indicated by the presence of endophytes (Marschner 2012). The growth of roots into the deeper soil is closely followed by the active colonization of the newer root just behind the meristematic tissues by the microbes attracted toward the root surface. The exudates oozed in the region directly behind the root tip and in the distal zone of elongation zone encourage the growth and proliferation of microorganisms and also appeal additional soil microbes toward the root surface. However, the exudation of metabolites is at a reduced pace and quantity in the root-hair and its neighboring region which furthers marks a decline in the intensity of microbial inhabitants (Marschner 2012). Thus, the fast-growing roots experience an abrupt variation in the microbial community of rhizoplane and rhizosphere from apical to basal regions alongside the root axis (Bowen and Rovira 1991). It is the alteration in category as well as the amount of carbon accessible as exudates in different root zones which stimulates the differences in the community structures (Baudoin et al. 2003; Marschner 2012). However, such differences in the microbial concentration alongside the root axis are vital for the overall nutrient revenue in the interior of the microbial load (Marschner et al. 2011). An upsurge in the microbiological density might lead to an overall nutrient immobilization, while a reduction in microbial load can lead to a net nutrient release.

The plant largely controls the microbial inhabitation of its root environment by secreting highly diverse root exudates. Their diversity and complexity can be taken into account by the fact that the root exudates of even a small plant species may comprehend more than 100 diverse metabolites (van Dam and Bouwmeester 2016). Furthermore, the attitude and class of root exudates only happen to be decisive for the dispersal of bionetworks and niche exactness of definite plant systems (Dakora and Phillips 2002). The release of these composites by the plant roots proceeds by as a minimum of two possible mechanisms, for instance, the exudates may be conveyed crosswise the cell membrane and then discharged into the adjacent rhizosphere, or the plant produces may also be secreted from the root edge cells and root edge-alike cells, which are known to discrete from the root structures as they mature (Hawes et al. 2000; Vicré et al. 2005). The root exudates may contain every possible plant-originated compound excluding some definite composites that find their key involvements in the process of photosynthesis. The rhizospheric microbiome is deliberated as a conglomerate of key engineers that have the potential to be employed to reconstruct the biodiversity and purposes in the tarnished environments. These microorganisms owe an imperative part in the management of growth, health, as well as ecological aptness of their host plant (Buee et al. 2009; Dutta and Bora 2019). Furthermore, these microbial systems have engrossed much attention and have become a subject for rhizospheric engineering due to their possession of key role in the management of both natural and accomplished agriculture soil ecosystems as they find involvement in diverse and significant progressions referring to soil structure formation, organic matter disintegration, toxin exclusion, xenobiotic deterioration, bioremediation, rhizoremediation, nutrient cycling, etc. A plethora of microbes inhabiting the rhizosphere has the capability of doing these jobs for their host plants. However, all the microbes inhabiting rhizosphere are not culturable, but the advances in the techniques of molecular biology and biotechnology have expedited the process of considering the role of other 99% microbes that cannot be cultured in laboratory situations. However, the major plant growth-promoting rhizobacteria that have been reported so far belong to the genera Azotobacter, Burkholderia, Arthrobacter, Chromobacterium, Caulobacter, Xanthomonas, Azospirillum, Enterobacter, Bacillus, Pseudomonas, Serratia, Flavobacterium, Klebsiella, Erwinia, and Micrococcus (Bal et al. 2013).

The rhizospheric microbiological inhabitants represent a subdivision of the microbiological society inhabiting the bulk soil. The secretion of exudates by plants allows the proliferation of some specific microbes in the rhizospheric zone as equated to the bulk soil. There have been several theories which have tried explaining the relative assembly of microbial communities in the rhizosphere. However, two main theories have emerged for a possible explanation. The first one is referred to as niche theory, which points out the significance of deterministic progressions, and the second one is deliberated as the neutral theory, which focuses on stochastic processes (Dumbrell et al. 2010). The niche-centered theory forecasts that the variations in the species community configuration are allied to the deviations in the ecological variables because species owe distinctive possessions that reward them the exploitation of matchless niches. The species copiousness in this theory will follow pre-emption, broken stick, log-normal, and Zipf-Mandelbrot models. On the other hand, the neutral theory envisages the structure and configuration of species communities to the geographic remoteness amid the samples on the account of their dispersal limitation, since several species are functionally comparable based on their capability to utilize niches. Consequently, their richness will follow a zero-sum multinomial (ZSM) distribution. Both the theories are well associated with ecological aspects, but none can provide any evidence in the favor of the dynamic nature of microbiological community association in rhizosphere (Mendes et al. 2014).

Since all the members of rhizospheric microbiome are not culturable, however, the culture-grounded approaches have advocated the supremacy of gram-negative microbes in rhizosphere. The proper designation of the microbiota to precise groups requires the use of advanced molecular biology techniques. Since microbial influences in the rhizospheric portion are repeatedly synergistic, thereby, the understanding of microbial system at the community level seems to be most ecologically significant. The community-level depiction of several agriculturally important crops like corn, pea, potato, rice, alfalfa, avocado, tomato, and corn has revealed that in most of the studies, but not all, the Proteobacteria was found to be the dominating group. However, the results varied among different classes of Proteobacteria , but mostly Gammaproteobacteria were found to overpass the other classes (Hawkes et al. 2007). Similarly, Uroz et al. (2010) also found the dominance of Actinobacteria and Proteobacteria in the oak rhizosphere soil. Likewise, the exploration of the rhizospheric community of three different cultivars of potato also revealed the dominance of the phylum Proteobacteria (46%), which was followed by Firmicutes (18%), Actinobacteria (11%), Bacteroidetes (7%), and Acidobacteria (3%) (Weinert et al. 2011). The rhizospheric community structure of alfalfa and barley as assessed by Kumar et al. (2018) was also largely represented by Proteobacteria (45.9%) which was followed by Bacteroidetes (21.4%) and Actinobacteria (10.4%). Similarly, the rhizospheric community analysis also proved the dominance of Proteobacteria with a share of 47% followed by Actinobacteria (23%), Firmicutes (6%), and Acidobacteria (5%). It also displayed the presence of eukaryote (3%) and archaea and virus (1%). The comparative analysis of rhizospheric soil as compared to the bulk soil confirmed the overexpression of phyla Actinobacteria, Acidobacteria, Chloroflexi, Cyanobacteria, Chlamydiae, Tenericutes, Deferribacteres, Chlorobi, Verrucomicrobia, and Aquificae in the rhizospheric soil (Mendes et al. 2014). The rhizospheric microbiome of any particular plant is known to be affected by different factors, and the microbial populations are known to react and acclimatize themselves to such factor, for instance, the loss of nitrogen-fixing symbiosis in L. japonicus modifies the assembly of the community accumulations in the roots as well as rhizospheric compartments (Zgadzaj et al. 2016; Sánchez-Cañizares et al. 2017). The patterns of exudates also vary a lot due to plant age, for instance, the GC-MS analysis of root exudates secreted by gnotobiotically nurtured A. thaliana displayed that the intensities of sugars and sugar alcohol secretion diminished during the plant development, although the degrees of amino acid and phenolic secretion augmented with time. The exudates comprising of sugars, organic acids, and amino acids intensely shake the configuration of microbiological plant populations, where the members of Actinobacteria and Proteobacteria represent the principal consumers of such compounds (Chaparro et al. 2014). The effect of exudates on shaping the rhizospheric diversity can be taken into consideration by the fact that a mutation of an ABC transporter, which finds active involvement in the process of exudation, altered the fungal as well as the populations in the rhizosphere of A. thaliana. Nevertheless, the incorporation of organic acids rather than sugars, even in the absence of plant systems, encourages bacterial fruitfulness and diversity. Therefore, the procurement of nutrient in any form acts as a strong driver for the microbial assemblage (Badri et al. 2009; Shi et al. 2011). The rhizospheric microbiome of a plant species is also affected by the presence of other plants. Interestingly, the microbial populations of plant systems cultivated in a mixed field are found to contain an enhanced level of microbial biodiversity, which in turn rewards the plant with an enlarged plant height and leaf surface area as equated to the plant cultivated in a monoculture (Lebeis 2015).

4 Plant-Microbe Rhizosphere Interactions

The plant systems have evolved in a realm of tiny microorganisms. The plants started influencing their rhizospheric microbiome from the very first day. The plant roots brought out numerous changes in the soils which ultimately resulted in the alteration of the physical configuration of the soil. Plant systems dug out the key nutrients from the soils, thereby giving a tough competition to the already inhabiting microorganisms. They also took out water from the soils, thereby modifying the soil moisture that too was faced by microorganisms. The plant debris resulted in the accretion of organic carbon that was later handled by the heterotrophic microorganisms, which resulted in the materialization of soil organic matter. The beginning of the process by which plants started releasing their photosynthates via roots favored the quick assimilation of microorganisms (Cotrufo et al. 2013; Lehmann and Kleber 2015; Doornbos et al. 2012). This further lead to the alterations in the physical as well as chemical environs of the rhizosphere, which in turn influenced the fitness of diverse microbial assemblies and communications amid microorganisms and thereby incited the evolution of new microorganisms that were better suited to the life in this thin zone of rhizosphere (Lambers et al. 2009). The sum of genotypic as well as phenotypic deviations in the plant attributes that support the plant-allied microbiomes responsible for upsurging the plant nutrient accessibility, precluding pathogenic microbes, or else refining plant aptness coupled with the plant performance sustains a fitness benefit. Therefore, the aptitude of plant systems toward the sustenance of a constructive microbiota is an attribute under selection. This close relationship of plant systems with the microorganisms is often regarded as an assimilated ecological entity acknowledged as a holobiont (Vandenkoornhuyse et al. 2015). This holobiont has been the unit under selection for several billions of years, thereby supervising the evolutionary pathway headed for plant traits supporting constructive microbiomes.

There is a vast array of microbial systems inhabiting the plant rhizospheric zone, and they are expected to interact with the plant systems in numerous ways. But most frequently only three distinctive classes of such host-microorganism associations are taken into consideration for the activities of the plant-allied microbiome: parasitic, which deleteriously affects the health of plant systems; mutualistic, which aids the plant growth by its growth promotion attributes; and the commensalism, which does not have any effect on the plant systems. However, these descriptions only take into account of the direct influence of the microbial systems on the plant systems and not the indirect belongings on the other community associates, consequently, exclusive of the influence of microbe-microbe communications happening in plant microbiomes. The microorganisms inhabiting the interior of plant tissues are capable of producing numerous growth-prompting molecules, improving nutrient procurement, or persuading defense from several biotic and abiotic stresses. While the beneficial and deleterious communications amid hosts and microbial species can be specifically elaborated, the notion targeting commensalism is not defined with much clarity. A true commensal certainly does not affect the plant health in any form, therefore, it is discreetly impossible to quantity, since it necessitates witnessing the absenteeism of a phenotype. In conclusion, the microbial systems can be deceitfully considered as commensals owing to their transient occurrence, provisional dormancy, or their performance of some formerly uncharacterized roles. Such kind of perceptions necessitates the performance of community-level investigation at the multiple time points and ecological situations (Berendsen et al. 2012; Lebeis 2015; Zapalski 2011). The interactions among numerous microbes inhabiting the rhizosphere also affect the composition of the rhizospheric microbiome. For example, diverse bacterial and fungal rhizospheric inhabitants act as antagonists for numerous soil-dwelling fungal or nematode phytopathogens by the possession of diverse mechanisms. These mechanisms may encompass antibiosis, competition, aptitude of parasitizing the plant pathogens, damage in the phytopathogenic activity via quorum sensing, and initiation of the systemic resistance in plant systems (Ali et al. 2017). However, here, only the account of plant-microbe interactions is taken into consideration.

4.1 Beneficial Interactions: The Good Microbiome

A major proportion of microbiological populations residing the rhizospheric zone have a vital part to perform in enhancing the configuration as well as production of the natural plant systems via safeguarding the persistence and forbearance against diverse biotic as well as abiotic stresses. This job is done by numerous tools, such as bio-fertilization, encouragement of root progression, management of stresses, rhizoremediation, and disease suppression. A large proportion of rhizospheric microbiomes behave synergistically, promote plant growth as well as development, expand the nutrient acquirement, enhance their tolerance, and induce different defense mechanisms in the plant systems. Therefore, these are deliberated as “the good” of rhizospheric microbiomes (Ali et al. 2017). The bacterial members of rhizosphere actively engaged in plant health elevation activities are designated as plant growth-promoting rhizobacteria (PGPR). The plant health and growth promotion trait of rhizosphere-residing bacteria is brought out by maintaining an active supply of numerous vital nutrients that otherwise are either inaccessible or narrowly obtainable by the plant systems, for instance, nitrogen, iron, phosphorus, and zinc. The mechanisms underlying the superior nutrient endorsement encompass phosphate solubilization, nitrogen obsession, solubilization of zinc, and iron chelation via fabrication of siderophores. Additionally, the PGPR also produces several plant hormones, such as indole acetic acid, cytokinin, and gibberellins. Furthermore, the other mechanisms may comprehend the possession of ACC deaminase activity, biofilm materialization, and production of various exopolysaccharides. The active involvement of rhizospheric dwellers in various nutrient cycles results in recovering vital nutrients like N, P, K, Zn, and Fe, thus enhancing their bio-obtainability to the plant systems (Ali et al. 2017; Sharma and Chauhan 2017; Backer et al. 2018). Broadly, such microbes are classified into three major classes according to their possession of plant growth promotion trait. First are the microbes that upsurge the accessibility of the nutrients to plant systems and are designated to be biofertilizers. The second type of microorganisms is responsible for increasing the plant growth by various indirect means such as by protecting from different plant pathogenic attacks. Such organisms are known to be biocontrol agents. The third class comprises microbes that are responsible for stimulating plant growth through secretion of different phytohormones as well as growth regulators, for instance, auxins, gibberellins, cytokinins, etc. Such microorganism is best regarded as biostimulants (Ali et al. 2017).

The PGPRs are also recognized to bring out the accession and assimilation of nitrogen to the plants which is considered as the succeeding most significant occurrence afterward photosynthesis in the plant systems. The process of biological dinitrogen fixation is extremely important to the global agricultural systems. In this process, the inactive dinitrogen from the atmosphere is reduced to ammonia in the occurrence of nitrogenase enzymes and is a doing of diazotrophic microbes (Sulieman 2011; Dixon and Kahn 2004; Franche et al. 2009). The nitrogen fixative microbial systems are commonly classified as (1) symbiotic nitrogen-fixing microbial systems (e.g., rhizobia and Frankia) (Zahran 2001; Ahemad and Khan 2012) and (2) nonsymbiotic (free-living, associative, and endophytes) nitrogen-fixing microbial systems like Cyanobacteria (Anabaena, Nostoc), Azotobacter, Azospirillum, Azocarus, etc. The symbiotic association necessitates a multifaceted communication amid the host microbial partners which may result in creation of some specialized structures like nodule formation for the intracellular colonization of bacteria (Bhattacharyya and Jha 2012; Giordano and Hirsch 2004).

PGPR also assist the plant by enhancing the availability of several vital and key nutrients. The method usually employed is the solubilization of the nutrients followed by their enhanced uptake. The solubilization of key nutrients takes place by secretion of some mild organic acids by the microorganism where the enhanced uptake proceeds by the secretion of some chelator molecules like iron. The plant systems usually face a problem which is low phosphate obtainability due to the occurrence of phosphate in insoluble forms. The phosphate-solubilizing bacterial strains convert the insoluble phosphate into its monobasic diabasic forms which are easily available to the plant systems. The phosphate-solubilizing bacteria dwelling the rhizosphere discharge some mild organic acids and enzymes called as phosphatases which facilitate the transformation of inexplicable forms of phosphate to the plant-accessible forms. The major phosphate-solubilizing bacterial strains are represented by Azotobacter chroococcum, Bacillus circulans, Cladosporium herbarum, Enterobacter agglomerans, Pseudomonas chlororaphis, P. putida, Rhizobium sp., Bradyrhizobium japonicum, Beijerinckia, Burkholderia, Pantoea, Flavobacterium, and Microbacterium (Ali et al. 2017; Vessey 2003; Lugtenberg and Kamilova 2009).

Iron is another essential nutrient required by the plant systems; however, its comparative insolubility in the soils restricts its accessibility to the plants. It plays a key role by aiding as a cofactor in different enzymes which catalyze numerous biological progressions such as nitrogen fixation, respiration, and photosynthesis. Plant roots favor iron absorption in the form of reduced ferrous ion, but the availability of ferric ion is much common in finely ventilated soils. Several rhizosphere-inhabiting bacteria have the attribute of siderophore production which functions to bind the ferric form of iron, and it is evident that plant species have the capability of absorbing bacterial Fe3+-siderophore complexes (Stein et al. 2009; Andrews et al. 2003; Lemanceau et al. 2009). The siderophores represent some lower molecular mass complexes possessing excessive empathy toward the chelation of ferric ions which is shadowed by the shift and its accretion in the bacterial cells. There can be different types of siderophores like phenol catecholates, hydroxamates, rhizobactin, and pyoverdine siderophores which differ in their structure as well as activity. In addition to this, several fungi are known to produce siderophores which include the rhodotorulic acids which are di- or tri-hydroxamates, the ferrichrome-type siderophores, and the fusarinines. The siderophore production not only provides the iron to the plants, but it also restricts the growth of various bacterial and fungal plant pathogens by restricting the iron availability to those microorganisms. A vast array of microorganisms have been reported for siderophore production that are largely represented by Agrobacterium tumefaciens, Erwinia, Bacillus subtilis, Pseudomonas stutzeri, Mycobacterium, Nocardia, Rhodococcus, Arthrobacter, Azotobacter, Penicillium, and Aspergillus (Osman et al. 2018; Sheng et al. 2020).

The rhizobacterial members of genera Bacillus and Pseudomonas have been reported to produce diverse plant growth regulators which further result in the development of fine root fibers by the plant systems, thereby amassing the entire surface area resulting in enhanced nutrient and water uptake. The different types of plant growth hormones secreted by microbes are found to be auxins, mainly indole-3-acetic acid, cytokinin, and gibberellins. These growth regulators are acknowledged to enhance the increase in root length, cell division process, seed and tuber sprouting, movement of water and nutrients, and secondary root development. Additionally, they also mediate geotropic as well as phototropic reactions and thereby confer resistance to different stresses. The microbes are also known to secrete inhibitors like ethylene which influence the hormonal equilibrium in plant systems. Ethylene is considered as a senescence hormone acknowledged for inhibiting plant growth during usual circumstances; however, at lower levels (0.05 ml/l), it is known for stimulating plant growth. This gaseous hormone is called as “stress hormone ,” and its level is known to upsurge during the plant exposure to different stresses. The rhizobacterial members are also known to produce 1-aminocyclopropane-1-carboxylase (ACC) deaminase enzyme which cuts the ethylene production in plant, thereby assisting the plant systems in stress recovery (Backer et al. 2018; Ahemad and Kibret 2014).

Plants being immobile living systems have to confront some abiotic stresses like drought stress, temperature stress, salinity stress, etc. These stresses cause a considerable decline in plant fitness and overall crop produce. The plant-allied valuable microbes are known to play an important role in stress abatement along with the expansion of such agricultural systems that are found to be resilient toward the climatic changes. Innumerable studies have proven that numerous rhizospheric microbes like Rhizobium and Azospirillum possess the trait of plant stress alleviation. The PGPRs are known to secrete several compounds that behave as osmolytes, for instance, the secretion of glycine-betaine, proline, ectoine, trehalose, polyols, and sucrose by PGPR actions in harmonization with the composites secreted by roots in response to various biotic as well as abiotic strains. The bacteria Pseudomonas pseudoalcaligenes, Bacillus pumilus, Pseudomonas putida, Enterobacter cloacae, Serratia ficaria, Pseudomonas fluorescence, Dietzianatro nolimnaea, Bacillus amyloliquefaciens, etc. are reportedly known for alleviating the salinity stress (Khan and Bano 2019). Similarly, on exposure to drought strain, plants experience the deposit of numerous stress-induced composites, like proline, polysugars, abscisic acid, and glycine betaine, along with an increment in the production of enzymatic as well as nonenzymatic antioxidants. The soil microbiota initiate diverse biological contrivances like accrual of compatible solutes, EPS fabrication, and spore formation. These mechanisms employed by the microorganisms assist the plant systems to cope with the drought stress. Similarly microorganisms employ a variety of stratagems to assist the plant systems in coping with different abiotic and biotic stresses (Priyanka et al. 2019).

The beneficial rhizospheric microflora also assists the plant systems to get rid of different recalcitrant and xenobiotic compounds, which have accreted in soil systems owing to the rapid pace of anthropogenic activities which further results in the soil humiliation and sterility. The coevolution of plant and their allied microbiota has effectively resulted in the reclamation and restoration of the degraded soils without instigating any detrimental by-products, unlike conventional methods. This process is often said to be rhizoremediation. Several root exudates secreted by plants, like linoleic acid, behave as surfactants which enhance the availability of pollutants to the microbial systems by forming a layer on soil particles which also upshot improved attachment of bacteria on the pollutant. The bacteria then secrete several compounds including enzymes and metabolites which function to breakdown the toxic pollutants into their nontoxic forms. The bacteria, namely, Bacillus licheniformis, Bacillus mojavensis, Achromobacter xylosoxidans, P. aeruginosa, Ochrobactrum sp., P. fluorescence, Microbacterium sp., Microbacterium sp., Rhizobium sp., Rhizobium, Pseudomonas, Stenotrophomonas, and Rhodococcus, have been reported to degrade various pollutants (Mishra and Arora 2019). Therefore, the possession of numerous and multidisciplinary beneficial attributes of plant-allied rhizospheric microbiota has projected them as an effective substrate for engineering the plant rhizosphere.

4.2 Harmful Interactions: The Bad Microbiome

The plant systems secrete root exudates for attracting beneficial microflora, but some pathogenic microbiota also gets attracted toward plant roots. These microorganisms parasitize the plant systems and result in several severe infections, therefore executing damaging effects on various crops of economic importance. This part of rhizospheric microbiome which affects the health of plant systems and thereby results in a considerable drop in the plant yield as well as economy represents “the bad” rhizosphere microbiome. The soil that endured pathogenic microbiota significantly deteriorates the crops, and among these fungal members of the rhizobiome are found to be most distressing. Consequently, this portion of rhizobiome seems to be a notable chronic menace toward global food production as well as economic steadiness. A vast variety of phytopathogenic fungi finding their origin from the rhizosphere have been reported; however, the most common pathogenic fungi take account of members of genera Phytophthora, Aspergillus, Verticillium, Fusarium, Mucor, Pythium, and Rhizopus. On the other hand, several bacteria have also been reported as pathogenic which largely belong to the genera Pseudomonas, Ralstonia, Erwinia, and Xanthomonas. The population and a variety of destructive and constructive microbes are interconnected to the measure and eminence of the rhizodeposits and to the aftermath of the microbiological communications happening in the rhizospheric zone (Somers et al. 2004; Tournas and Katsoudas 2005).

There are four major classes of phytopathogens, namely, virus, bacteria, fungi, and nematodes (Agrios 2005); however, only two of these are considered to be key performers in the soils, namely, fungi and nematodes. Nevertheless, bacterial pathogens on a narrow scale are also deliberated to be soil-borne, possibly for the reason that nonspore formers are not able to endure well in soils for longer times. In addition to this, bacterial pathogens also necessitate an injury or an indigenous breach for their penetration into the plants and thereby initiate the infection process. However, some bacterial pathogens are still able to infect the plant systems, for instance, Ralstonia solanacearum is responsible for bacterial wilt of tomato and Agrobacterium tumefaciens for the crown gall disease. A fewer filamentous bacterial pathogens also exist and infect the plant systems and are better adapted for their survival in soils. However, only fewer viruses are capable of infecting the roots. Their chances of infection are restricted by their requirement of vector and wound in the plant tissues for the initiation of infection. However, nematodes and fungi like Olpidium and Polymyxa act as the vehicles for viral particles (Campbell 1996; Nester et al. 2005; Raaijmakers et al. 2009). The pathogenic fungal species are causing major harms to crops in the form of various diseases, thereby affecting the overall economy of the field. The major sinks of the crop economy find their origin from several genera like Pythium, Fusarium, Verticillium, Rhizoctonia, and Armillaria (Ali et al. 2017).

The microbiota inhabiting the rhizosphere is also composed of many nematode species that are found to be parasitic to the plant systems. While a major proportion of the nematodes inhabiting the soils is free-living, 7% of the overall soil-lodging nematodes are found to be pathogenic to diverse plant species. The plant-parasitic nematodes have been found to affect different crops of much economic importance such as wheat, soybean, potato, tomato, and sugar beet. The nematode parasitism produces different signs in plant systems like leaf chlorosis and patchy, wilting, arrested growth coupled with the defenselessness against other major pathogens. The most pathogenic of all these nematodes are said to be root-knot nematodes and cyst nematodes which belong to the Heteroderidae family due to their broad range of host plants. The other major category of parasitic nematodes is migratory endoparasitic nematodes which migrate through roots and detrimentally feed on the plant cells, thereby causing substantial necrosis in the plant tissues. These are largely represented by the rice root nematode (Hirschmanniella), lesion nematode (Pratylenchus), and burrowing nematodes (Radopholus). These nematodes are attracted toward the plant roots by several of the root exudates like alcohols, ketones, organic acids, terpenoids, thiazoles/pyrazidines, cyclic adenosine monophosphate, esters, ions, amines, amino acids, and other aromatic compounds (Moens and Perry 2009; Jones et al. 2013; Ali et al. 2015; Rasmann et al. 2012).

These soil-originated pathogenic microbes have evolved in very hard situations, and therefore these are well fitted to the rhizospheric zone as equated to other microorganisms. They have invented several methodologies in their evolutionary journey to have hard edifices like resting spores, which aid their survival for longer periods in the nonappearance of the host crop.

The rhizospheric soil encompasses numerous microorganisms, somewhat lesser in statistics, which are found to be human pathogens. Such unscrupulous microbial pathogens are “the ugly” ones owing to their most damaging nature by unswervingly infecting the humans. These ugly microbes may either be native to the soils and also be dropped by human deeds, for instance, carried by animal as well as the bird fecal material, manure solicitations, by agricultural machineries, use of slaughterhouse wastes, sewage water, and medical wastes. The major human opportunistic pathogens dwelling the plant rhizosphere are of dermatological significance affecting the skin, hair, nails, etc. The opportunistic human pathogens are mainly represented by fungi like Microsporum canis, Trichophyton mentagrophytes, Aspergillus spp., Coccidioides, Blastomyces dermatitidis, and Trichophyton rubrum. However, the human pathogenic bacterial members especially the spore formers also inhabit the rhizosphere, for instance, Clostridium tetani, C. botulinum, Bacillus anthracis, Actinomyces israelii, and Clostridium perfringens, and some nonspore formers like enterotoxigenic strains of E. coli also inhabit rhizosphere (Berg et al. 2005; Chapman 2005; Baumgardner et al. 2011; Blackburn et al. 2007; Ali et al. 2017). The presence of numerous plant pathogenic microbial systems and unscrupulous human pathogens in the rhizospheric zone has prompted a need to engineer the rhizosphere where only beneficial microbiota can thrive by kicking out the plant and human pathogens so that the release of plant photosynthates via roots can be properly utilized by the plant systems.

5 Rhizospheric Engineering

The plant systems regulate the occurrence of microbial populations in the rhizospheric zone. Plants have also advanced several functions and stratagems for the alteration of rhizosphere and rhizobiome. It has also been proven that both beneficial and pathogenic (plant, human) microbes inhabit the rhizosphere. The configuration, comparative copiousness, and spatial and chronological dynamics of the rhizospheric microbial inhabitants not only affect the plant health and growth but also lay a strong influence on the health of human beings (Ryan et al. 2009; Mendes et al. 2013). The domestication of plant systems was mainly done using artificial selection by selecting crops based on traits excluding reproductive fitness, thereby deviating the whole process from the natural selection. The food crops were mainly selected based on huge seed size, condensed bitterness which is a principal defense mechanism, and some other traits, which unintentionally altered the plant traits regulating the microbiome. Therefore, the domestication process of crops has resulted in the alteration of the microbiomes conscripted by the plant systems (Leff et al. 2016; Pérez-Jaramillo et al. 2016). The advent of employing nitrogen-based fertilizers has also resulted in a paramount deviation from the natural selection. The application of nitrogen-based fertilizers made it sure that the yield of crops was not unswervingly associated with a plants’ capability of supporting microbial nutrient cycling. The N fertilization leads to a sharp reduction in the microbial biomass as well as their variety (Treseder 2008; Ramirez et al. 2010), concomitantly leading to the promotion of copiotrophs above oligotrophs (Fierer et al. 2012). The plant selection following explicit fertilizer establishments has promoted the unlinking of soil microbiota from the plant health. The application of ammonium-grounded fertilizers tends to condense the rhizospheric pH, whereas the application of nitrate-based fertilizers leads to an increase in the pH, thereby resulting in an alkaline rhizosphere. It is evident that alterations in soil pH can modify the soil chemistry in the zone surrounding the roots and thus impact the progression along with the configuration of microbial societies (Ryan et al. 2009). The selection of plant systems facing extraordinary fertilization management has resulted in the selection of genotypes supporting microbial N mineralization (Schmidt et al. 2016). Consequently, the present varieties may have experienced a loss in their aptitude of supporting microbiota responsible for degrading the organic forms of nitrogen and solubilizing the mineral nutrients like phosphorus (Wallenstein 2017).

Therefore, the major research interest in this field is precisely leaning toward the development of different approaches that could reshape the rhizospheric microbiota in favor of those microbial systems that have the potential of improving plant health as well as productivity and can also avert the propagation of different plant and human pathogenic microbiota already inhabiting the rhizosphere. Several research programs have already proven that plant’s genetic makeup along with soil variety is an important driver for shaping the rhizospheric microbiota (Berg and Smalla 2009; Bakker et al. 2012). Moreover, the fascinating roles played by microorganisms in various natural processes like soil organic materialization, nutrient proclamation, and pathogen burden have projected them for manipulating the microbiome as key for the rhizosphere engineering (Wallenstein 2017). The impact of soils on the rhizospheric microbiota has already been validated for different plant species (Berg and Smalla 2009). The soil systems are composed of extremely multifaceted and assorted environs that considerably affect the physiology of plant systems, a configuration of root exudation, and concurrently the rhizospheric microbiome. The pH of soil systems has also a significant part to play in determining the rhizospheric microbiome. The abundance along with a variety of bacterial populations has been found to fluctuate by the ecosystem type where the soil pH is the key driver. The bacterial variety is utmost in the neutral soils and subordinate in the soils having an acidic pH (Fierer and Jackson 2006; Mendes et al. 2013). Based on the genetic configuration of plant systems also, innumerable methodologies have been suggested for reshaping the microbial configuration of rhizosphere in the quest to redirect the microbial movement. The term “rhizosphere engineering” thereby denotes the alteration of plant’s root and adjoining environment in the quest to generate a “biased” milieu that will unambiguously improve the crop yield as well as the plant endurance. Root exudates play an essential role in enticing different plant pathogenic microbes and activation of their virulence factors. Therefore, altering the amount of root exudates through plant breeding experiments or by genetic alteration seems to be an apparent methodology for redirecting rhizospheric microbiome. The other strategy for reshaping the rhizosphere involves various soil amendments like the addition of compost and biochar which favor the colonization by beneficial microbial communities. Other strategies include the introduction of beneficial microbes in soil onto seeds and planting materials (Bhattacharyya and Jha 2012; Mendes et al. 2013). The understanding of the actions involved can help propose the different techniques which can allow the modification of the rhizosphere for an improved plant fitness and enhanced soil output. The different methodologies and representations of rhizospheric engineering are discussed under.

5.1 Soil Amendments

The alteration of the rhizospheric soil, and in turn its microbial constitution which has remained the most involuntary concern of the human activities, such as the frequent farming of some definite crops, may bring about the appearance of disease-oppressive soil systems, and several soil pollutants have also been reported for radically distressing the configuration of soil as well as plant-allied microbiota. The expansion of various novel practices in the field of microbiology and microbial ecology has delivered several prospects for modifying the soil microflora in a way analogous to the discerning “rhizosphere engineering” that happens in nature (Ryan et al. 2009). The amendments in soils seem to be the easiest way of engineering the rhizosphere. A vast array of soil amendments is employed for upsurging the plant productivity which also proves to be an important tool for shaping the rhizospheric microbiome (Fig. 21.1). This section takes account of the different types of soil amendments that are often employed for getting a biased rhizosphere.

Fig. 21.1
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Diagram depicting the different types of soil amendments employed for shaping the rhizospheric microbiome

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5.1.1 Soil Amendments with Compost

The addition of compost to the soils is also known for altering the microbial composition of rhizosphere. It increases the soil suppressiveness toward the soil-borne pathogens. However, the soil suppressiveness is dependent on the type of compost added. It also enhances the number of antagonists in the rhizosphere (De Brito et al. 1995). It further improves the physical as well as biochemical belongings of the soil, upsurges the soil water balance, and enhances the nutrient supply to plants, thus altering the soil properties and making it fit for microbial inhabitation. The short-term application of composts increases the rhizosphere soil carbon mineralization and microbial biomass, and this carbon mineralization increases the progression of roots and thin root hairs (Zhang et al. 2014) which further allow the plant systems to harbor beneficial microbiota. The compost brings a source of carbon for the existing rhizospheric microbiota in the form of soil organic matter, and it also acts as a source of diverse classes of microorganism which later inhabit the plant rhizosphere. It also alters the soil chemistry as well as soil structure in a substantial manner and thereby significantly affects the configuration of plant-allied microbial communities (Green et al. 2007). The soil organic matter represents a noteworthy basis of utilizable carbon for different rhizospheric inhabitants (Toal et al. 2000), and it has also been advocated that the incorporation of composts to the soil can upkeep microbes that are not even endured by exudates. This capability for compost-originated organic matter to endure some microbes advises that the “rhizosphere effect” does not act similarly on all microbial inhabitants (Boehm et al. 1997). De Brito et al. (1995) noticed that the compost incorporation to soil augmented the occurrence of bacteria in the rhizosphere of tomato that exhibited antagonism against various soil-borne pathogens like Rhizoctonia solani, Pyrenochaeta lycopersici, Fusarium oxysporum f. sp. radicis-lycopersici, and Pythium ultimum. The suppression of various pathogenic microbes by addition of compost is known to bring about the recruitment of definite microbes as the suppressive soils tend to lose their suppressive activity on their pasteurization and sterilization (Weller et al. 2002; Haas and Défago 2005). The addition of compost and organic matter enhances the microbial activity in the soil which inhibits the growth of pathogens either directly by its antagonistic activity or indirectly by the possession of competitive actions of recruited soil microorganisms. The suppression incurred to the soil systems either can be general or may also be specific. In case of general suppression, a basal shield contrary to an extensive collection of pathogenic microbes is established, and the defeat is not accredited to any precise microbe (Weller et al. 2002). However, the possession of specific suppression is attributable to the accomplishments of precise microbes that act contrary to specific pathogens and is found to be more operative than general suppression. The compost amendments in the soils not only redesign the structures of a microbial community but also lead to the establishments of new equilibria (Hadar and Papadopoulou 2012). The composts are also known to contain various bacterial and fungal biocontrol agents that later inhabit the plant rhizosphere and are known to advance the regularity of disease control. Antoniou et al. (2017) assessed the consequence of compost addition on the rhizospheric community of tomato along with its effect on the suppression of fungal pathogens. The compost added to the plant was able to suppress the fungus, namely, Fusarium oxysporum f. sp. lycopersici and Verticillium dahliae. It was also observed that the compost lost its disease suppression ability upon sterilization. Furthermore, it was found that the phyla Firmicutes and Ascomycota were dominating the compost, whereas the phyla Actinobacteria, Proteobacteria, Bacteroidetes, and Mucoromycota were rarely isolated. The addition of compost significantly altered the microbiological configuration of the rhizospheric zone as experienced by a reduction in the Ascomycota and Firmicutes, while Actinobacteria, Bacteroidetes, and Proteobacteria were augmented. Surprisingly, the number of Proteobacteria was found to be augmented by 57 times in the rhizosphere samples, while Actinobacteria by 6.1 times as equated to the unplanted compost sample. Innumerable studies have evidenced that the incorporation of compost in the agricultural soils protects the plant systems from some pathogenic microbes such as Pythium ultimum, Pythium irregular, Phytophthora nicotianae, Sclerotinia minor, and Sclerotinia sclerotiorum. The mechanisms may include the direct suppression of the pathogens or activation of the disease resistance genes in plant systems (De Corato 2020). Countless studies have testified a relative increment in the members of Proteobacteria and Actinobacteria upon compost addition, thus making it the most dominant group in the rhizosphere. Proteobacteria are also acknowledged for playing a serious role in the global cycling of carbon, nitrogen, iron, and sulfur, whereas Actinobacteria are supposed to subsidize the global carbon cycle by degrading the plant biomass, and because of their aptitude of decomposing organic matter in the soils, they are also proficient for fabricating several key enzymes like cellulases, hemicellulases, chitinases, glucanases, and amylases (Mickan et al. 2018; Yang et al. 2019). Conclusively, the amendments of compost in the soils prove to be an effective tool for reshaping the rhizosphere biology and, in turn, the beneficial rhizospheric inhabitants for improved plant health and yield.

5.1.2 Soil Amendments with Biochar

Biochar is a very steady product of thermal deterioration of organic materials in the lack of air (pyrolysis) and is distinguished from charcoal by its use as a soil amendment. The temperature of pyrolysis lies in the range from 300 to 1000 °C. The biomass employed for pyrolysis is principally composed by organic composites like cellulose, hemicellulose, and lignin (Kavitha et al. 2018). It has also been designated as a promising measure to upgrade the soil fertility besides other environmental amenities such as carbon sequestration for the extenuation of climate changes. The addition of biochar is acknowledged for the enhancement of the fertility of soil systems predominantly by uplifting the pH of acidic soils or by enhanced nutrient retention via cation adsorption and by uplifting the water retention capacity of the soil. The desired depth for the application of biochar lies in the range of 4–6 cm (Lehmann et al. 2011; Yu et al. 2019). The biochar amendments in the soils are known to alter the diversity as well as an abundance of the biological community. The alterations induced by the biochar amendment in the microbial community configuration may not only distress nutrient cycling and plant progression but also the dynamics of organic matter present in the soil systems (Wardle et al. 2008; Kuzyakov et al. 2009; Liang et al. 2010). The biochar apertures function as a microenvironment for the proliferation of microbial systems. The microorganisms utilize carbon, nutrients, gases, and water offered by the biochar for growth as well as reproduction. The soil application of biochar at a proportion of 10 t per hectare has resulted in a noteworthy upsurge in the biological nitrogen fixation by red clove as equated to the control. Its amalgamation in the soil is also known to affect the arbuscular mycorrhizal fungi in a positive manner (Jaafar 2014; Mia et al. 2014). Biochar also reduces the tensile strength of the soil, therefore making the root as well as mycorrhizal nutrient mining extra operative. The reduced tensile strength also facilitates the easy seed germination and also simplifies the movement of invertebrates through the soil, thereby modifying the predator/prey dynamic (Lehmann et al. 2011). The biochar addition supports the growth of PGPRs like Bacillus insolitus, Aeromonas hydrophila, and A. caviae which are known to mitigate the salinity stress by the secretion of exopolysaccharide responsible for binding sodium ion that results in a reduced uptake by the plants along with the production of an enzyme called 1-aminocyclopropane1-carboxylate deaminase which also relieves the salinity stress (Ashraf and Harris 2004; Ali et al. 2014). In addition to it, the microbial copiousness has also been confirmed in the biochar-amended soils by different methods, like total genomic DNA extraction, plate count, substrate-induced respiration, fumigation-extraction, phospholipid fatty acid extraction, and staining and direct surveillance of discrete biochar particles. Furthermore, it also enhances the rate of reproduction of microbial populations (Lehmann et al. 2011). The microbial communities associated with the nitrogen transformations are known to be altered upon biochar incorporation indicating a reduced soil nitrogen loss and improved nitrogen utilization as indicated by a reduction in the number of Nitrososphaera in the rice fields upon biochar amendment (Liu et al. 2017). Moreover, the biochar addition is also known to uplift the network of beneficial fungi in the rhizospheric zone (Wang et al. 2019). Win et al. (2020) evaluated the effect of biochar on the rhizospheric communities using the next-generation sequencing methods and observed that biochar augmented the copiousness of Proteobacteria as well as Actinobacteria in the rhizoplane particularly after 2 weeks of transplantation. On the contrary, there was a decrease in the number of Acidobacteria and Bacteroidetes. The members of Xanthomonadaceae experienced an increment of 2.8-folds in their numbers after 2 weeks of transplantation followed by Desulfuromonadales (1.8-fold), Burkholderiales (1.8-fold), and Actinomycetales (1.4-fold) along with a concomitant decline in the relative abundance of Sapropirales (1.8-fold) and Nitrososphaerales (2-fold). Similarly, Cheng et al. (2018a, b) also observed that the supplementation of the soils with the biochar augmented the diversity as well as an abundance of bacteria. The comparative copiousness of Adhaeribacter, Rhodoplanes, Pseudoxanthomonas, and Candidatus Xiphinematobacter augmented in the biochar-amended soil; however those of Lacibacter, Pirellula, and Kaistobacter faced a decline. The addition of biochar is also acknowledged for influencing the root metabolome and is known to alter the levels of some amino acids as well as organic acids. Therefore, it is not only the rhizosphere microbiome that is altered upon soil amendments with biochar, but the rhizosphere metabolome is also reshaped. Chen et al. (2017) observed that the biochar addition along with a simultaneous nitrogen reduction caused a 1.75-fold increase in the levels of isoleucine, a 2.16-fold surge in malonate, and a 2.15-fold rise in acetate in exudates. Similarly, Bornø et al. (2018) also observed that the exudates of particularly glucose and fructose were intensely altered by the biochar application, specifying that the plant reaction to biochar application can modify the configuration of root exudates discharged into the rhizosphere. This altered exudation process in turn plays a key role in engineering the rhizospheric microbiome (Fig. 21.2).

Fig. 21.2
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A portrayal depicting a GM plant engineered for the secretion of specific root exudates which later harbors definite microbial populations and alleviate the heavy metal stress

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5.1.3 Other Soil Amendments

A large number of human practices are known to alter the rhizospheric microbiome in an unintentional way, for instance, addition of fertilizers, addition of substrates for fueling bioremediation processes, use of pesticides and other agrochemicals, etc. The application of glyphosate has been shown to alter the denitrification process in the grass sward along with a surprising increment of 20- to 30-fold in the denitrification process as equated to the herbicide-untouched grass. The denitrification process in the soil is predominantly attributable to the facultative anaerobic bacteria; thereby, any increment in the process suggests a possible alteration in the diversity and number of accountable microbes in the rhizospheric zone (Tenuta and Beauchamp 1996; Qian et al. 2018). The application of diclofop-methyl leads to a reduction in the nitrification of urea nitrogen in soils. This weedicide is potent enough to inhibit the enzyme acetyl-CoA carboxylase activity and thereby can lead to a reduction in the fatty acid synthesis in the crop. In addition to it, the persistence of residual DM particles in the soil systems is known to affect an extensive range of plant metabolic pathways and thus can lead to an augmented exudation of organic acid (Rensink and Buell 2004; Qian et al. 2012; Chen et al. 2017). The plant root exudates are the crucial influencers of rhizospheric microbiota configuration; therefore, the testified impact of diclofop-methyl on the exudation nurtures the probability that multifaceted plant-microbiome communications could restrain the DM poisonousness and could also alter the copiousness of specific microbes distressing the biogeochemical cycles of nutrients. Qian et al. (2018) reported that the application of DM on rice altered the levels of 28 different exudates in the rice rhizosphere. The altered exudation also affected the rhizospheric microbiome and resulted in an increase in the fraction of Proteobacteria from 42.1% in the control to 55.4% after 5 days of DM exposure. However, the comparative richness of phyla, Firmicutes and Acidobacteria, faced a decline from 22.0 and 16.9% in the control to only 8.9 and 13.9%. Additionally, the comparative richness of the genera Azospira, Clostridiales, and Rhodocyclaceae increased from 7.1, 0.3, and 1.1% in the control to 21.0, 2.4, and 2.3% of total rhizospheric microbes.

The wastewater-borne pollutants are also known to alter the rhizospheric configuration of the holobiont. The wastewater-borne sulfonamides are known to alter the microbiome composition in the constructed wetlands planted with Cyperus alternifolius, Cyperus papyrus, or Juncus effusus. A noteworthy decline in the microbial diversity has been testified along with a precise inhibition of microbes involved in the nitrogen and sulfur cycle. However, the microbes like Methylosinus, Methylotenera, Methylocaldum, and Methylomonas which are potent for degradation of sulfonamides are found to be increasing in the rhizospheric zones of the plants (Man et al. 2020). The irrigation with treated wastewater is also known to alter the composition of rhizobiome. The soil ammonia-oxidizing bacterial populations are altered irrespective of the ammonium concentration or the presence of plants. The treated wastewater brings a reduction in the comparative richness of Actinobacteria along with a simultaneous upsurge in the comparative copiousness of Gammaproteobacteria (Oved et al. 2011; Frenk et al. 2014). Zolti et al. (2019) also reported an upsurge in relative copiousness of Gammaproteobacteria and a decline in Actinobacteria, in the root microbiome receiving irrigation with treated wastewater. The assessment on more precise levels revealed the abundance of Pseudomonadales and a reduction in Streptomycetales and Pseudonocardiales. Similarly, the wastewater effluent containing aged nanoparticles has also been acknowledged for influencing rhizospheric microbiota. In a study by Liu et al. (2018), it has been claimed that the copiousness of cyanobacteria was amplified by 12.5% as demonstrated predominantly by an upsurge of Trichodesmium spp., and the lavishness of unknown archaea was heightened from 26.7% in the control to 40.5% in the soil watered with wastewater effluent containing aged nanoparticles.

Several other organic amendments, such as seed meal for the control of fungal pathogens, also alter the rhizospheric microbiome. The soil amendments with Brassicaceae seed meal preparations for the suppression of apple replant disease altered the rhizobiome in a significant way. The amendment not only suppressed the pathogen Pratylenchus penetrans but also elevated the level of Proteobacteria and Acidobacteria in the rhizosphere. In addition to it, the microbial genera engaged in numerous nitrogen-cycling progressions , like Bradyrhizobium, Rhodopseudomonas, and Nitrospira, were found to exhibit more abundance. Similarly, the fungus Basidiomycota got reduced in abundance in the apple rhizosphere after the treatment, whereas the abundance of Zygomycota got increased (Mazzola et al. 2015).

The addition of fertilizers also changes the structure of rhizosphere microbiome. The soil amendments with high levels of nitrogen fertilizers negatively affect the soil diazotrophs. The discharge of root exudates is reliant on the plant physiological status along with the nutrient obtainability. For instance, maize has been reported to discharge subordinate amounts of amino acids via roots during nitrogen scarcity (Carvalhais et al. 2011, 2013). Therefore, the application of nitrogenous fertilizers alters the nutrient status of the soil and thus affects the rhizospheric microbiome. The analysis of root exudates of maize during nitrogen fertilization has revealed a tremendous increment of 30-folds in the sugar alcohols, 11-folds in sugars, and 7-folds in phenolics. This altered exudation process affected the rhizospheric microbiome by elevating the levels of Bacillales, Nitrosomonadales, and Rhodocyclales and by reducing the abundance of Chloroflexales, Gemmatimonadetes, and Phycisphaerae (Zhu et al. 2016).

6 Engineering the Plant

The plant systems happen to be the strategic elements for shaping the microbial populations in the rhizospheric zone. The plant’s ability to employ a diversity of occupations and stratagems to alter its rhizosphere in the quest to circumvent environment-associated stresses has attracted the interest of researchers for modifying the rhizosphere by engineering the plant systems. The understanding of the actions taking place assists in the development of techniques for modifying the rhizosphere for attaining improved plant healthiness and enhanced soil output efficiency. The plants can be genetically engineered for altering the soil organic anion efflux along with its transference from root cells by altering plants with an inordinate aptitude to produce organic anions coupled with their conveyance outside the cell. The plants are also potent enough to be genetically amended for the fabrication of several recombinant proteinaceous molecules, root exudates, and several other metabolites which target a biased rhizospheric colonization (Ryan et al. 2009; Mohanram and Kumar 2019). Nevertheless, the engineering of plant systems drives beyond the presently extensively nurtured, genetically altered plant systems that are resistant to a few pests or resilient to some herbicides.

The role of root exudates in shaping plant microbiome has attracted the attention of plant breeders and plant biotechnologists on a global basis for engineering the plant systems in the quest to get definite root exudates in higher concentration. As early as 1978, Petit et al. recommended to harness the benefit of the close connection prevailing amid the plants and their accompanying microbiota for framing the exudation process. This would offer a selective benefit to certain microbes which would help them in their establishment in the rhizospheric zone, a stratagem later designated “biased rhizosphere” or “artificial symbiosis ” (Savka et al. 2002). The earlier reports on engineering plant systems for a biased rhizosphere mainly target the engineering of plant systems to produce opines. The presence of opines in the rhizospheric zone powerfully shakes the native microflora. To be sure, such opine-secreting transgenic plants lead to an increment in the population of opine-consuming associates that may range from 100 to more than 10,000-folds in the non-sterile soils (Mansouri et al. 2002). This phenomenon can result in alterations of the bacterial members that persist evident even in the nonexistence of the selective pressure of opines (Oger et al. 2000) which further validate the excellence of opines as discerning substrates for microbial inhabitants in the rhizospheric zone. For instance, the transgenic lotus plants genetically altered for the production of two opines, namely, mannopine and nopaline, altered the composition of rhizospheric microbiome along with a specific increment in the bacterial communities able to exploit these molecules as sole carbon source (Oger et al. 2004).

The plant metabolism is redesigned for engineering the plant systems for desirable root exudates. The genes directing the synthesis of root exudates are firstly recognized in the plant systems, and then their expression levels are altered for redesigning the rhizosphere for upgraded features. For instance, the GM rice and tomato engineered with the vacuolar H+-pyrophosphatase gene AVP1 from the Arabidopsis plant displayed almost 50% more citrate as well as malate efflux as compared to their wild types after their treatment with aluminum phosphate. This was later deduced as a probable mechanism for enhancing resilience toward aluminum-ion-induced strain and to advance the plant aptitude to consume the unsolvable phosphorus (Ahkami et al. 2017; Yang et al. 2007). Similarly, a gene encoding for citrate synthase from Citrus junos plant when cloned and overexpressed in Nicotiana benthamiana led to a threefold increment in the enzyme activity which further supported the accumulation of citrate in a concentration that was found to be twofolds higher as equated to the wild-type plant systems. Certainly, the root systems of genetically altered plants were found to be more tolerant to aluminum toxicity, and, surprisingly, their roots sustained to lengthen at levels of 100 mM Al, which were enough to constrain growth in wild-type plants (Deng et al. 2009). Likewise, the citrate synthase gene originating from Pseudomonas aeruginosa when transferred into papaya also led to an augmented accrual of citrate in the cytoplasm (Rengel 2002) which was further complemented by enlarged efflux of citrate into the vicinity of roots along with an improved forbearance of transformed plants to Al. The secretion of specific root exudates has also been reported for increased plant tolerance toward the deficiency of nutrients. For instance, the transferring of rye chromosome 5R or only a minor segment of chromatin from the long arm of the chromosome 5R to wheat upsurges its lenience toward the copper paucity (Schlegel et al. 1997). The plant’s increased tolerance toward copper deficiency after the chromosome transference is also coupled by the fact that genes for mugineic acid synthase and 3-hydroxymugineic acid synthase, the enzymes involved in biosynthesis of common phytosiderophores, are located on the rye chromosome 5R (Rengel 2002). Furthermore, the root exudates are also supposed to play a significant role in the abovementioned process.

The plant systems are evolved with different mechanisms to discharge the exudates into the rhizospheric zone, comprising diverse kinds of passive as well as active transport systems. Conventionally, the exudation has been deliberated to be a passive progression, arbitrated via different pathways: the conveyance over the root membrane by diffusion, ionic channels, and vesicles transport (Baetz and Martinoia 2014). The pitch shaped by their dissimilar levels amid the cytoplasm of root cells and the rhizosphere is a major factor in shaping the exudation process which is also a subject to be affected by the permeability of root membrane, the veracity of root cells, and the polarity of the compounds to be exuded (Badri and Vivanco 2009). The presence of ion channels for secretion of several root exudates also provides a selective prospect for engineering the plants. The ionic channels are held accountable for discharging the carbohydrates along with some precise carboxylates like malate and oxalate, which are oozed not by diffusion, but via a transport machinery facilitated by proteins. Two different anionic channels have been described: SLow Anion Channels (SLACs), originally named S-type (Slow-type), which need several seconds to be activated, and QUick Anion Channels (QUACs), originally named R-type (Rapid type), which can be activated in a few milliseconds (Dreyer et al. 2012). The aluminum-activated malate transporters (ALMT) and multidrug and toxic compound extrusion (MATE) membrane transporters are extensively studied among all the transporters (Sharma et al. 2016; Kang et al. 2011; Vives-Peris et al. 2020). The two approaches that have been tried to upsurge the discharge of organic ions from the roots are engineering the plant systems with an improved ability to synthesize organic ions and genetically altering the plant systems with a heightened aptitude to convey organic ions outside the cell (Ryan et al. 2009). The first approach targets the expression of genes concerned with the synthesis of particular ions, whereas the second approach targets the genes encoding proteins facilitating the movement of organic ions through the plasma membrane. The genetic engineering of plants grounded based on the second approach takes account of genes encoding the transport proteins. The foremost gene that was recognized to translate a transport protein facilitating the efflux of organic anions from plants is TaALMT1 from Triticum aestivum (Sasaki et al. 2004). This gene codes for the first fellow of an innovative membrane protein family that functions as an anion channel to mediate Al3+-activated malate efflux from roots. Thus, it represents an important tool for altering the malate release in the plant rhizosphere. Similarly, the MATE genes are found to efflux a vast array of small organic composites comprising secondary metabolites like flavonoids and alkaloids (Omote et al. 2006). They have also been found to enable citrate efflux from the plant cells. The Arabidopsis and tobacco plants transformed with SbMATE1 and HvMATE genes, respectively, have been reported to deliberate Al3+-stimulated citrate efflux along with an augmented tolerance of Al3+ stress (Magalhaes et al. 2007; Furukawa et al. 2007). The examples have exhibited the key part of transport proteins in engineering the plant systems for getting a biased rhizospheric zone. Similarly, the plant systems can also be engineered for altering the rhizospheric pH as the plant systems are known to back the rhizospheric acidification by engendering electrochemical gradient potential crosswise the cell membrane of root cells after the efflux of H+. This acidification assists in the augmentation of the plant’s contact to Fe3+ and P which are otherwise not accessible to plants (Hinsinger et al. 2003). The efflux of H+ ions from the plant cells is principally under the control of a large family of H+-ATPase. Therefore, the manipulation of plant systems for the overexpression of these genes in the quest to amend the rhizospheric pH also seems to be an open opportunity. The expression of the AVP1 pyrophosphatase in Arabidopsis beyond the normal levels persuaded a highly acidified rhizospheric environ, speciously by increasing the action of the cell membrane H+-ATPase (Yang et al. 2007). Therefore, the involvement of diverse biotechnological approaches can be utilized to engineer the plant systems for getting a biased rhizosphere owing to the ability of the engineered plants to produce the desired root exudates, acidify the rhizospheric zone, and therefore harbor the desired set of microbial systems.

7 Engineering of Microbial Partners

The particular aim of microbiome engineering is to influence the microbiota in the direction of an assured type of microbial community that owes the potential of optimizing plant functions of interest. Furthermore, the engineering of microbial partners is always motivated to harnessing the advantage of naturally evolved plant-microbiome communication networks (Quiza et al. 2015). The directing force toward the alteration of rhizospheric microbiome in the quest to upsurge the plant functioning and productivity is the plenty of evidence that has unveiled the critical role of plant-microorganism connection to the healthiness, output-efficiency, and the complete situation of plant systems. Therefore, the only objective of modifying the plant microbiome is to drive the plethora of rhizospheric interactions in the direction of enhanced constructive aftermaths for the plant systems. The plant root exudation-mediated microbial colonization of rhizospheric microbiome is largely explored, but what is of more interest is that the presence of specific microbes in the rhizosphere is also identified to amend and shape the exudation process, for instance, antimicrobial-resistant Pseudomonas is potent enough to block the fabrication of plant antimicrobial compounds (Bais et al. 2008; Hartmann et al. 2009; Oburger et al. 2013). Thus, the parameter dealing with the engineering of microbial partners requires a prompt knowledge of rhizospheric interactions. However, the efforts for revealing rhizospheric communications are predominantly focused toward the aptitude of a single plant root exudate to touch the single bacterial or fungal rhizospheric inhabitant. The unblemished constraint tackling this kind of attitude is the removal of the microorganism from any environment that would surely pot the existence of interspecies interactions into ignorance (Ziegler et al. 2013). The other major restrain in this approach is the inability of several rhizospheric microbes to grow in the laboratory and the inadequacy of the culture-dependent approaches for the qualitative scrutiny of rhizosphere microbiome. Interestingly, in spite of these several methodologies, targeting rhizosphere microbiome engineering necessitates the involvement of microbial isolates at hand, thereby pointing the requirement for the escalation of cultivability of rhizospheric microbes. Therefore, the possession of a distinct functional capacity by several microbial isolates puts forward the approach of inoculating these microbial cultures in the plant rhizosphere in the quest to engineer the plant microbiome for improved plant well-being and output (Ryan et al. 2009; Quiza et al. 2015). However, the perseverance, as well as the serviceability of the inoculated isolates, needs to be further measured to ascertain positive influences when used as a definite stratagem for manipulating the rhizospheric microbiome (Stefani et al. 2015). In addition to this, the inoculation with genetically altered microbial strains also represents an important strategy for manipulating the rhizospheric microbiome. The recombinant strains are genetically altered for any particular desired trait, and in several circumstances, the recombinant strains have the potential to address complications allied with the swift diminution of the population density coupled with their undersized persistence. The recombinant strains may bring out the augmentation of several inhabitants of the endogenous community by the transferal of genetic material via horizontal gene transfer. However, the release of GM strains in the environs necessitates a thorough assessment to appraise the impending risks associated (Ryan et al. 2009). However, the disruption of existing microbial communities of the rhizosphere before the inoculation favors the establishment of biological functions in the rhizosphere. The different approaches for altering the rhizosphere by targeting the microbial partner of the holobiont are explained in detail in the subsequent paragraphs.

7.1 Rhizosphere Engineering by Microbiome Manipulation

The manipulation of rhizospheric microbiome in a direct manner seems to be an easy and more feasible method for engineering the rhizosphere. The inoculation of potent microbial strains seems to be an imperative choice for altering the rhizospheric microbiota. The existence of several novel tactics is potent enough to augment the competence as well as perseverance of the newly introduced microorganism into the soil systems (Bakker et al. 2012). The inoculation process follows some screens and selection perimeters along with a precise evaluation of the different plant health elevation attributes of the retrieved microbial isolates. Furthermore, their survival and growth in the carrier and their efficacy to perform in the natural environments are also assessed before the inoculation (Okafor 2016). The colonization followed by dominance in the rhizospheric zone by the microorganisms is very critical for both beneficial and pathogenic microbes (Bakker et al. 2012). The aptitude of PGPR is being harnessed from several decades as amendments in the form of attributable to their employment as eco-friendly substitute to chemicals, thereby acting as protecting shield against the long-lasting negative impact on different chemicals on the environmental health. However, the employment of this technique has not picked up the anticipated pace regardless of having numerous proven benefits. Therefore, the farming community has lost interest in this technology and thus still relies on the usage of chemical fertilizers (Dubey and Sharma 2019). Several limitations in the abovementioned process came across either with the monoinoculation or even with a consortium assembled with a group of two or more bioinoculants. The direct inoculation of any microbial culture in the rhizosphere is estimated to tackle a substantial degree of competition from the surroundings. It may also alter the already prevailing equipoise in the rhizospheric zone and, thus, can upset the plethora of valuable natural connections (plant-microbe and microbe-microbe interactions) prevailing in the soils. However, some strategies for enhancing the rhizosphere microbiome focusing on the co-inoculation with numerous microbial strains or mixed cultures of arbuscular mycorrhizal fungi (AMF), ectomycorrhizal fungi (ECM), PGPR, and endophytes, enabling combined niche exploitation, cross-feeding, enhancement of one organism’s colonization ability, modulating plant growth, and achieving niche saturation and competitive exclusion of pathogens have become successful also (Satyanarayana et al. 2019). The inoculation of microbial culture along with some organic amendment like compost has also proven to be successful and has produced desirable results. The microbial strains that are to be inoculated are the result of the study of any particular plant’s microbiome as the plant microbiome consists of several energetic microorganisms that have the potential to alter the plant physiology as well as development and can also prompt the resistance systems against pathogenic microbes along with the elicitation of diverse tolerance mechanisms against numerous plant stresses (Santoyo et al. 2017; Yaish et al. 2017; Yuan et al. 2016). The whole plant microbiome is not capable of assisting plant growth as only a few microbial strains possess these beneficial attributes and the synergistic effects between two strains or more have also been reported for their plant growth supportive attributes (Rojas-Solís et al. 2018; Timm et al. 2016). Therefore, the desired microbial strains are maintained in the form of bioformulations for preserving their viability by shielding them from hostile environmental situations. There are different modes of applications of bioformulations in the field such as biopriming of seeds, foliar spray, seedling dip, and soil drenching. However, the inoculation of the desired microorganisms in the rhizosphere not only increases the number of the inoculated microbes but results in the alteration in the rhizospheric environmental conditions, and therefore the change in the diverse array of communications taking place in the rhizosphere brings out an overall change in the rhizospheric microbiome. For instance, Wan et al. (2017) reported that the inoculation of tomato rhizosphere with the biocontrol agent Bacillus amyloliquefaciens altered the rhizospheric composition and increased the abundance of Pseudomonas and Massilia. Similarly, Bacillus amyloliquefaciens when inoculated in the sorghum rhizosphere significantly enhanced the yield and also affected the rhizosphere microbiology as the proportion of Tremellomycetes was reduced by 8.87% in the continuous cropping soil (Wu et al. 2019). Likewise, the inoculation of Pseudomonas putida Rs-198 in the pepper rhizosphere increased the abundance of Blastococcus, AKYG587, Pseudomonas, Cyanobacteria, and Chloroflexi (He et al. 2019). The PGPR Paenibacillus mucilaginosus when co-inoculated with the rhizobia Sinorhizobium meliloti in the rhizosphere of Medicago sativa also altered the rhizobiome as displayed by a relative increment in the abundance of Firmicutes as well as Acidobacteria (Ju et al. 2020). The inoculation with AMF also changes the profiles of rhizospheric microbial community, for instance, the rhizosphere of Prosopis juliflora when inoculated with Glomus intraradices and a mix of G. intraradices and G. deserticola also significantly affected the bacterial and fungal community structure (Solís-Domínguez et al. 2011). Similarly, the inoculation of the AMF in the rhizospheres of Salvia officinalis L., Lavandula dentata L., Thymus vulgaris L., and Santolina chamaecyparissus also altered the bacterial and fungal communities of rhizosphere. Moreover, the ability of the AM fungus to shape the rhizosphere bacterial community structure was independent of the host plant species (Rodríguez-Caballero et al. 2017). Similarly the inoculation of maize with the phosphate-solubilizing fungi, namely, Aspergillus niger P39 and Penicdlium ozalzcum P66, also lead to an increased bacterial diversity in the rhizospheric zone as assessed using DGGE fingerprinting (Guang-Hua et al. 2007). Therefore, it can be concluded that the members of rhizospheric microbiota which are often selected from the core microbiome on the basis of their several growth promotion attributes not only directly benefit the plant systems by their valuable possessions but also serve the plant systems by creating a unique environment in the plant rhizosphere. The inoculated microbes assist the growth of plant systems by reshaping the microbial community of the rhizosphere where some genera face a relative increment in their proportion, while the others have to bear a concomitant decline. Thus, this approach inoculating desirable microbes proves to be an important tool for engineering the rhizosphere.

7.2 Rhizospheric Engineering by Genetic Manipulation of Microbes

The microbial strains used for inoculation in the quest to engineer the rhizosphere must be established in the rhizosphere and should uphold biologically active populations to outcompete the already adapted occupant microbial systems. However, microbial systems employ a lot of stratagems for successfully inhabiting the new environment, for instance, synthesis of cell surface molecules; at various times the colonization process is not found to be much effective (Ryan et al. 2009). Therefore, the genetic engineering of several microbial strains for various desired traits seems to be a viable option for enhancing their fitness before their inoculation (Fig. 21.3). The genes responsible for the growth promotion attributes of microbial systems have demonstrated to be effective targets for strain enhancement, either by amending the timing or degree of their expression or by transferring and expressing them in alternate hosts with other desirable attributes (Ryan et al. 2009). However, the early efforts comprise the insertion of a heterologous gene encoding a siderophore receptor into a Pseudomonas fluorescens strain to render it more competitive in soil (Dessaux et al. 2016). This methodology targets the gene insertion tactic for increasing the number of outer membrane siderophore receptors in microbial strains for making them more efficient on iron acquisition and therefore inhabiting the rhizosphere, for instance, the insertion of the siderophore receptor for ferric pseudobactin 358 into P. fluorescens WCS374 resulted in a strain that was found to be more competitive than the WCS374 parental strain for the occupation of the radish rhizosphere (Geetha and Joshi 2013; Raaijmakers et al. 1995). The rhizobacteria are also genetically engineered for the production of several key enzymes and have demonstrated improved plant growth promotion attributes, for instance, Pseudomonas fluorescens CHA0 altered with the acdS gene coding for the enzyme ACC deaminase significantly improved the root length in canola seedlings and also provided enhanced defense against the phytopathogen Pythium (Wang et al. 2000). Similarly, the genetically altered B. subtilis OKBHF significantly increased the height, fresh weight, and flower along with the fruit number in tomato plants along with a concomitant reduction in the disease rigorousness due to Cucumber mosaic virus. The Bacillus strain was genetically engineered for the gene coding for the HpaGXooc which is a member of the harpin group of proteins and is responsible for the biocontrol activity (Wang et al. 2011).

Fig. 21.3
figure 3

Effect of inoculating plants with GM microorganisms altered for various traits on the plant health

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The plant systems also face several abiotic stresses, and it is an unhidden fact that several PGPR strains have got unique abilities to aid plant systems during their exposure to different stresses. The competent microbial strains which prove to be effective in coping with the abiotic stresses are isolated and identified, and the molecular cascade of events taking place during the microbial elimination of plant stress is unveiled in the quest to engineer microbial strains with an improved capability of assuaging the plant stress responses. A cadmium-resistant Pseudomonas aeruginosa transformed with metallothionein gene has been validated for its tremendous capability of adsorbing cadmium ions via extracellular accrual and was also found to owe an improved aptitude for the immobilization of cadmium divalent ions from the external source. The inoculation of this genetically altered microorganism in cadmium-polluted soil considerably heightened the plant biomass as well as the chlorophyll content in leaf (Huang et al. 2016; Jishma et al. 2019).

The colonization of plant root by the inoculated microorganism represents an important parameter to be considered for genetically altering the microbial systems. The colonization of root surfaces is driven by a molecular cascade of events and also depends on various factors like phenomenon of chemotaxis and biofilm formation (Yaryura et al. 2008). The disruption of gene abrB created a genetically altered strain of Bacillus amyloliquefaciens SQR9 which resulted in enhanced root colonization therefore with enhanced biocontrol ability (Weng et al. 2013).

The plants facing insect attacks can also be inoculated with the genetically engineered endophytic microbes transformed with the genes coding for precise insecticidal proteins. Such endophytes are also designated as living vectors meant for the expression of anti-pest proteins in plant systems. The first attempt to insert a heterologous gene into an endophytic microbe was made by Fahey (1988). The other endophyte Clavibacter xyli subsp. cynodontis was also genetically manipulated with an endotoxin gene originating from Bacillus thuringiensis. The genetically improved bacterium was capable of secreting toxin inside the plant that protected the plant systems from insect attacks with a specific reduction in the attacks of Ostrinia nubilalis (Tomasino et al. 1995; Lampel et al. 1994). The nitrogen-fixing bacterium Bradyrhizobium has also been transformed with the endotoxin gene from B. thuringiensis and was later inoculated into the roots of Cajanus cajan, where it not only upgraded the nitrogen fixation process but also provided protection to the plant systems against Rivelia angulata larvae (Nambiar et al. 1990). Similarly, the endophytic Bacillus subtilis WH2 which was genetically engineered to express anti-pest Pinellia ternata agglutinin by insertion of PTA gene into plasmid pP43NMK displayed insecticidal activity against white-backed planthopper Sogatella furcifera when inoculated in the rice rhizosphere (Qi et al. 2013). Thus, the genetically altered microbes represent an important candidature to be considered for engineering the plant rhizosphere owing to their enhanced performance as compared to their wild relatives. They can be genetically altered for improved colonization of the plant roots as well as for other plant-growth-aiding traits. Moreover, the employment of GM microorganisms could result in the enhancement of many members of the endogenous population by the transmission of genetic information via horizontal gene transfer.

8 Engineering of Interactions

The involvement of root-associated microbiome makes the holobiont a single and complete unit. The association of microorganisms to the plant tissues is a complex process which happens in the soil by way of chemical interactions that takes place with the active involvement of both the partners (Farrar et al. 2014). Taking into account the complication of these communications, a fine understanding of these chemical networks amid all members is indispensable to untangle how microbial inhabitants harmonize their activities and intermingle with the plant roots. Therefore, the portrayal of these interactions is an essential step for understanding the connotations as well as occupations of microbial populations (Kumar et al. 2016). However, many molecules along with the mechanisms involved that synchronize the foundation of precise rhizospheric interactions have already been unveiled and explored in literature. The understanding of such interactions is staggering as the signaling molecules owe the aptitude of upsurging plant functions of interest and provide a unique methodology to access control over the microbial inhabitants if properly understood and harnessed (Guttman et al. 2014; Quiza et al. 2015). The plant’s sole purpose of shaping the rhizospheric microbiome is to fascinate favored microbial associates and to deter the pathogens along with the undesirable contestants. These activities happen as a result of different signaling molecules secreted by the plant systems in the form of root exudates. In addition to plant systems, numerous microbes also discharge different signaling compounds in the rhizosphere. These signaling molecules play important roles not only in the life cycles of these organisms but also in their evolution as well as complexity of life (Cornforth et al. 2014; Parks et al. 2014; West et al. 2015). Furthermore, the successful colonization of plant roots by the competent rhizobacteria is possible only due to this bidirectional signaling. Consequently, the collective interests of both the donor and the recipient in the quest to disseminate the unswerving information prompt an operative signaling arrangement to procure numerous health benefits (Kumar et al. 2016). Thus, this bidirectional signaling which accounts for ecological interaction between plant and microbial systems also provides a platform for rhizospheric engineering by manipulating the interaction taking place in the rhizospheric zone. The plant-allied microbial partners yield and exploit diffusible quorum-sensing molecules (e.g., N-acyl-homoserine lactones, AHLs) for signaling each other and thus to order their gene expression (Berendsen et al. 2012). The AHLs of bacterial origin have also been reported to affect root development in the plant systems (Ortíz-Castro et al. 2008) along with the elicitation of the phenomenon acknowledged as induced systemic resistance (ISR) which permits the plant systems to withstand the pathogenic attacks that possibly will be disastrous without the occurrence of such factors of bacterial origin. The plant systems have also developed the ability to utilize the microbial communication systems for manipulating the gene expression in their accompanying microbial populations, such as various plant-allied bacterial members, which owe some LuxR-like proteinaceous molecules which are motivated from different signals originating from plant systems (Ferluga and Venturi 2009). A small proportion of bacterial communities is diverse owing to their ability to quench the signaling process by deteriorating numerous compounds of plant as well as microbial origin in the rhizosphere, thereby leading to the disruption of quorum-sensing process (Tarkka et al. 2009), and other members have also been reported for degrading the compounds, like ethylene, that negatively affect the plant health (Bais et al. 2008). Such members of microbiological community provide an ostensible opportunity for engineering the rhizospheric interactions in the hunt to shape a perfect rhizosphere supporting healthy plant systems. For instance, the members of genus Pectobacterium are highly plant pathogenic, and their pathogenicity depends on the fabrication of enzymes that degrade the plant cell wall and are popularly known as macerating enzymes (Liu et al. 2008). The microbe produces these enzymes at great cell density via quorum-sensing mechanisms. The bacterial cell synthesizes a signal molecule, and the concentration of that molecule upturns with the cell density. The quorum-sensing signal is professed after attaining a threshold cell concentration which further prompts the production of the macerating enzymes and in turn the humiliation of the plant tissues. The biocontrol of this plant pathogen is usually based on the alteration of the interactions, i.e., by inhibiting the quorum-sensing mechanism (Faure and Dessaux 2007). Several soil microbes having the potential to degrade the QS signal, for instance, Bacillus cereus, Bacillus thuringiensis, and Rhodococcus erythropolis, have been reported to condense the maceration signs under laboratory conditions (Uroz et al. 2003). It has been found that the bacterium R. erythropolis does not hinder the progression of the pathogen, but proficiently averts the accretion of the QS signal and henceforth the deliquescence of the plant tissues (Cirou et al. 2007, 2011, 2012).

Another example of successful engineering of interactions is the successful transformation of soil bacterium Burkholderia cepacia with a plasmid encoding toluene degradation (Fig. 21.4). The reinoculation of yellow lupine plants with the transformed bacterial strain sustained the plant growth that too without the appearance of any symptoms of phytotoxicity even at the elevated levels (1000 mg/l) of toluene, contrary to the control plants that displayed symptoms of phytotoxicity at the toluene intensities above 100 mg/l. Some PGPRs are known to aid the plant growth by forming a biofilm around the plant root cells. This biofilm formation happens as a result of microbial response toward the plant root exudates. The addition of root exudates responsible for prompting biofilm formation along with the inoculation of microbial culture is known to enhance plant-microbe interactions and therefore also encourage the biofilm formation (Zhang et al. 2015). Furthermore, the combinatorial addition of several microbial strains has also been reported for their improved efficacy as well as improved plant growth assessment parameters. In addition to it, the combinatorial addition has also been proven for supporting greater microbial diversity in plant rhizosphere (Gupta et al. 2019) which probably has happened due to reshaping of the biotic interactions happening in the rhizospheric hotspot. The plant-microbe interactions especially the symbiotic association between plant systems and the rhizospheric microbiota are also engineered for in situ bioremediation of an extensive array of organic pollutants like parathion, trichloroethylene, toluene, and PCBs using genetically altered rhizobacteria or endophytic bacteria (Wu et al. 2006). In a study, the Arabidopsis thaliana phytochelatin synthase gene (PCSAT) was expressed in a micro-symbiont, Mesorhizobium huakuii subsp. rengei, which lives in the nodules of Astragalus sinicus. The symbiont expressing the PC synthase possessed the ability to upsurge the cadmium accretion by 1.5-fold in the nodules (Sriprang et al. 2003). Similarly, an antifungal bacterium Pseudomonas putida 06909 engineered for plant-microbe symbiotic relationship also exhibited enhanced cadmium-binding properties. The genetic engineering-mediated expression of a metal-binding peptide (EC20) not only upgraded cadmium binding but also alleviated the cellular toxicity of cadmium (Wu et al. 2006). Thus it can be concluded that the interval of interactions between plants and microbes happens to be very critical as it is the process of interaction only which kicks the plant systems as well as microbial systems toward a state of interdependence where both the members can harness the beneficial attributes of each other. Therefore, the engineering of interactions can reshape the plant-microbe interactions for enhanced plant productivity as well as superior plant health.

Fig. 21.4
figure 4

Inoculation of a stressed plant with the genetically engineered microbial partners of holobiont for improved plant-microbe interactions

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9 Conclusion and Future Prospects

The rhizosphere is one among the most complex microbial habitats. Plants have evolved into a microbial world where they extended their fine network of roots into the soil already inhabited by a diverse community of microbes. The rapid colonization of the plant roots by the microbes followed by the plant-mediated release of photosynthates via its roots has put both the life forms in a state of interdependence where both these survive as a single unit called as holobiont. Plants are largely known for engineering their rhizospheric microbiomes which differ by the cultivar, age, and variety of plants. However, a large proportion of the rhizospheric microbiome is still represented by the Proteobacteria and Actinobacteria , and the microbial population varies at the genus and species levels. Plants secrete root exudates to harbor a great diversity of microorganisms. The rhizospheric microbiota responds to these exudates by the phenomenon of chemotaxis and actively colonizes the plant roots. But the prevalence of bad and ugly microbiome proves to be problematic at different times and puts the plant systems in a state of stress. However, the valuable possessions of the beneficial rhizospheric microbiota, for instance, their ability to own plant growth promotion traits and xenobiotic degradation, improve soil structure, and sustain the plant health and productivity, have attracted the attention of researchers to create a “rhizosphere bias”. Where only the microbiota beneficial to the plant systems can thrive and aid the plant growth. The rhizosphere can be engineered for the beneficial microbiota by several soil amendments and by direct inoculation of the selected PGPR isolates. However, only a little proportion of rhizospheric microbiome is culturable; therefore, the development of novel processes which can study the valuable microbial possessions in its natural habitat should be a point of major concern. The amendments should be decided after unveiling the requirements of unculturable microbiota. The artificial addition of root exudates is also known to be the important soil amendment, but on the flip side, all the root exudates secreted by the plants at different times haven’t been unveiled yet. The interactive effect of all the root exudates should be worked out along with their precise effect on both culturable and non-culturable rhizospheric microbiota. The plant systems are genetically engineered for the production of the desired root exudates, ion efflux, and other metabolites. The advancement in techniques for cheaper production of such metabolites is the need of the hour. Moreover, the artificial production of root exudates at an industrial scale could save a lot of money in the agricultural sector by boosting the overall production. The identification of different biotic and abiotic parts of rhizosphere can also unveil some hidden rhizospheric interactions which can further prove to be an important asset for the agricultural sector. The genetic engineering experiments in the plants have proven to be of only a little success; therefore, the development of robust methodologies which can reveal some novel pathways for metabolic engineering of the plant systems should be addressed. Ultimately, the rhizosphere is a highly dynamic habitat where predictions work the least; thus, this dynamic microbial habitat is a subject to dynamic research.