Keywords

14.1 Introduction

Soil is considered to be the reservoir for various microbes and organisms like ants, moles, and nematode (Dhanjal et al. 2017). Recent advances in sequencing techniques and elevation in number of microbial libraries have expanded the aura of the tree of life, as it is dominated by microbes (Anand et al. 2019). The horizontal gene transfer and mutation events have evolved wide array of variation among the microbial community. This significantly increases the diversity within species and endows them their functional characteristic (Bengtsson-Palme et al. 2017a). Here, soil plays the major role in recycling the nutrients (phosphorus and nitrogen) and imparting protection against abiotic and biotic stress (Dhanjal et al. 2018). Although the agricultural activities have increased the yield of crop, simultaneously it has also deteriorated the biological and physical properties of the soil (Gomiero 2017). Even usage of fertilizer aids in maintaining the soil fertility, but on tillage microbial communities get disrupted (Dong et al. 2012). The degradation of soil due to anthropogenic activities has emerged as a global concern and sustainable agriculture has become the need of the time for sustaining the life of humans on this earth. Thus, to sustain the life, plant–microbiome plays significant role in improving soil quality and plant growth, and providing resistance from stress (Rashid et al. 2016; Kumar et al. 2019a).

Plant–microbiome is essential as they contain distinct properties like production of secondary metabolites as well as phytohormone and nitrogen fixation and many more. Therefore, it represents the microbial community which is directly or indirectly associated with plants. Hence, they have been generally characterized into epiphytic, endophytic, and rhizosphere microbiome (Igiehon and Babalola 2018a; Kour et al. 2019; Kumar et al. 2019b; Rana et al. 2019a; Rana et al. 2019b). The soil contains both types of microbes, i.e., pathogenic and nonpathogenic in nature (Finkel et al. 2017). Nonpathogenic involves the symbiotic and neutral microbes which plays variety of roles in diverse fields like biodegradation, biofuel production, biocontrol, biotransformation, seed production, phytoremediation, and many more (Dwibedi and Saxena 2019). These potentials of microbes prompt us to understand the hyper-diversity of these unexplored plant microbial communities, not only for sustaining the ecosystem but also to preserve these biodiverse microbial communities beneficial for mankind (Braga et al. 2016). Hence, untapping and deep understanding of these plant microbes as whole have become important to explore the positive interactions for sustainable agriculture, especially during microbiome-dependent cropping approach (Busby et al. 2017). In this chapter, we will discuss the challenges and efforts put forward to advance our knowledge about different properties of microbes and how these properties affect plants. Further, we will also discuss about the soil microbiome improving the crop production.

14.2 Composition and Function of Plant Microbiome

Plants are surrounded by a variety of microbes and vary according to their location like anthosphere, carposphere, phyllosphere, rhizosphere, and spermosphere (Shade et al. 2017) (Fig. 14.1). Here, we categorized the bacteria into three broad categories as follows.

Fig. 14.1
figure 1

Compartmentalization of plant microbiome

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14.3 Plant Microflora Below the Ground

Root microflora generally get horizontally transferred as they are predominantly present in soil (Lareen et al. 2016). Most dominating microbes belong to the family of Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria, and Verrucomicrobia (Mendes et al. 2013; Kour et al. 2019; Suman et al. 2016; Verma et al. 2017b). There is a possibility of vertical transmission through seeds. Seeds also serve as reservoir for microbes, which allows them to multiply in the roots during plant development (Shahzad et al. 2018). Root system of plant provides distinctive niche to soil microbes residing in the rhizosphere (roots and certain portion above the ground) (Raaijmakers et al. 2009). Recently, Donn with his colleagues reported about the changes in bacterial community surrounding the roots of wheat and found 10-fold increase in population of actinobacteria, copiotrophs, oligotrophs, and pseudomonads at rhizosphere. Moreover, they also reported that over time, variation takes place in rhizoplane and rhizosphere community but there is no variation in soil microbial population (Donn et al. 2015). Similar results were also seen for Brachypodium distachyon rhizosphere which reported about the predominance of species of Burkholderiales, Sphingobacteriales, and Xanthomonadales family (Kawasaki et al. 2016). There have been reports which claimed that root exudates like amino acids, fatty acids, organic acids, plant growth regulators, phenolics, putrescine, sterols, sugars, and vitamins also affect microbes present in the rhizosphere, proclaimed as rhizosphere effect (Hunter et al. 2014). For example, secondary metabolite benzoxazinoids (BXs) synthesized by the roots of maize amends the composition of root-associated microbes, out of which members of Actinobacteria and Proteobacteria family were highly affected (Neal et al. 2012; Kudjordjie et al. 2019). Moreover, other researchers are investigating the mechanisms responsible for the assembly of microbial community and effects of substrate and root exudation on microbial community. Hence, this confirms that composition of rhizosphere microbes gets influenced by plants species and root exudates (Jacoby et al. 2017; Yadav et al. 2015a; Yadav et al. 2015b).

Various bacterial endophytes have colonized the roots of plants internally (Santoyo et al. 2016). These bacterial endophytes enter the root tissues via passive processes or root abrasion and active mechanisms (Santos et al. 2018). The transmission and colonization of these bacterial endophytes inside the plant depend on various factors like ability of endophytes to colonize plant and distribution of plant resources (Kandel et al. 2017). Various microbes have gained access to root tissues, for instance, Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, Planctomycetes, Proteobacteria, and Verrucomicrobia are the bacterial taxa which have gained access to grapevine roots (Morgan et al. 2017; Verma et al. 2016; Yadav et al. 2016). On the other hand, members of Bradyrhizobiaceae, Comamonadaceae, Rhizobiaceae, and Streptomycetaceae family are the one predominantly found in rice roots (Edwards et al. 2015).

14.4 Plant Microflora Above the Ground

Floral parts, leaves, and vegetative parts present above the ground provides distinctive environment for epiphyte and endophyte microbes (Frank et al. 2017). The endophytes predominantly translocate themselves through xylem to different parts of plants, which can either be fruit, leaves, or stem (Hardoim et al. 2015). With respect to location on the plant, aboveground microbes distribute themselves with other members of endophytic community (Nair and Padmavathy 2014). It has been observed that phyllosphere microbes obtained from the soil get influenced by external stimuli and later shows the profound effect (Carvalho and Castillo 2018). Subsequently, various microbes have been found in the phyllosphere and endosphere up to species level (Schlaeppi and Bulgarelli 2015). For example, on analyzing the carposphere and phyllosphere microbes of grapevine uncovered the presence of Acinetobacter, Bacillus, Citrobacter, Curtobacterium, Enterobacter, Erwinia, Frigoribacterium, Methylobacterium, Pantoea, and Pseudomonas species (Kecskeméti et al. 2016; Verma et al. 2017a; Verma et al. 2017b; Yadav et al. 2019; Yadav et al. 2018a; Yadav et al. 2018b; Yadav et al. 2018c). On the other hand, endophyte analysis of grape berries uncovered that Bacillus, Burkholderia, Dyella, Mesorhizobium, Propionibacterium, Pseudomonas, and Ralstonia species are the dominant (Campisano et al. 2014).

There is a study conducted on 300 different varieties of maize to analyze the leaf microbiome that revealed the predominance of methylobacteria and sphingomonads taxa (Wagner et al. 2019), whereas in apple flowers there is predominance of Enterobacteriaceae and Pseudomonas species (Steven et al. 2018). Various other studies conducted on almond, apple, grapefruit, pumpkin flower, and pumpkin also revealed the abundance of Pseudomonas species (Aleklett et al. 2014). Lately, seed-associated microbes have highlighted the abundance of Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria (Qiao et al. 2017). Usually, microbes found on aboveground have originated from air, seed, and soil and adapted themselves to sustain their life on or inside the tissue of plant, where various factors like environmental condition, soil, and management influence microbial composition (Raaijmakers et al. 2009). Compartment-specific assembly with the host illustrates the strong relationship among the aboveground microbes and plant on the basis of functionality, but still there is a need to understand this association deeply (Garcia and Kao-Kniffin 2018). Aboveground microbes and endophytes are recognized for their ability to alleviate stress tolerance, increase disease resistance, and promote plant growth (Kumar and Verma 2018).

14.5 Satellite and Core Microflora

Core microflora or core plant–microbiome (CPM) refers to those microbes that closely linked with particular type of plant and are independent of soil and environmental conditions (Lakshmanan et al. 2014). Bradyrhizobium, Microvirga, and Sphingobium were found to be the core microbiome of Solanum tuberosum (potato) (Pfeiffer et al. 2016). Another study revealed that Hyphomicrobiaceae, Micrococcaceae, and Pseudomonadaceae sps. are the core microbes found in grapevine (Zarraonaindia et al. 2015). The CPM contains those microbial taxa that are essential for plant and have established themselves in plant during the course of evolution (Jacoby et al. 2017). The enhancement of microbial taxa through evolutionary selection process contains the genes responsible for survival and holobiont of the plant (Rosenberg and Zilber-Rosenberg 2018).

Distinctively, the microbial taxa found in less affluence and fewer locations are referred to as satellite taxa. They are described based on their habitat, geography of habitat, and their regional population. These taxa are perceived as the regulators of important mechanisms in an ecosystem (Banerjee et al. 2018). Few researchers found that microbial taxa having the scarce population play a crucial role in obstructing the entrance of undesirable microbial taxa in soil. Parallelly, the scarce bacterial population produces different antifungal chemicals which guard the plants against soil-induced infectious organisms (Ciancio et al. 2016). Various researches demonstrate that forfeiture of scarce microbial population compromises with plants’ efficiency (Garcia and Kao-Kniffin 2018). Researchers also found that microbial taxa regulate vital mechanisms that can be unequal to their population number (Pineda et al. 2017). Numerous ecological factors should be taken into account to comprehend mechanisms of plant–microbiome taken in response to certain environmental tensions (Braga et al. 2016).

14.6 Factors Affecting Plant Microbiota

The microbial organization in plant’s tissues is linked with various organic and inorganic constituents. These constituents can be type, pH, salinity, structure, moisture, organic matter, and exudates of soil, respectively (Jacoby et al. 2017; Yadav et al. 2015c; Yadav and Yadav 2018). These constituents above are important for parts of the plants which are present beneath the ground level. Other constituents such as infectious agents, environmental conditions, and human activities affect the microbial community of above- and belowground plant parts (Mendes et al. 2013). Using high-throughput approaches like a shotgun and 16S rRNA sequencing, Bulgarelli with his colleagues examined the root microbial community of various barley species and concluded that root exudates and innate immune system determine the organization of root microbiota (Bulgarelli et al. 2015). Various host-influence factors such as growth stage, age, and wellness of plants affect organization of plant microbiota by the formulation of root exudates and plant signaling processes (like induced and acquired systemic resistance, respectively) (Ortíz-Castro et al. 2009).

14.7 Function and Role of Plant Microbiome

Plant–microbiome consists of all neutral, beneficial as well as pathogenic microbes. There are few plant growth-promoting (PGP) bacteria which promote the growth of plant by synthesizing different phytohormones such as gibberellin, cytokinin, and auxin (Egamberdieva et al. 2017; Yadav 2017a, b; Yadav 2019; Yadav et al. 2017a). However, few PGPB produce ACC deaminase (1-aminocyclopropane-1-carboxylate deaminase) which regulate the level of ethylene (stress hormone) in plant (Glick 2014). Literature survey revealed that Arthrobacter spp., Bacillus spp., and Pseudomonas spp. are the ACC deaminase producer, which enables them to enhance the growth of plant (Souza et al. 2015). On analyzing the root microflora of soybean and wheat, it showed the dominance of Pantoea spp., Paraburkholderia spp., and Pseudomonas spp. These species promote the plant growth because of the properties like phytohormones (ACC deaminase, indole acetic acid), nitrogen fixation, and phosphate solubilization mechanism to enhance the stress tolerance and improve nutrient uptake (Rascovan et al. 2016). Schematic representation of the function performed by microbiome is illustrated in Fig. 14.2.

Fig. 14.2
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Schematic overview of function and impact of plant–microbiome on the host plant

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On the other hand, there are few bacteria which show disease symptoms because of the production of phytohormones and phytotoxic compounds (Olanrewaju et al. 2017). For instance, Pseudomonas syringae is a plant pathogen which affects various plants like green bean, olive, tobacco, and tomato (Hirano and Upper 2000). Erwinia amylovora, another pathogenic bacterium, causes fire blight disease in ornamental plants. Ralstonia solanacearum, Xylella fastidiosa, and Xanthomonas sps. are the bacterial species that are associated with various diseases of banana and potato (Vrancken et al. 2013). There are certain factors which determines the severity as well as outcome of disease like biotic factors (like plant microflora), favorable environmental factor, host susceptibility, and population size of pathogens (Lareen et al. 2016). Both aboveground plant microflora and belowground microflora have been found to increase the resistance in host via commensal interactions of pathogen or due to modification in plant defense system (Igiehon and Babalola 2018b).

The plant microbiota uses diverse biocontrol mechanism like antibiotic production, siderophore production, lytic enzyme production, and pathogen-inhibiting volatile compound production to prevent the disease and pathogenic invasion (Compant et al. 2005). Few plants modulate the hormone level and induce resistance in plant to protect them from plant pathogens. Therefore, agricultural lands containing disease-suppressing microbes build pressure on pathogens and make it the disease-suppressive soil (Gómez Expósito et al. 2017). Particularly, Bacillus, Burkholderia, Enterobacter, Paenibacillus, Pantoea, Paraburkholderia, Pseudomonas, and Streptomyces have been found to play the main role in pathogen suppression (Yadav et al. 2017b). Carrión and his colleagues revealed that Paraburkholderia graminis PHS1 produces cysteine desulfurase and dimethyl sulfoxide reductase (sulfurous volatile compounds), which provide suppressive ability against fungal root pathogens (Carrión et al. 2018). On the other hand, Durán and his colleagues highlighted the role of endospheric bacteria belonging to Enterobacter and Serratia family, which have the biocontrol activity against Gaeumannomyces graminis (Durán et al. 2017).

14.8 Advancements in Plant–Microbiome Research (PMR)

Prediction about the advances in plant–microbiome research is quite difficult (Thijs et al. 2016). But following are the three points which help us in shaping the future of both applied and basic studies of soil microbiome.

14.8.1 Upgradation of Culturing Techniques

The advent of molecular techniques has rapidly increased the genomic data of uncultured microbial taxa persisting in the soil, for which closely related strains are currently unknown (Warinner et al. 2017). There is an exponential increase in data because of culture-independent approach like single-cell genomics or by the assembling of individual genome obtained via metagenome analysis (Blainey 2013). Although we have the genomic information of all the microbes present in the soil, still we lack to understanding about their functionality. Therefore, categorizing them in ecological taxa considering their genomic data is risky (Peršoh 2015). Additionally, the slow-growing microbe is another challenge. Therefore, approaches which use genomic data to intercept the information about ideal cultivation and isolation of uncultured microbes will unquestionably be helpful for the field to me in forward direction (Streit and Schmitz 2004).

14.8.2 Role of Viruses in Soil Microbiome

Approximately, 107–109 virus particles are found in one gram of soil, and this number is less than the number of viruses found in the aquatic ecosystem (Jacquet et al. 2010). Apparently, these viruses found in soil are highly diverse and remained unexplored (Williamson et al. 2017). Marine studies have revealed that phages play chief role in nutrient dynamics, as they maintain the nutrient dynamics by killing the 20–40% microbial population present in the water column (Sime-Ngando 2014). Various researches have demonstrated soil to be the reservoir for phages which specifically targets bacteria like Rhizobium spp. and Xanthomonas spp., still the effect of these viruses on activity and composition of soil remains comprehended (Buttimer et al. 2017). According to statistics, > 90% of viruses found in soil mainly get absorbed by clay as well as other soil surfaces, which leaves very low number of viruses in soil. Additionally, it is also uncertain that these viruses are capable enough to infect the plant–microbiome (Andika et al. 2016). Due to advancement in viral metagenomic field and development of new techniques, there is an enumeration in viral population, and it has prompted us to explore new viral community as well as study the effect of these viruses on microbial processes and populations (Jacquet et al. 2010). Basically, it clear to develop a holistic understanding of how these microbes (directly or indirectly) interact with each other instead of studying the individual microbial group (Tshikantwa et al. 2018).

14.8.3 Importance of Horizontal Gene Transfer

There are three main mechanisms of horizontal gene transfer, i.e., conjugation, transduction, and transformation, by which microbes their gene from one generation to another (Von Wintersdorff et al. 2016). Genes contains the sequence of various different traits like arsenic detoxification, antibiotic resistance, and xenobiotic degradation. Therefore, mobile genes may cause evolution of new phenotypic characteristic and may generate close relation with dissimilar genomes (Janssen et al. 2005). However, horizontal gene transfer can impose dilemma during the attempt of linking particular gene to targeted phylogenetic lineages. This definite control of horizontal gene transfer, its frequency in soil microbial communities, and their effect on the soil population are the topics which nurtures this expedition and motivate us to work in this direction (Andrews et al. 2018).

14.9 Use of Plant–Microbiome as a Biocontrol Agent

Worldwide, plant diseases have been held responsible for farmers’ losses. FAO stated that 25% of crop loss occurs due to plant diseases and pests. Therefore, there is need for control plant disease (Savary et al. 2012). To achieve this, specific plants which are resistant to various diseases are bred along with different cultivation techniques like use of pathogen-free seeds, crop rotation, or by using biological and chemical agents (Cheng and Cheng 2015). All these plant protection methods influence the microbiome of plant; hence, information gathered from plant protection strategies should be taken into consideration during cultivation (Berg et al. 2014). In various cases, the onset of disease takes place due to imbalance of plant–microbiome and obstructs the desired objective of whole microbiome. Hence, analyzing metabolic pathway and plant–microbiome of the host plant unlock new opportunities to advance biocontrol approaches (Thijs et al. 2016).

Overall, better understanding unfolds the information about the diverse microbes which aid in plant growth and produce antagonistic chemicals against phytopathogens (Bargaz et al. 2018). Mosses are known to have unique microbial diversity and harbor microbes with exceptional antagonist potential because of their ecology (Bragina et al. 2012). Moreover, medicinal plants are also to be known to nurture diverse microbes as their secondary metabolites determine the composition of microbiome (Berg et al. 2015). Because of large diversity among microbes, it is believed that endophytes, especially seed endophytes, can emerge as the unique biocontrol agent (Ryan et al. 2008). Till now, largely bacteria as well as fungi have been used for biocontrol purposes (Whipps 2001). Recently, Archaea have been exploited to become the member of plant–microbiome but its biocontrol potential is still under evaluation (Müller et al. 2015).

As stated above, microbes linked with plant develops a network which gets influence during pathogen invasion. Therefore, these networks will enable us to develop new model and enhance disease management of the plant–soil microbes (Hassani et al. 2018). Even researchers have developed a framework to decipher these microbiome networks and showed the benefit of these frameworks to test their hypothesis for targeted microbes responsible for particular plant disease. They proposed four types of network analysis: (a) first type involves the general analysis of network to discover the aspiring taxa to maintain the existing microbial community; (b) second type involves the analysis majorly focusing on host as well as plant response; (c) third type involves the identification of pathogenic taxa which are directly or indirectly associated with prior known taxa of pathogens; and (d) last type involves the identification of those taxa which are associated with disease (Poudel et al. 2016).

Now, most of the biocontrol agents are screened through in vitro antagonisms effective against particular pathogen. As this screening allows the identification of potent biocontrol agent, still intense debate is going on about this screening approach (Larran et al. 2016). The chief reason is that biocontrol and plant growth-promoting (PGPR) microbes during in vivo evaluation show no antagonisms, whereas in the case of in vitro studies it shows modest result (Beneduzi et al. 2012). Different high-throughput techniques have been developed for plant assays but were found to be ineffective as includes artificial characters (Rasheed et al. 2017). For instance, rapeseed treated with Paenibacillus showed plant growth in natural soil, whereas no negative effect was observed in sterile soil under gnotobiotic conditions. Therefore, there is need for testing the potential of biocontrol and plant growth-promoting strains in soil as well as evaluation of their effect on soil type and plant species also be done (Bashan et al. 2014). Another research study showed the presence of similar genera of Pseudomonas in lettuce rhizosphere in three different soil samples from the field. This confirms that soil types do not play any role in biocontrol activity and rhizo-competence (Schreiter et al. 2018).

Additionally, targeted enhanced diversity is also being exploited as biomarker for screening purpose by researchers. These applicability and development in biological control is attaining attention globally (Atanasov et al. 2015), whereas previously only one microbe was used in biocontrol strategies, which explains about inconsistency. But recent advancements have enabled us to develop microbiome-dependent biocontrol strategy (Ab Rahman et al. 2018). In 1999, Emmert and Handelsman stated Gram-positive bacteria to be potential candidate in biocontrol practices. On assessing the registered products for biocontrol and along with those that are in pipeline, almost all the products are bacillus based (Emmert and Handelsman 1999). There is technical reason for using Bacillus sps. as the base product in contrast to other Gram-negative bacteria, as form spores under unfavorable condition for survival. This spore formation increases their shelf-life (Berg et al. 2017). On examining the plant-associated microbes which harbor large number of bacterial species, it make us realize that we are seeing the very small portion of taxonomic diversity for biocontrol purpose (Chowdhury et al. 2017).

Moreover, the researchers have reported that 2% mean population is occupied by Bacillus species from the total bacterial community in the soil (Li et al. 2017). As an exception, another researcher published a paper in which they stated that 37% of Bacillus and Paenibacillus species are found in arid soil (Köberl et al. 2013). Still, the debate is going on comprehending the role of Bacillus on the plant and against its pathogen, or does it trigger the plant growth hormones or induce resistance as they are involved in plant–microbe interaction. It is already known that Bacillus and Paenibacillus strains synthesize various antibiotics and secondary metabolites (Mhlongo et al. 2018). As per studies, strains and spores of both Bacillus and Paenibacillus are predominantly found in the environment and this might be reason for reducing number of plant-associated microbial community. Hence, more emphasis is given on increasing the microbial diversity within products during biocontrol activity. This prompts to develop new strategies to explore the antagonistic potential of microbes associated with plants (Yadav et al. 2017c).

Nowadays, antibiotic resistance is becoming the global concern and making our treatment ineffective as a result people is suffering from disability, prolonged illness, and at last death (Laxminarayan et al. 2013). Regrettably, strategies used in agriculture like use of antibiotics in livestock are increasing the resistance level. These livestock aid in transferring the resistance in plant production system, which causes the enrichment of resistant bacteria in the rhizosphere (Founou et al. 2016), even though many microbes have developed resistance and are highly prevalent in the environment. Therefore, risk management studies to suppress the emergence of resistant microbes have become our first priority (Larsson et al. 2018). Though the different biocontrol products have shown lower persistence on soil and plant, usage of spore-forming bacteria will change the whole scenario (Paul et al. 2019). Additionally, soil microbes are found to be bacterial antagonists in nature. In particular, Paenibacillus have been found to contain not only the antibiotic synthesis gene but also contain antibiotic gene, justifying about their antagonistic ability within the microbiome (Cycoń et al. 2019). Therefore, further investigation is required to understand the mobilization of resistant gene through different ways of horizontal gene transfer (Bengtsson-Palme et al. 2017b).

14.10 Studies Related to Plant Microbiomes

Even though plant–microbiome is a broad topic, microbial group associated with plant is an active research area. The major reason is the exponential increase in publications in recent year on this topic as well as research targeting the niche of specific plant and how interaction takes place among particular microbial community (Naylor and Coleman-Derr 2018). Additionally, it has been observed that microbial assembly varies according to environmental conditions and plant species. This creates curiosity to learn more about how microbes are acquired by plant, either the microbes are subsequently passed to next generation or recruited from the environment (Yu and Hochholdinger 2018).

In spite of the role of the microbes in promoting the plant growth and nutrient cycle, we still require to gain more insight about microbial interaction which makes up the plant microbiome. This will allow us to comprehend the functioning of plant microbiome to changing agricultural practices and environmental conditions (Garcia and Kao-Kniffin 2018).

Various studies are being conducted to extend the link the shift in environmental condition with microbiome response (Purahong et al. 2018). For instance, the researcher conducted on the grape vineyard using culture-independent method revealed the presence of dynamic microbial community on different stages of plant lifecycle, enlightening the effect of agrochemicals on the plant (Morgan et al. 2017). Numerous studies have associated microbiome with physiology of plant, as microbes found in plant–microbiome in desert aid in providing the resistance to plant to survive in unfavorable conditions (Vurukonda et al. 2016). In 2012, Marasco and his colleague proposed that plant microbiomes are essential to develop resistance against drought stresses (Marasco et al. 2012). Another effective interaction was reported by another research group, where the described role of microbiome determines the composition of plant root exudates. These examples highlight the role of soil microbiome not only in plants but also in their evolutionary mechanism, regulated by host–microbe interaction (Lareen et al. 2016).

14.11 Conclusion and Future Prospects

The microbial communities possessing beneficial traits act as a powerful tool to elevate the sustainable agriculture by reducing the usage of fertilizes and combatting plant diseases to enhance the crop yield. The potential of microbiome is to elicit the plant growth, generate stress resistance, and improve plant health. Various microbial inoculants have been developed to achieve field success by either designing smart microbial consortia or engineering the microbiota with beneficial characteristics. In order to upsurge the crop yield and support the enhanced technologies, new plant breeding practices and suitable formulations are required. To achieve these goals, there is need to gather insight about the plant–microbiome interaction, microbial community of soil, and their stability during environmental changes. As single microbes are the key regulators within microbial community, therefore comprehensive investigation on these microbes along with microbial community of soil can assist us in expanding the horizon of this field. Moreover, the knowledge gained will enable us to completely comprehend the impact of these microbes on disease resistance, nutrient cycles, and yield of the crop. Furthermore, it will prompt us to explore novel strategies for microbiome engineering to move toward the sustainable agriculture.