Keywords

4.1 Introduction

The substantial pressure on land for agricultural farming due to increased urbanization, rapid changes in the agroclimatic conditions, and rising population led to the emergence of alarming food security globally. In addition, yield losses in agricultural crops caused by plant pathogens/pests such as viruses, bacteria, fungi, oomycetes, nematodes, insects, and mollusks pose a significant risk. Estimates reveal that the crop loss due to plant pathogens in Western countries is approximately 25% while that in developing countries is as high as 50% (Dubey et al. 2015; reviewed by Aboutorabi 2018). Annually it is estimated that plant diseases, either directly or indirectly, account for losses worth 40 billion dollar worldwide (Roberts et al. 2006). These plant pathogens are major biotic constraints of food production and have led to severe disasters in the past significantly impacting human history, for instance, the Irish potato famine resultant of Phytophthora infestans (1840s), the Great Bengal rice famine resultant of Cochliobolus miyabeanus (1943), the Bengal brown leaf spot disease of rice due to Helminthosporium oryzae (1940s), and the USA epidemic of southern corn leaf blight, caused by Bipolaris maydis (1970–1971), among others. While effective management stratagems such as the development of resistant varieties and genetically engineered cultivars and usage of agrochemicals were employed to tackle these diseases, they do have loopholes. Developing a disease-resistant variety through conventional breeding is time-consuming, and the resistant trait is effective against only a few diseases. Likewise, crop plants engineered for resistance via genetic engineering face environmental risks and public concerns and have not been approved by national governmental policies. So far, the effective means of disease control had been achieved by the use of agrochemicals. However, they are cost-intensive, hazardous, and environmentally unfriendly as they severely affect soil fertility, microfauna, and human health (Aktar et al. 2009; Prashar and Shah 2016). The extensive usage of chemical pesticides results in their accumulation in plant tissues, inhibition of beneficial microbes, environmental contamination, and the emergence of disease-resistant pathovars. The reckless usage of chemicals is detrimental to organisms across all taxonomical hierarchies (Kawahara et al. 2005; Rastogi et al. 2010; Mnif et al. 2011; Schwartz et al. 2015). Some of the biotic catastrophes encompass algal bloom (Heisler et al. 2008), coral bleaching (Danovaro et al. 2008), mass death of bees (Kasiotis et al. 2014), food chain contamination (Chen et al. 2007), avian reproductive loss (Jagannath et al. 2008), and mad cow disease (O’Brien 2000). In India, the rising trend of farmer suicide is partly linked to the depressive effects of the pesticides (Chitra et al. 2006). Organophosphates have been consistently linked to cancers and neurological disorders (Rastogi et al. 2010; Neupane et al. 2014). In this regard, much attention has to be paid toward alternative disease management strategies that are free from environmental risks and other related issues. The recruitment of biological control agents (BCA) as control measures against phytopathogens seems to be a quite promising approach.

Among the various phytopathogens, root pathogens significantly affect the root system and interfere with nutrient utilization and water uptake of plants, thus causing severe yield losses. Generally, root systems secrete specific exudates to the soil which improve plant nutrient availability and encourage the interaction with the rhizospheric beneficial microbes (Broeckling et al. 2008; Carvalhais et al. 2011; Trivedi et al. 2017). The rhizospheric area is the nutrient-wealthy zone of the soil due to a variety of chemicals such as auxins, peptides, amino acids, and sugars, liberated by the roots (Carvalhais et al. 2011; Takahashi 2013). Several crops are vulnerable to root diseases caused by bacteria and fungi (Alstrom and Van Vurde 2001; Maheshwari 2012). A diverse range of microorganisms thrive in the rhizosphere. Bacteria compete for the rhizospheric niche due to its resistance to climatic and edaphic fluctuations, unlike phylloplane region (O’Callaghan et al. 2006). The bacteria residing in this habitat are known as rhizobacteria (Prashar et al. 2014; Alsohim et al. 2014; Ali et al. 2014).

Biological control is the technique which attempts to mitigate the plant disease by the use of a bacterium, virus, fungus, or a combination of them to the plant or the soil (D’aes et al. 2011; Maheshwari 2012; Guo et al. 2014). The biological control agents (BCA) inhibit the phytopathogen by various offense modalities (Pearson and Callaway 2003). The most important benefit of using BCAs is that they are specific for a pathogen and are likely to be inoffensive to nontarget species. Microbial antagonists which are used to suppress diseases in plants are termed as biocontrol agents (Maheshwari 2012). The plant diseases are generally suppressed by the antagonistic effect of bioagents which occupies the same rhizospheric zone and utilizes the same food as the pathogens (Berendsen et al. 2012; Prashar et al. 2014). In the last few decades, there have been many details of the wide range of applications of BCA for the plant root diseases management (Kloeppe et al. 1999; Kokalis-burelle 2002; Mavrodi et al. 2012). The data has been presented in Table 4.1. Eco-friendly and sustainable attributes of biocontrol have spurred intense research on the potential candidates.

Table 4.1 Biocontrol agents (BCA), their target phytopathogens, and the host plants
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For BCA to be marketable, apart from efficacy, two other key factors that must be fulfilled are safety and affordable cost. It is not easy to find such candidates, and biocontrol paradigms still lag behind in replacing the detrimental chemical-driven agro-market. Biological control can be achieved at several levels such as partial, substantial, and complete.

Crop plants have to deal with a gamut of pathogens, insects, and herbivores. Root diseases are major problems, which can sabotage the plant health. It is because the roots are vital for nutrition uptake and are in direct contact with an array of soil microorganisms. Soil-dwelling pathogens include Rhizoctonia, Verticillium, Phytophthora, Fusarium, Pythium, Sclerotinia, Rosellinia, etc. (Hussain and Khan 2020; Karima et al. 2012; Matny 2015; Mostert et al. 2017). How BCA might be used to control the root pathogens and to benefit farmers in developing countries is the focus of this article.

4.2 Merits and Demerits of Biological Control Agents (BCA)

BCA has two opposite facets like all remedies. While low-cost, mild, and eco-friendliness are its positive traits, its unpredictable efficacy is a major hurdle.

4.3 Mechanisms Adopted by Biological Control Agents

The BCA activity is mediated either directly by the antagonism of soilborne pathogens or indirectly by triggering plant defense responses (Pozo and Azcon-Aguilar 2007; Jamalizadeh et al. 2011). Direct antagonism results from physical contact with the pathogen or pathogen selectivity through the mechanisms expressed by the BCA. Elicitation of plant host defense system by BCA is considered as a direct form of antagonism. BCA employ several modalities to challenge the phytopathogens (Rahman et al. 2017). Such strategies include antibiosis through the production of antimicrobial compounds, competition for available nutrients and niches, disruption of pathogen signaling, and the elicitation of plant defenses (Sturz and Christie 2003; Bais et al. 2004; Compant et al. 2013). The schematic diagram below shows some of the pathogen-vanquishing modes of BCA (Fig. 4.1). The pathogen-disarming pathways have been described in the following sections.

Fig. 4.1
figure 1

The strategies exerted by the BCAs for the management of phytopathogens

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4.3.1 Microbial Antagonisms

The microbes considered as ideal candidates for BCA have the ability to proliferate in the rhizospheres, a niche which defends the roots and acts hostile to pathogens. The advantageous microbes colonize the roots and secrete pathogen-antagonizing metabolites into the root system where they directly aid in the suppression of pathogenic bacterial growth (Shoda 2000). This microbial antagonism between beneficial microbes and pathogens is the most significant strategy of disease control, in which the metabolically active populations of beneficial microbes offer protection either by direct antagonism or by priming of host plant defenses (Nihorimbere et al. 2011). It also involves antibiosis, where the secretion of diffusible antibiotics, volatile organic compounds, toxins, and extracellular cell wall-degrading enzymes (such as chitinase, β-1,3-glucanase, beta-xylosidase, pectin methylesterase) is key to pathogen control (Shoda 2000; Compant et al. 2005).

4.3.2 Parasitism

Parasitism, the concept of one organism living off another, is ubiquitous. BCA exploit parasitism to control pathogens. They produce cell wall-lysing enzymes such as chitinases and glucosaminidases to degrade the cell wall of fungal pathogens, followed by penetration and killing (Guigon-Lopez et al. 2015). Trichoderma has been discovered to parasitize Macrophomina phaseolina and Pythium myriotylum, among others (Kubicek et al. 2001). A nematophagous fungus Pochonia chlamydosporia uses its proteases to infect the eggs of nematodes. The fungal infectivity of the nematode is enhanced by chitosan (Escudero et al. 2016).

4.3.3 Competition

When two or more than two organisms demand the same nutrition from one source for survival, the interaction becomes competitive. BCA exploit this nexus to deter pathogens. They prevent the establishment of pathogen by utilizing the same nutrients which are needed for the development and infectivity of the pathogen. A microbe must be able to tap the accessible nutrients in the form of exudates, leachates, or senesced tissue in order to thrive in the phyllosphere or rhizosphere. The niche surrounding the rhizosphere is a significant source of carbon (Roviara 1965), where the photosynthate allocation can be as high as 40% (Degenhardt et al. 2003). The nutrient abundance around root surfaces attracts a large diversity of microbes, both favorable and pathogens. Effective BCA compete for these nutrients and protects the plants from phytopathogens (Duffy 2001). This competition approach has been proven to be successful particularly for soilborne pathogens such as Fusarium and Pythium that infect through mycelial contact as compared to the pathogens that directly germinate on plant aerial surfaces. For instance, Enterobacter cloacae, a BCA, reduces the growth of Pythium ultimum by enhancing the catabolism of nutrients (van Dijk and Nelson 2000; Kageyama and Nelson 2003). Migration of BCA to the root surface is governed by the chemical attractants of the root exudates such as organic acids, amino acids, and specific sugars (Nelson 1990; Welbaum et al. 2004; De Weert et al. 2002). For example, Pseudomonas fluorescence consumed iron required for the pathogen Fusarium oxysporum, and Chryseobacterium sp. WR21 restrained Ralstonia solanacearum by claiming root exudates for itself (Huang et al. 2017).

4.3.4 Production of Antimicrobial Compounds

4.3.4.1 Antibiotics

The role of antibiotics as BCA has been recognized. Among others, polymyxin, circulin, and colistin are antibiotics generally produced by a number of Bacillus species, Antibiotics such as phenazines, phloroglucinols, pyoluteorin, pyrrolnitrin, cyclic lipopeptides, and hydrogen cyanide (HCN) affect pathogenic fungi as well as Gram-positive and Gram-negative bacteria. For antibiotics to act as effective BCA, they must be produced in proximity to the pathogens and in adequate amount (Weller et al. 2007; Mavrodi et al. 2012). Some of the antibiotics documented to suppress plant pathogen growth include 2, 4-diacetyl phloroglucinol (DAPG) (against Pythium spp.) (Weller et al. 2007), agrocin 84 (against Agrobacterium tumefaciens) (Kerr 1980), iturin A (against Botrytis cinerea and Rhizoctonia solani) (Kloepper et al. 2004), and phenazines (against Gaeumannomyces graminis var. tritici) (Thomashow et al. 1990). Several species of the genus Pseudomonas elaborate antifungal metabolites phenazines, pyrrolnitrin, DAPG, and pyoluteorin (Bloemberg and Lugtenberg 2001). Phenazine has redox activity, which can suppress phytopathogens such as F. oxysporum and Gaeumannomyces graminis (Chin-A-Woeng et al. 1998). Pyrrolnitrin produced by Pseudomonas chlororaphis DF190 and PA23 inhibits the fungus Leptosphaeria maculans, which causes blackleg lesion in canola (Ramarathnam et al. 2011). Trichoderma has emerged as an epitome of antagonism (Verma et al. 2007). The efficacy of Trichoderma virens-produced agrocin K84 in the management of Pythium damping off of cotton seedlings has been widely observed. Bacillus methylotrophicus R2-2 and Lysobacter antibioticus 13-6 inhibited tomato root-knot-causing nematode Meloidogyne incognita (Zhou et al. 2016). Lipopeptide class of surfactants secreted by Pseudomonas and Bacillus species have been intended as BCA for their antagonistic effect on bacteria, fungi, oomycetes, protozoa, and nematodes, among other pests. The role of antibiotics as effective BCA has been demonstrated by the inability of soilborne root disease suppression by the mutant strains of biocontrol bacteria that fail to produce phenazines and ploroglucinols (Keel et al. 1992; Thomashow et al. 1990).

4.3.4.2 Iron-Chelating Siderophores

Bacteria and fungi-derived siderophores can inhibit plant pathogens by competing for iron, copper, zinc, and manganese (Leong and Expert 1989; Bloemberg and Lugtenberg 2003). Siderophores are iron-chelating compounds, and they aid in the transport of iron across cell membranes (Neilands 1981; Hider and Kong 2010). The ability of BCA to compete for nutrients can limit the growth of pathogens (Handelsman and Parke 1989; Nelson 1990; Harman and Nelson 1994). Iron being an essential growth element for all life forms, its deficit in soil niche and on plant surfaces creates a furious competition (Leong and Expert 1989; Loper and Henkels 1997). Iron deficiency induces BCAs to produce siderophores to acquire ferric ion (Whipps 2001). Siderophore as a mechanism of biological control was first demonstrated by plant growth-promoting strains of Pseudomonas fluorescens such as A1, BK1, TL3B1, and B10 against the pathogen Erwinia carotovora (Kloepper et al. 1980). Siderophores with higher affinity for iron and sequestration ability have been widely observed in fluorescent pseudomonads (Loper and Buyer 1991; Sullivan and Gara 1992). Significance of P. fluorescens siderophores in plant pathology suppression has been demonstrated in the past (Costa and Loper 1994; Leong and Expert 1989). Owing to their potential role in disease suppression, engineered bacterial strains with enhanced production of siderophores could be developed.

4.3.4.3 Biocidal Volatiles

Volatile organic compounds (VOCs) are lipophilic substances with high diffusion tendency through biological membranes (Pichersky et al. 2006). The VOCs emitted by soil bacteria act above the ground as well as within the soil. Some VOCs act as signaling molecules and play critical role in communications (Kai et al. 2009). Microbial VOCs as a weapon of defense against pathogenic fungi have received substantial attention in recent times (Mackie and Wheatley 1999; Strobel et al. 2001; Fernando et al. 2005; Gu et al. 2007; Zou et al. 2007; Liu et al. 2008; Wan et al. 2008; Arrebola et al. 2010). VOCs from soil bacteria can impede the growth of phytopathogenic fungi (Alström 2001; Wheatley 2002). For example, the VOCs produced by rhizobacteria inhibit the growth of pathogenic fungus Sclerotiana sclerotiorum (Giorgio et al. 2015). Volatiles produced by the bacterial strains, Bacillus megaterium KU143 and Pseudomonas protegens AS15, significantly inhibited the growth of Aspergillus candidus, Aspergillus fumigatus, Penicillium fellutanum, and Penicillium islandicum in stored rice grains (Mannaa and Kim 2018). Volatile compounds from Trichoderma was able to restrain plant pathogens (Fusarium oxysporum, Rhizoctonia solani, Sclerotium rolfsii, Sclerotinia sclerotiorum, and Alternaria brassicicola) (Amin et al. 2010; Meena et al. 2017). However, correlation of VOCs with BCAs, plant pathogens, and plants, along with biotic and abiotic, factors is explored to a limited level (Campos et al. 2010).

4.3.4.4 Lytic Enzymes (Chitinases and Glucanases)

The prevention of potential plant pathogen is usually done by the battery of hydrolytic enzymes produced by the microbes extracellularly. For example, chitinase and β-1, 3-glucanase cleave chitin and β-1, 3-glucan, the major components of fungal cell walls (Lam and Gaffney 1993), resulting in its weakening followed by death (Chernin and Chet 2002). The production of chitinase by S. plymuthica, Serratia marcescens, Paenibacillus sp., and Streptomyces sp. was found to be inhibitory against Botrytis cinerea, Sclerotium rolfsii, and Fusarium oxysporum f. sp. cucumerinum (Ordentlich et al. 1988; Frankowski et al. 2001). Similarly, laminarinase produced by Pseudomonas stutzeri digest and lyse mycelia of F. solani (Lim et al. 1991). The cell walls of F. oxysporum, R. solani, S. rolfsii, and Pythium ultimum are destroyed by the β-1, 3-glucanase synthesized by Paenibacillus and B. cepacia (Fridlender et al. 1993). The genetic evidence for the role of these enzymes in biocontrol was demonstrated by the genetic modification of E. coli with ChiA. The ChiA transformants showed disease in a number of incidences of southern blight of bean caused by Sclerotium rolfsii (Shapira et al. 1989). Similarly, ChiA from S. marcescens (Haran et al. 1993) transformed into Trichoderma harzianum was strongly able to inhibit Sclerotium rolfsii than the native strain. Trichoderma, a saprophytic fungus, produces a multitude of lysing enzymes and antagonizes pathogens by creating pressure on the available nutrients and space (Olmedo-Monfil and Casas-Flores 2014). A step forward in the paradigm of biocontrol was established by the generation of transgenic plants harboring gene for endochitinase from T. harzianum with increased resistance to plant pathogenic fungi (Lorito et al. 1993). These demonstrations suggest the importance of these enzymes in biocontrol and which could be enhanced using chitinolytic enzymes. In addition, search for other enzymes secreted by the biocontrol agents and their introduction into non-biocontrol microbes or via genetic engineering of plants against a broad range of phytopathogenic fungi could serve as an effective means of control measure.

4.3.4.5 Detoxification of Virulence Factors

The detox system revolves around the interaction of a protein produced by a BCA with another toxin produced by pathogen to decrease its virulence potential of the toxin on a temporary or permanent basis. For instance, Alcaligenes denitrificans and P. dispersa are involved in the detoxification of albicidin toxin produced by Xanthomonas albilineans (Zhang and Birch 1996, 1997; Walker et al. 1988; Basnayake and Birch 1995). Similarly, fusaric acid, a phytotoxin produced by various Fusarium species, is hydrolyzed by strains of B. cepacia and Ralstonia solanacearum (Toyoda and Utsumi 1991; Toyoda et al. 1988).

4.4 Priming and Induced Systemic Resistance

Resistance mediated by plants against various biotic stresses comprising both beneficial and non-beneficial and abiotic factors is distinct. Induced systemic resistance (ISR) in plants resembles systemic acquired resistance (SAR) if bacteria and pathogen remain separated. The complexity of ISR has been explored in a plant model Arabidopsis with three different pathways. Out of three, two involve in the release of pathogenesis-related (PR) proteins with an alternate route induction. In one of the pathways, PR proteins are produced in response to pathogen attack, while in the other pathway, they are produced in response to wounding or necrosis-inducing plant pathogens. In the pathway induced by pathogen, resistance is mediated by salicylic acid (SA) produced by plants, contrary to the wounding pathway that relies on jasmonic acid (JA) as the signaling molecule. Salicylic acid-mediated defense is triggered by pathogen infection that leads to the production of PR proteins such as PR-1, PR-2, chitinases, and some peroxidases (Kageyama and Nelson 2003; Park and Kloepper 2000; Ramamoorthy et al. 2001). These PR proteins can effectively destroy the invading cells and/or augment the cell membranes to withstand infections. On the contrary, the third pathway is rhizobacteria-induced systemic resistance (ISR), leads of systemic resistance, which is elicited by naturally present nonpathogenic bacteria associated with root. The induction of elicitors like volatile compound, protein, and antibiotic by biocontrol agents enhances the gene expression of jasmonic acid/salicylic acid/ethylene pathways (Hase et al. 2008). Trichoderma-emitted terpenes and compound such as 6-pentyl-2H-pyran-2-one-stimulated strains tended plant growth (Lee et al. 2016). BCA like Pythium oligandrum suppresses Ralstonia solanacearum-caused wilt disease in tomato by inducing an ethylene-dependent defense response (Hase et al. 2008). A number of compounds like polyacrylic acid, ethylene, and acetyl salicylic acid, various amino acid derivatives, the herbicide phosphinothricin, and harpin produced by Erwinia amylovora induce resistance of host plant against soilborne pathogens (Wei and Beer 1996). Application of biocontrol fungi, bacteria, bacteriophages, and compounds that induce ISR in the plant has been reported as an effective alternative tool for soilborne disease control.

4.5 Emerging Biocontrol Strategies

4.5.1 Usage of Plant Exudates to Attract Beneficial Biocontrol Microbes

The composition and function of rhizosphere microbial populations are significantly impacted by the exudate secreted by the root. Certain beneficial microbes are attracted by specific root exudates to meet the specific needs. The role of plant chemical exudates in favoring specific microbiomes has been well explored in the past (Rahman et al. 2017). For instance, specific nitrogen-fixing rhizobacteria are attracted by flavonoids released from legumes (Cooper 2007), and some beneficial rhizobacteria aid in activating plant defense responses to combat foliar diseases (Ryu et al. 2004). The application of soil microbiomes in agriculture has been extensively practiced as a strategy to enhance plant nutrition and disease resistance (Cao et al. 2011; Kavoo-Mwangi et al. 2013). The correlation between different exudate profiles and an attraction of different microbial populations was established in hormone-treated plants and defense signaling mutants (Carvalhais et al. 2013, 2015). Furthermore, signaling by strigolactone, a plant hormone, attracted mycorrhiza and other microbes that aid in phosphate solubilization, water supply, and defense (Rahman et al. 2017). The organic compounds malate, succinate, and fumarate aid in the attraction of a beneficial microbe Pseudomonas fluorescens and protect the plant from various pathogen attacks (Oku et al. 2014). Based on the successful demonstrated evidences, the implementation of plant exudates could be one of the viable approaches to attract beneficial microbes to control different plant diseases. In addition, the rhizosphere microbial population could be manipulated by simply spraying plants with signaling chemicals or altering the genotype via plant breeding to attract beneficial microbes (Carvalhais et al. 2015; Wintermans et al. 2016).

4.5.2 Use of Substrates to Maintain Beneficial Biocontrol Microbes

Substrates are the nutrients required for the growth and metabolism of microbes. Beneficial biocontrol microbes can be cultured using specific substrates. The majority of plant-associated microbes can be grown using systematic bacterial isolation approaches (Bai et al. 2015). This is advantageous to harness the beneficial microbiomes from the natural soil microbiota for the biocontrol of plant diseases by providing the right substrates. The nutritional flexibility of beneficial microbes, especially bacteria, renders them suitable for different types of environments.

4.5.3 Phyllosphere Biocontrol

Foliar diseases by fungal pathogens can significantly affect various crop plants (Madden and Nutter 1995; Dean et al. 2012). A better grasp of the role of foliar microbiomes could be a crucial step toward crop protection. Microbial biocontrol agents serve as an eco-friendly alternative to synthetic chemical control (Maksimov et al. 2011). Spray application of microbial biocontrol agents has been found to be effective on foliar diseases, including blights, leaf spots, and mildew (Heydari and Pessarakli 2010). The potential of microbial formulation in controlling stem rot pathogen of avocado plants has been tested (Demoz and Korsten 2006). Several bacteria could inhibit the growth of tomato plant bacterial stem rot pathogen Erwinia chrysanthemi under greenhouse condition (Aysan et al. 2003). Reduced fungal growth was noted on flowers of blueberries treated with the bacterial strain (B. subtilis QRD137) producing the biological products Serenade (Scherm et al. 2004). Plants defend themselves by producing antimicrobial compounds on the leaf surface or by enhancing the proliferation of beneficial microbes through the release of diverse phytochemicals (Vorholt 2012). It has been demonstrated in the past that leaf-colonizing microbes can prevent foliar disease progression in plants (Morris and Monier 2003). Niche occupation is believed to play an important role in the development of crop protection against pathogens (Lindow 1987). The implementation of innovative strategies such as profiling of phyllosphere microbiome (Vorholt 2012) and their interactions with the plant and microbe–microbe interactions can reveal new insights toward plant pathogen mitigation.

4.5.4 Breeding Microbe-Optimized Plants

Plants have evolved to interact with certain type of microbes. For instance, different ecotypes of Arabidopsis showed about fourfold increment in yield when inoculated with the bacterium Pseudomonas simiae WCS417r (Wintermans et al. 2016). This demonstrates that the outcome of the beneficial interaction is influenced by the genetic profile of the plant (Smith et al. 1999). Breeding of plants optimized to attract and maintain encouraging the colonization of beneficial microbes is the prime objective of this approach. The adoption of genetic engineering can lead to the generation of microbe-optimized plants capable of producing exudates attractive to the beneficial bacteria (Trivedi et al. 2017).

4.5.5 Engineering Microbiome, Plant-Optimized Microbes/Microbiomes

This strategy involves engineering or breeding individual microbes or microbial consortia harboring beneficial microbes followed by their maintenance for application on crop plants meant for different soil types. This leads to the formulation of plant-/soil-optimized microbes and plant-/soil-optimized microbiomes that can serve as an inoculum for different crops in different soils. This strategy is rather new, but soil microbiomes have shown evidence of promoting plant–microbe interactions (Berendsen et al. 2012). Naturally occurring plant microbiomes play a protective role in the face of disease development (Bulgarelli et al. 2013).

4.5.6 Pairing Plant Seed with Optimal Microbiome and Soil Amendment Practices for Specific Soil Type

Efforts have been made and are still underway by the researchers to find the microbes that suit a particular crop to grow better. Smearing of seeds with promising microbes for specific soil type is one of the ideal strategies for optimizing plant–microbe interactions. The microbiomes coating the seeds assist the plants to absorb nutrients and as BCA offering protection against pathogens. In order to ensure that beneficial microbes are maintained, certain soil amendments may be essential.

Formulations of beneficial bacteria such as Rhizobium for legume seed treatment have already been in market. Apart from promoting the development of nitrogen-fixing nodules on leguminous plant roots, they also aid in the suppression of pathogens. The effectiveness of granular and aqueous extracts of vermicompost-based bioformulations enriched in microbial growth-promoting compounds has been demonstrated in the past (Kalra et al. 2010). Likewise, Rice et al. (1995) successfully cultured the phosphate-solubilizing fungus Penicillium bilaii with Rhizobium. Enhanced soybean nodulation was noted when co-inoculation of Bradyrhizobium and Bacillus megaterium was conducted (Liu and Sinclair 1990). Recently it was demonstrated that mixtures of rhizobacteria enhanced biological control of multiple plant diseases, promoting plant growth (Liu et al. 2018).

4.6 Current Scenario and the Need of Adopting of BCA in India

Food security is a topmost priority of all countries (Porter et al. 2014), and it is urgent for developing countries with rapid population growth. To meet the nutritional requirement of the ever-growing number of consumers, the production of food crops must be raised. But the excessive reliance on chemical fertilizers and pesticides is an unsustainable paracrine that comes with heavy price in terms of environment as well as organism health.

Despite the rising awareness of the environmental threats, in the developing countries like India, classical biocontrol programs are generally not used for agricultural practices. Therefore, it is important to extensively explore and evaluate their biocontrol potential against pathogens. Pilot program on the mass production of some BCA like Trichoderma can help in managing crop pathologies (Korolev et al. 2008; Cumagun 2014). Trichoderma can modulate the host plant signaling to combat cucumber mosaic virus (Vitti et al. 2015), Fusarium (Wang et al. 2005), and Botrytis cinerea (Elad et al. 1998), among other pathogens.

In Karnataka, the tomato plant wilt caused by Ralstonia solanacearum was abrogated by Pseudomonas fluorescens under greenhouse conditions (Vanitha et al. 2009). So, BCAs hold promises in promoting Indian agriculture, while reducing the dependency on the vicious chemical pesticides.

In order to assist the farmers in adopting new technologies, the government should take several approaches. The use of local languages to generalize literature and enhance financing to the biocontrol projects; if needed, the importing of BCA, promotion of research and development on biocontrol, and formulating manuals of BCA–plant host can be promising initiatives in this regard.

4.7 Future Prospects

In the present scenario of crop production, biocontrol is of utmost importance; however, its application needs to be optimized. Novel BCA can be screened from root microbiome (Lareen et al. 2016). Addition of resistance inducers like Bion (benzo(1,2,3) thiadiazole-7-carbothioic acid S-methyl ester) (BTH) and salicylic acid (SA) improved the efficiency of BCA such as Trichoderma hamatum, Trichoderma harzianum, and Paecilomyces lilacinus (Abo-Elyousr et al. 2009). BCA with synergistic function against phytopathogens might result in desirable outcome.

The research in this area is still confined to the laboratory, and very little attention has been given to formulate profitable bioagents. Moreover, the few cost-effective products have not been used conveniently by the farmers owing to the limited available information regarding their usage. Therefore, initiatives toward the popularization of biological control are required. BCAs which appear promising in laboratory settings often fail when implicated in the field. A myriad of physiological and ecological factors has been recognized causal for the futility. To improve the selection and characterization of BCA, biotechnology and other molecular tools are gaining importance to potentially solve the problem in the near future. For augmenting the efficacy of BCA, different methods such as mutation or protoplasm fusion could be a good intervention. A better understanding of the BCA mechanism and the evaluation of environmental factors is critical for viable marketability. Also, every technology leaves behind a trail of menace, so it is important to account for them, before things go out of control. For example, if BCA turn against the host plant, certain situations must be monitored. This concern is not without foundation, as Pythium touted as a BCA is a phytopathogen as well (Mavrodi et al. 2012; Alsohim et al. 2014). So, efficacy of the BCA mostly hinges on the plant host status, pathogens, and environmental conditions. The temperature, soil water level, moisture, oxygen, carbon, nitrogen, trace elements, indigenous microflora compositions, and the density of BCA have been found to be critical players in the pathogen control performance (Raaijmakers et al. 2002; Innocenti et al. 2015). The nematicidal effect of Pseudomonas fluorescens can be affected by the cyanobacterium Calothrix parietina (Hashem and Abo-Elyousr 2011). Alteration of relations from symbiosis to mutualism to parasitism, with changing milieu, has been reported (Redman et al. 2001). Introduction of alien species often poses environmental risks, so the impact must be assessed. Antibiotics as the driver of “drug resistance” are a grave problem. Similarly, BCA are capable of spreading perils, so they ought to be used in a controlled manner.

4.8 Conclusion

The importance of biocontrol agents in phytopathogen suppression has been known since decades back. However, the laboratory findings have not been successfully implicated in the field. In-depth understanding of the various strategies leading to positive plant-beneficial microbe association is imperative. The combination of microbial biofertilizers, biocontrol microbes, and soil amendments and the planting of microbe-optimized crops can forge positive plant–microbe interactions. In addition, potent bio-formulations and effective application methods need to be developed for successful implementation against a broad range of pathogens on a commercial scale in a cost-effective manner. This is an under-investigated area that deserves major research efforts, as it is paramount for enhancing crop yields and ensuring food security in a sustainable manner.