Exploring the efficacy of antagonistic rhizobacteria as native biocontrol agents against tomato plant diseases

Abstract

As the environmental and health concerns alert the necessity to move towards a sustainable agriculture system, biological approach using indigenous plant growth-promoting rhizobacteria (PGPR) gains a strong impetus in the field of plant disease control. In this context, the present review article addresses the usage of rhizospheric antagonistic bacteria as a suitable alternative to control tomato fungal diseases namely Fusarium wilt and early blight disease. Biological control has been considered to be an eco-friendly, safe and effective method for disease management. The inherent traits of PGPR to antagonize a pathogen through various mechanisms has been investigated extensively to utilize them as potent biocontrol agents (BCA). Hence, the article provides a detailed account on different biocontrol mechanisms displayed by BCA. It is also suggested that the use of bacterial consortium ensures consistent performance by BCA in field conditions. Likewise, this review also deals with the opportunities and obstacles faced during commercialization of these antagonistic bacteria as biocontrol agents in the market.

Introduction

Tomato (Solanum lycopersicum), a dicotyledonous plant belonging to Solanaceae family, is considered as the ancestor of cultivated tomatoes. It is a short duration crop and re-enumerative vegetable, appreciated with high nutritive esteem and antioxidant curative and therapeutic properties (Nour et al. 2018; Azeez et al. 2019). Hence, it is a versatile vegetable in the Indian culinary tradition. It exerts several beneficial effects on health as it is rich in vitamin A, B and C, minerals, organic acids and a considerable amount of total sugar (Salim et al. 2017). Moreover, it is also used commercially to produce various food products, such as ketchup, soup, paste and powder (Paul and Kehinde 2012; Manivannan and Tholkappian 2013). Therefore, it leads to increased demand in improved quality, high yield, better storage durability and promising disease and pest management system for tomato plants. In order to keep a balance between crop production and demographic food demand, the growers and scientists tend to emphasize sustainable and biological agricultural production (Syed et al. 2018). One of the major constraints faced during their cultivation is the assault of pathogens both in fields as well as greenhouse condition (Sanoubar and Lorenzo 2017; He et al. 2020).

The crop is affected by various pathogenic diseases leading to a decrease in its nutritional contents and the overall economy (Danish et al. 2014). Late blight induced by Phytophthora infestans is one of the damaging ailments of tomato bringing about huge financial loss (Singh et al. 2017). Sclerotinia rot brought about by Sclerotinia sclerotiorum, is another significant infection influencing the tomato crop profitability. Several studies on wilt, crown and root rot diseases in tomato caused by Fusarium species have been reported (Laurence et al. 2014; McGovern 2015). Root knot caused by the nematode Meloidogyne sp. is another destructive and widespread disease in tomato (Zhou et al. 2016). It not only influences the crop yield directly but also makes the plants increasingly prone to fungal and bacterial infections (Ashraf and Khan 2010). Bacterial leaf spot is a common bacterial ailment of tomato caused by Xanthomonas campestris. It is exceptionally ruinous in both greenhouses as well as in field conditions, causing 10–50% yield loss (Singh et al. 2017). Ralstonia solanacearum is a soil-borne plant pathogen that causes bacterial wilt in tomatoes and hampers their yield (Huang et al. 2013). Clavibacter michiganensis infection systemically causes wilting and canker on the stem, while blister-like spots are developed in locally infected leaves causing a substantial economic loss (Agrawal et al. 2012). Among the fungal diseases encountered by tomato plants, wilt disease and early blight disease caused by Fusarium oxysporum. f. lycopersici (FOL) and Alternaria solani (AS), respectively, are known to be the most deleterious ones (Pawar et al. 2016).

Mere cultural sanitation is not much effective since the pathogens are pandemic. Although current agricultural practices have been subject to the utilization of agrochemicals as a solid technique for harvest insurance, expanded chemical utility has caused a few negative impacts including resistance development among pathogens to the applied agents and their non-target natural effects (Ghazanfar et al. 2016). These reasons have prompted a quest for substitutes for chemical inputs. Biological control is considered as a successful option for lessening the seriousness of the diseases (Linu and Jisha 2017).

The utilization of rhizobacteria that colonize the underlying foundations of harvest plants and smother soilborne ailments is turning into an elective choice as compared to the utilization of chemical fungicides as referenced before. The utilization of plant growth-promoting rhizobacteria (PGPR) as soil inoculants for control of soilborne infections, can be a suitable organic option. Rhizobacteria with biocontrol viability frequently give long haul security from soilborne pathogens at the root surface since they have the ability to quickly colonize the rhizosphere and spread down the root from a solitary seed treatment or soak application into the soil (Haldar and Sanghamitra 2015).

Currently, a large number of bacterial strains have been isolated and identified for their advancement as biocontrol agents against tomato diseases. Punja et al. (2016) utilized Bacillus subtilis strain under greenhouse conditions to control the postharvest fruit infection. B. subtilis strains were likewise used by Kilani-Feki et al. (2016) for the suppression of Botrytis cinerea, the causative agent of tomato fruit rot. Gowtham et al. (2016) used ten rhizobacterial strains to deal with the Fusarium wilt in tomato and observed that two distinct strains Bacillus amyloliquefaciens and Ochrobacttrum intermedium significantly repressed the incidence of wilt and furthermore enhanced the vigour index of seedlings. Singh et al. (2017) have depicted the efficacy of Pseudomonas fluorescens strains against different diseases, such as damping-off, root rot, stem canker and leaf blight of tomato. Higher accumulation of phenolic compounds in leaf tissues induced by P. aeruginosa against A. solani makes it an effective BCA against this pathogen (Hariprasad et al. 2013). Abo-Elyousr et al. (2019) reported that the PGPR (B. subtilis, B. amyloliquefaciens, P. fluorescens and P. aeruginosa) and their formulations could successfully control the wilt and canker disease of tomato caused by Clavibacter michiganensis subsp. michiganensis, in vitro and under greenhouse conditions. Attia et al. (2020) investigated a new strategy by using PGPR in the induction of systemic resistance of plants diseases. They were confirmed to be efficient in the reduction of early blight disease-causing A. solani which infected tomato plants following the assessment of invitro antagonistic activity. The isolated bacterial strains namely Bacillus subtilis SBMP4, Lysinibacillus fusiformis NBRC15717 and Achromobacter xylosoxidans NBRC15126 could increase the induction of systemic resistance in the tomato plant and thereby reduce the percent disease severity by 13.0%. They also recorded a protection percentage of 84.3% when compared to non-treated plants.

Incorporation of microorganisms for disease control/plant growth promotion in cropping systems and the elimination of chemical utility is reliant on effective selection, screening and safety analysis of potential PGPR strains. Moreover, information on targeting diseases, cost of mass-scale production and registration procedures also need to be amended likewise to raise the market status of these biocontrol entities. This review is an attempt to explore the role of antagonistic rhizobacteria in biological control of tomato plant diseases namely Fusarium wilt and early blight. Moreover, the hurdles and benefits of commercializing these microbes in the agriculture sector are also included in this review article.

Fusarium wilt and early blight diseases of tomato

Fusarium wilt is considered as the deadliest disease confronted by tomato plants throughout the world, particularly in the uplands (Fig. 1a). The causal agent is Fusarium oxysporum f. lycopersici (FOL) (Sacc.). They are well-established soil-borne pathogens ubiquitous in all soil types. They are saprophytic and are able to survive in the soil for a prolonged period (Mj et al. 2017). At least 32 countries have reported this disease, among which warm climate countries have been severely affected (Bawa 2016). Srinivas et al. (2019) reviewed that Fusarium wilt is characterized by 60–70% of fruit yield loss with wilted plants containing yellowed leaves. FOL invades plant’s vascular system and binds inside xylem vessel, which results in impaired water transportation, finally leading to wilting of the foliage (Boukerma et al. 2017) (Fig. 1b). The symptoms of the disease appear as slight vein clearing. The infection develops yellowing of leaves which is restricted to one side of the plant or a single shoot followed by defoliation of the older leaves. The browning of vascular tissue is the characteristic feature, which is used as an identification tool for the disease (Ajilogba and Babalola 2013). Since the pathogen inhabits in the soil by producing resistant spore structures, it is a challenging task to manage this disease (Sundaramoorthy and Balabaskar 2013; Hussain et al. 2016).

Fig. 1.

Symptoms of Fusarium wilt disease caused by Fusarium oxysporum. f sp. lycopersici. a Field view of infected tomato plants; note the yellowing of the oldest leaves. b Discolouration of vascular tissue in Fusarium infected tomato plants

‘Early blight’ (EB) of tomato is another fatal disease which occurs worldwide (Hadimani and Kulkarni 2016). Alternaria solani (Ellis & Martin) Sorauer, is the causative organism which has been recognized as a serious foliar pathogen of tomato (Patel et al. 2011; Ghazanfar et al. 2016). Around 79% yield loss in tomato have been reported in India, Canada, the United States and Nigeria due to the early blight damage (Maurya et al. 2015). This disease results in yield reduction both in quantity and quality. Under humid conditions followed by warm and wet weather, tomato plants are susceptible to this disease (Sadana and Nidhi 2016). The disease mainly affects the leaves, stems, flowers and tomato fruit which leads to reduced plant health and vigour (Thakkar and Saraf 2015) (Fig. 2a–c). Moreover, severe infection leads to the complete death of the plant. Sparse foliage results in fruit sunscald, which in turn disposes the fruit quality. Alternaria solani reproduces asexually through the production of a reproductive structure called conidia. This resistant structure can thrive under adverse conditions and germinates during favourable environmental conditions. Conidial germination requires a temperature of 8–32 °C. The germ tube produced, invades the host tissue through stomatal openings or wounds resulting in the establishment of the infection. Lesions appear after 2–3 days of infection and sporulation occurs after 3–5 days. The spores or conidia disperses to other healthy plant parts through rain splashes and wind thereby resuming the disease cycle. This fungus leads a polycyclic disease cycle when excess moisture occurs through rain, mist, fog, irrigation etc. (Patel et al. 2011).

Fig. 2.

Symptoms of early blight disease caused by Alternaria solani in tomato plants. a Development of concentric rings in tomato leaves due to early blight disease. b Early blight on tomato stem showing elongated concentric rings. c Early blight disease on tomato fruit showing black spore masses

Control measures

The ruinous diseases namely early blight and Fusarium wilt should be effectively treated to improve the market yield and diminish the economic loss (Hassanein et al. 2010). The emergence of new phytopathogenic races is another threat to deal with (Khiareddine and Riad 2015). Currently there are different disease control strategies which comprises of pathogen exclusion and eradication through cultural, chemical (quarantine measures and eradication) control, use of resistant varieties, botanicals and also by native biocontrol agents. Cultural practices include perpetuation of a pathogen-free condition in the field, by long crop rotation, sanitation, removal of affected plant debris from the field etc. Beyond pathogen exclusion and eradication, it is arduous to control these diseases because the soil pathogenic fungi produce resting structures which persist for a longer period of time. The major steps involved in the control measures of the above-mentioned diseases are described here.

Chemical control

Today, agriculture is intensely dependent on the use of chemical pesticides for disease control. They are routinely and frequently applied to control fungal pathogens (Cwalina-Ambroziak and Ryszard 2012). Application of protective and systemic fungicides inhibit spore germination and thus reduces disease incidence. Benomyl, carbendazim, prochloraz, bromuconazole (Amini and Sidovich 2010), Nativo (Akhtar et al. 2017) are fungicides of FOL. Fungicides used against early blight disease include Mancozeb (Desta and Yesuf 2015) copper oxychloride, chlorothalonil (Sahu et al. 2013), carbendazim, antracol (Kumar et al. 2017) Thiophanate–methyl etc. (Gharasheed 2016). Moreover, these fungicides are applied to the field in every 7–10 days without considering epidemiology. Eventually, the soil as well as the crop receives an excessive amount of fungicide. The strong demand of the public and scientific community for eco-friendly management tends to shift from the use of chemical fungicides. Although other disease management practices like cultural sanitation and usage resistant breed plants prevail, they do not exhibit complete diminishment of these diseases. The apparition of fungicide resistance in phytopathogen and usage of three to four fungicides in order to avoid any fall or ineffectiveness can be a major concern.

Disease-resistant varieties

During the nineteenth century, plants resistant to diseases were recognized and their breeding was successfully done. Disease resistant varieties checks the pathogen attack thereby restricting disease incidence. It is an economical and environment friendly method. Likewise, it eliminates the additional effort to prevent pathogen attack. Recent developments in molecular markers and molecular assisted selection technology (MAs) fostered the advances in tomato genetics and breeding (Foolad and Panthee 2012). Adhikari et al. (2017) reviewed that the use of resistant varieties is an effective control measure of EB of tomato. There are a few breeding experiments in the pipeline to develop resistant varieties, however, the absence of qualitative genes and markers along with the association of undesirable traits are the major challenges to be tackled. Hence there is no commercial cultivar with sufficient resistance to EB. Apart from this, FOL resistant varieties are available in the market (Hanson et al. 2016). The resistant gene I-1 (S. Pimpinellifolium “PI79532”), I-2 (S. lycopersicum × S. pimpinellifolium hybrid “PI126915”), I-3 (S. pennellii “LA716”) and I-7 (S. pennellii “PI414773”) from wild tomato has been reported to confer wilt resistance against different races of FOL. (Catanzariti et al. 2015; Lee et al. 2015).

Plant extracts or metabolites as biocontrol agents

Botanical fungicides are another appealing option with a negligible negative impact on the environment. They are plant-derived compounds with pesticidal activity. Botanical fungicides are selective and biodegradable with low residues. Hence, these herbal products can be fostered in organic and sustainable agriculture (Yoon et al. 2013). There are various reports which recommend the use of botanical fungicides. The chloroform extract of Piper betle. L. was observed to be strongly inhibitory to FOL population when amended in the soil (Manoj et al. 2010). Yeole et al. (2016), reported that out of the seven plant extracts screened against the same fungus, Syzyjium asromaticum methanolic extract showed encouraging results with 100% inhibition to spores. Furthermore, reduced disease incidence and lipid peroxidation were found in tomato seedlings treated with aqueous neem and willow extract from Egypt (Farag et al. 2011). The use of plant extracts to check pathogen growth have also fortified these days since it does not give rise to environmental and health hazards (Mamgain et al. 2014). Plant extracts of Azadirachta indica, Allium sativum, Parthenium lysterophorus, Datura stramonium were reported as potential growth inhibitors of A solani (Raza et al. 2016). Ravikumar and Garampalli (2013) have communicated the capabilities of aqueous extract of Crotalaria trichotoma (16.6%), Azaridacta indica (10%), Capsicum annum (7.1%), Datura metel (6.6%), Polyalthia longifolia (6.3%) and Citrus aurantifolia (5.5%) as an antifungal agent against EB. Moreover, Majorana syriaca and Hibiscus sabdariffa extracts have shown strong inhibitory action to this fungus when compared to standard fungicides (Goussous et al. 2010). Few literature reports suggest the importance of neem extract as a powerful phytofungicide. Hassanein et al. (2010) has supported it with the report of effective suppression of FOL and AS with different concentration of neem extracts. Despite these benefits, they have limitations as well. The major challenge is that, a huge amount of plant source needs to be exploited which poses a threat to their population. The synthesis and purification of these active compounds is a tedious process. When it comes to the field, easy decomposition and short shelf life are the other challenging factors. Moreover, the effect of most of the botanical fungicides are moderate thereby demanding repeated applications.

Microbes as biocontrol agents

It is desirable to control plant disease with high specificity towards the target pathogen and with low mass production cost (Kumar et al. 2011). There are some microorganisms present in nature that can antagonize pests. These organisms can be exploited as biopesticides. They include biofungicide, bioherbicide and bioinsecticide. Usually, these kinds of microbes are seen in close association with the host plant. Hence, investigations to utilize the beneficial microorganisms as biocontrol agents gain significance to subside the fatal effects of such plant diseases (Linu and Jisha 2017). (Fig. 3) describes the desirable characteristics of a biocontrol agent which is in demand in the agriculture sector.

Fig. 3.

Schematic diagram showing desirable characteristics of a biocontrol agent (Carmona-Hernandez et al. 2019)

Biological control has been used over two millennia and since the end of the nineteenth century, it has been commonly used in pest management. Khan et al. (2012) used Paenibacillus lentimorbus strains for repressing early blight disease in tomato brought about by Alternaria solani. Specific strains, such as B. subtilis, B. amyloliquefaciens, B. pasteurii, B. pumilus, B. mycoides and B. cereus brought about significant reduction in various diseases by inducing systemic resistance (Bouizgarne 2013). Endophytic actinomycetes were utilized for the biocontrol of Rhizoctonia solani causing damping-off in tomato. These strains significantly restrained the pathogen development and enhanced the growth parameters of tomato (Goudjal et al. 2014). Mj et al. (2017) suggested that, successful biological management of Fusarium wilt of tomato can be carried out using vermicompost biofortified with selected biological control agents (BCAs) i.e. Trichoderma harzianum, Pseudomonas fluorescens and Bacillus subtilis. The application of Burkholderia gladioli pv. agaricicola strain 12322 could enhance disease protection and improve the consistency of biological control against tomato wilt disease caused by Verticillium dahlia (Elshafie et al. 2017). Lian et al. (2017) proved that, Streptomyces pratensis LMM15 could be a potential biocontrol agent for controlling tomato gray mold because the incidence of tomato grey mold decreased by 46.35% in association with an increase in proline content and malondialdehyde (MDA) and changes in the defence-related enzymes on tomato leaves were observed when the strain was sprayed on the tomato leaves 24 h prior to inoculation with pathogens. Arenas et al. (2018) evaluated the efficacy of Mexican strains of Trichoderma spp. and its antagonistic effect on F. oxysporum on tomato seedlings. It was observed that the Trichoderma harzianum strain presented the highest growth rate with a mean of 1.25 cm/day, proving to be the most aggressive strain to control F. oxysporum with a development rate of 3.80 mm/day.

The types of biological control can be classified into natural, conservation, inoculative (classical) and augmentative biocontrol. Pest reduction in natural biocontrol has been occurring since evolution using natural enemies, whereas conservation biocontrol involves human actions to stimulate and protect the performance of the same. Inoculative (classical) mode is the first type of biocontrol being practised widely, in which natural enemies are released into new areas, where the pest was accidentally introduced. Massive rearing of natural enemies in biofactories and its release into the market for immediate pest control made augmented biocontrol more desirable (van Lenteren 2012). This approach is considered to be an environment-friendly and food-hygienically-safe plant protection method (Sandheep et al. 2012). Furthermore, understanding the mechanisms of biological control through the interactions between the biocontrol agents and the pathogens may help in improving and developing biocontrol strategies.

Plant growth-promoting rhizobacteria: tapping for BCA

The rhizosphere is the narrow region of soil surrounding the living plant roots that are directly influenced by root secretions and associated soil microorganisms. It is a zone of mutual cooperation between plant, soil and microorganisms, such as biochemical interactions and exchange of signal molecules, nutrient transformation, genetic exchange, the release of root exudates, etc. (Haldar and Sanghamitra 2015). Hence, it is known as a unique niche for microbial activities and diversities (Venant et al. 2011). The diverse group of bacteria colonizing the rhizospheric habitat are called rhizobacteria. They are potent microbial competitors in the root zone. They influence plant growth directly or indirectly (Tank and Meenu 2010; Beneduzi et al. 2012). The direct mechanism involves the beneficial activities done by PGPR that support the plant growth directly. These mechanisms promote plant growth, but the ways in which it influences will vary species to species as well as strain to strain (Kundan et al. 2015). The PGPR nurture the plant by transforming the nutrients present in the soil through biogeochemical cycling. They also facilitate transport of these nutrients into the plant which aids plant growth directly. They enhance plant growth directly by producing plant hormones, (Glick 2014; Miransari and Smith 2014; Damam et al. 2016), fixing atmosphere nitrogen (Singh et al. 2015), solubilizing minerals, such as phosphorous (Kannapiran and Sri 2011; Stephen and Jisha 2011; Sagervanshi et al. 2012; Karpagam and Nagalakshmi 2014; Mahantesh et al. 2015; Sanjoth and Sudheer 2016), synthesizing siderophores that may solubilise and sequester iron (Radzki et al. 2013) and avail nutrients to plants beyond controlling soil-borne plant pathogens (Akhtar et al. 2012; Nadeem et al. 2014). In addition to plant growth promotion, it also has a significant role in resisting the phytopathogenic microorganisms (Son et al. 2014). Chen et al. (2013) discovered that Bacillus subtilis exhibited above 50% biocontrol efficacy on tomato plants against the plant pathogen Ralstonia solanacearum under greenhouse conditions through robust biofilm formation. Abdallah et al. (2016) inoculated seven distinctive endophytic strains isolated from the native Nicotiana glauca plants and discovered 88–94% significant reduction in yellowing and wilt symptoms and 95–97.5% in vascular browning of tomato plants. Antifungal activity of several Bacillus sp. against plant pathogenic fungi were accounted for, elevating them to be utilized as promising candidates for the biological control (Attia et al. 2020). You et al. (2016) discovered Trichoderma-mediated growth inhibition of Botrytis cinerea and their application in soils promoted growth of tomato. A combination of biocontrol isolates Mitsuaria sp. TWR114 and nonpathogenic Ralstonia sp. TCR112 exerted a synergistic suppressive effect resulting in enhanced biocontrol efficacy against tomato bacterial wilt (Marian et al. 2019). Maung et al. (2017) demonstrated the effectiveness of Bacillus amyloliquefaciens Y1 not only in the control of Fusarium wilt disease, but also for the enhancement of plant growth in cultivated tomato. Elsayed et al. (2020) revealed that the strains, Bacillus velezensis B63 and Pseudomonas fluorescens P142 were promising candidates for biocontrol of bacterial wilt caused by Ralstonia solanacearum under field conditions through significantly lowered R. solanacearum densities in tomato shoots and in the rhizosphere.

Biocontrol mechanisms (indirect mechanisms)

PGPB as BCA has certain advantages over other disease control methods such as they are eco-friendly and non-toxic indigenous microorganism and its application is sustainable to both environment and human health. The important mechanisms involved in the antagonism by BCA involves antibiosis, competition, induced systemic resistance of the host plant, hydrolytic enzyme production, HCN production and siderophore production (Bhattacharyya and Jha 2012) (Fig. 4). In addition, they can alleviate various stress conditions, such as salinity, drought, flood, heavy-metal toxicity, etc. in plants, thus empowering them to survive in such stress conditions (Heidari and Amir 2012). Even though several free-living rhizobacteria are considered as plant growth beneficial rhizobacteria, all the strains under the same species do not possess the same metabolic capacities to enhance plant growth. It is significant to know the potentialities of rhizosphere microbiota besides its mechanism of action involved in sustainable crop production (Bhattacharyya and Jha 2012).

Fig. 4.

Different mechanisms by which plant growth-promoting rhizobacteria (PGPR) accomplish biocontrol against phytopathogens

The antagonistic traits exhibited by the PGPR over various pathogens augment possibilities for their use as biocontrol agents (Pathak et al. 2017; Tariq et al. 2017). Well-known BCAs in suppressing tomato disease include strains of Pseudomonas (Toua et al. 2013), members of the genera Arthrobacter, Azoarcus, Azospirillum, Bacillus, Burkholderia, Enterobacter, Gluconacetobacter, Herbaspirillum, Klebsiella, Paenibacillus, Pseudomonas and Serratia (Maheshwari 2011). Various literatures suggest that consortium of BCA helps to reduce disease incidence through synergistic action. It has been reported that Bacillus subtilis, Bacillus megatarium, Bacillus polymyxa, Pseudomonas fluorescens and Trichoderma harzianum in combination with dinitrogen fixers of Azotobacter sp and Azospirillum sp were identified as successful biocontrol agents against soil-borne pathogens F oxysporum and Verticillium dahliae causing fungal wilt disease of tomato (Saad et al. 2016). Serratia plymuthica, Bacillus coagulans, Paenibacillus macerans, Bacillus pumilis and Pantoea agglomerans were tested for inhibitory effects on Alternaria solani, early blight pathogen on tomato (Yazici et al. 2011).

Antibiosis

Antibiotics are chemical substances produced by microorganisms against microorganisms. Interaction between the organisms leads to the production of these chemical substances in order to survive in predation, competition etc. (Ulloa-Ogaz et al. 2015). Bacterial antagonists impose suppression of phytopathogens by extracellular secretion of these metabolites that have inhibitory property, even at low concentration (Goswami et al. 2016). In fact, it is an efficient and most effectively studied characteristic of biocontrol (Ramadan et al. 2016).

The well-characterized antibiotics for biological control are 2,4 diacetylphologlucinol (DAPG), phenazine, pyrrolnitrin, pyoluteorin, tensin, tropolone, oomycin A, cyclic lipopeptides and HCN (Babalola 2010). The majority of Bacillus antibiotics shows activity against plant pathogenic fungi Alternaria solani and Fusarium oxysporum (Maksimov et al. 2011). HCN production mediated biocontrol has been proved by B. subtilis against FOL (Akintokun and Taiwo 2016). However, B. subtilis was reviewed as a potential BCA, capable of inhibiting the growth of fungal pathogen due to their ability to produce a vast array of antibiotics, such as zwittermicin, bacillomycin, fengycin, bacilysin and difficidin (Mangalanayaki et al. 2016). Jain and Das (2016), reviewed the positive correlation between HCN production and plant protection in tomato wilt disease. Bacillus isolate TNAM5 was found to be effective in suppression of FOL by the production of diffusible and volatile antifungal compound ammonia and HCN (Prashar et al. 2013). Similarly, it was observed that B. subtilis inhibited AS by the secretion of antifungal metabolites (Bellishree et al. 2015). A similar result was observed by Phichai (2014), against Alternaria spp. wherein B. subtilis could secrete several antifungal metabolites such as subtilin, bacitracin, bacillin and bacillomycin which had an inhibitory effect on the fungal pathogen.

However, too much dependence on antibiotic-producing bacteria as a BCA may be a disadvantage since there is a problem of antibiotic resistance. In order to overcome this threat, researchers are using potent biocontrol strains that could synthesize one or more antibiotics such as Bacillus and Pseudomonads (Glick 2012; Beneduzi et al. 2012).

The biological control of plant phytopathogens by endophytes was reported in the late 50s where, a Micromonospora isolate from tomato showed antagonistic activity against Fusarium oxysporum f.sp. lycopersici (Manikprabhu and Li, 2016). Bacterial endophytes such as Bacillus and Streptomyces species (Frank et al. 2017) both exhibited secondary metabolites showing antimicrobial activity against plant pathogens. As a result, Bacillus spp. endophytes were proposed for crop management (Aloo et al. 2018). Similarly, Streptomyces spp. endophytes are widely reported as phytopathogens biocontrol agents. For example, Kennedia nigriscans-endophytic Streptomyces sp. strain NRRL 30562 was recently reported to produce antibiotics as munumbicins A, B, C and D active against plant pathogenic bacteria and fungi (Castillo et al. 2002). Mohamad et al. (2018) evaluated the antimicrobial activity of endophytic bacterial populations from Chinese traditional medicinal plant licorice and characterized their bioactive secondary metabolites against Verticillium dahlia. The results revealed that the genus Bacillus, particularly B. atrophaeus and B. mojavensis, were the most effective biocontrol agents with most strains exhibiting broad antibacterial and antifungal activities. Around 13 compounds were produced during co-cultivation with V. dahlia which included putative compounds possessing antimicrobial activity such as 1,2-benzenedicarboxylic acid, bis (2-methylpropyl) ester; 9,12-octadecadienoic acid (Z,Z)-, methyl ester; 9- octadecenoic acid, methyl ester, (E)- and decanedioic acid, bis(2-ethylhexyl) ester.

Competition

The BCA should be able to withstand and multiply in a natural environment since effective colonization and enhanced competition play a significant role in biocontrol (Raguchander et al. 2011). For the successful establishment on rhizosphere, microorganisms must effectively compete for nutrient availability and niche. Competition among pathogenic and non-pathogenic microbes is an essential matter in biocontrol (Heydari and Mohammad 2010). It has been known that plant associate microbes give protection to the plant by accelerated rhizosphere colonization than the pathogen. The biocontrol agents deplete the limited available substrates making it unavailable to the pathogens. Simultaneously, they produce metabolic compounds that are detrimental to the pathogens (Trapet et al. 2016; Khilyas et al. 2016; Tabassum et al. 2017).

According to Khan et al. (2012), the antagonism depicted by Paenibacillus lentimorbus against AS was enforced due to strong competition between them for niche and nutrient utilization. Lugtenberg et al. (2001) revealed that the tomato foot and root rot pathogen FOL reside deep inside the soil. Hence, an efficient BCA must be able to protect deeper root parts by effective colonization to reach the growing tips and suppress the pathogen. Pseudomonads are reported as highly efficient competitors for root exudates among the rhizobacterial communities (Barea et al. 2005). Some of the root exudates include antimicrobial compounds which provides a suitable ecological niche for PGPR which in turn can detoxify them. This implies that PGPR competence is majorly reliant on their ability to take advantage of the specific environmental condition or to get adapted to variable circumstances (Compant et al. 2005). Kuiper et al. (2001) demonstrated that the competitive colonization ability of root colonizing Pseudomonads was considerably dependent on their increased uptake of a tomato root exudate, putrescine. In addition, Prasanna et al. (2013) reported that competitive colonization of Anabaena variabilis RPAN59 and A. laxa RPAN8 were positively correlated with the reduced fungal population of FOL. Biocontrol Bacillus strains namely 3F-II, 3F-VII, 13F-III, 15F-III inhibited EB in tomato and the enzymatic profile indicated that they were potential ecological competitors (Pane and Zaccardelli 2015).

Apart from competitive root colonization, another important mechanism of pathogen suppression via nutrient competition by PGPR involves the secretion of compounds, such as siderophores that efficiently sequester iron and deprive the pathogen from this important element (Singh et al. 2017). Several siderophore-producing rhizobacteria were evaluated and reported as biocontrol agents including species of Pseudomonas (Weller 2007), Bacillus and Enterobacter (Solanki et al. 2014). Heidarzadeh and Baghaee-Ravari (2015) proved that siderophore production by B. pumilus played a crucial role in suppressing Fusarium wilt disease by depleting iron.

Induced systemic resistance

Plant beneficial bacteria in the rhizosphere interact with the host plant to stimulate the defence against various pathogens. Induced resistance (IR) is the enhanced physiological state of defence, elicited by broad-spectrum biotic and abiotic stimuli. Induced resistance is classified into Induced Systemic Resistance (ISR) and Systemic acquired resistance (SAR). When plants innate defence mechanisms are evoked due to biotic challenges (Choudhary and Johri 2009), it is known as ISR. In SAR, plants render more resistance to uninfected plant parts while encountering broad spectrum of pathogens (Pieterse et al. 2014). SAR occurs through salicylic acid-mediated signalling pathway whereas ISR occurs predominantly through jasmonate- or ethylene-sensitive pathway (Fu and Dong 2013). Plant growth beneficial rhizobacteria colonizing plant roots can evoke resistance against a broad spectrum of plant diseases. This strategy has gained attention over the recent years. Few literatures have suggested that, some strains of Pseudomonas, Bacillus, Serratia and Trichoderma elicit ISR against different pathogens (Mandal and Ramesh 2011). BCA demonstrates disease suppression caused by fungal, bacterial, viral and in some cases insects and nematodes by eliciting such induced resistance.

It is evident that the Bacillus genus is an ideal biocontrol agent and the mostly exploited biopesticide to control plant diseases (Ongena et al. 2007). Pseudomonas also induces systemic resistance in plants. It was observed that Pseudomonas fluorescens protected tomato plants from the pathogens F. oxysporum and Phytophthora infestans by means of systemic resistance (Santoyo et al. 2012). Ongena et al. (2007) provided strong evidence of ISR mediated biocontrol of tomato gray mold disease by the use of potential B. subtilis, an efficient lipopeptide producer. Pseudomonas gladioli triggered defence molecules against Alternaria solani through induced systemic resistance in tomato (Jagadeesh and Jagadeesh 2009). Khan et al. (2012) assessed the ability of Paenibacillus lentimorbus to control early blight disease in tomato by inducing host resistance. Induction of systemic resistance has been established by the application of vermicompost biofortified with bioagents—Bacillus subtilis and Pseudomonas fluorescens against F. oxysporum by the accumulation of PAL, PO, PPO free phenol and SOD in tomato plants (Mj et al. 2017). B. cereus, Streptomyces cereus and S. marcescens were proved to be effective in host’s resistance against wilt disease by the activation of defence enzymes peroxidises (POX), polyphenol oxidases (PPO), glucanases (GLU), chitinases (CHI), phenylalanine ammonia-lyases (PAL) and lipoxygenases (LOX) (Gledson et al. 2014). P. fluorescens has also been reported as a strong BCA against the pathogen by inducing key enzymes POX, PPO and superoxide dismutase (SOD), β-1,3 glucanases (Dorjey et al. 2017). Reduced disease severity coupled with enhanced enzyme production elicited by B. subtilis, B. atrophaeus and Burkholderia cepacia mixtures indicated its mode of action for the vascular suppression through direct biocontrol and ISR (Shanmugam and Kanoujia 2011).

P. putida and P. syringe stimulated a systemic response against A. solani by inducing high rates of enzyme activity of PAL, PO, PPO as well as the accumulation of phenolics (Ahmed et al. 2011). Similarly, Chowdappa et al. (2013) reported that B. subtilis OTPB1 isolate was able to inhibit A. solani by enhanced systemic resistance. The defence-related enzymes, PO, PPO and SOD were significantly higher in inoculated tomato seedlings, compared to uninoculated control. Indigenous isolate P. fluorescens TK3 was recommended as the best biocontrol agent for early blight pathogen (Moges et al. 2012). The study reviewed that disease suppression of Pseudomonad was by induction of systemic resistance. Exopolysaccharides (EPS) are polysaccharides synthesized by bacteria which are secreted in the external environment. EPS helps to endure drought condition, protection from stress (Qurashi and Anjum 2012) and defence against phytopathogens (Tewari and Naveen 2014). The significant role of bacterial EPS as an elicitor for the induction of systemic resistance has already been reported in different crop species. It is reported that application of Bacillus EPS obtained from natural biofloc at 200 ppm could effectively reduce the wilt disease incidence (Thenmozhi and Dinakar 2014).

Hydrolytic enzyme production

Production of hydrolytic enzymes is an efficient mechanism to eradicate the pathogen growth through lysis of pathogenic cell wall. Different polymeric compounds present in fungal cell wall, such as cellulose, hemicelluloses, chitin, proteins and DNA can be degraded by producing lytic enzymes such as cellulase, chitinase, protease, etc. The cell wall degradation of fungal pathogens by the secretion of these enzymes is an antifungal activity aiding in the biocontrol of phytopathogens (Jadhav et al. 2017; Mabood et al. 2014; Aeron et al. 2011). The soil-borne fluorescent Pseudomonas has gained more attention in this regard because they can produce different kinds of cell wall degrading enzymes, such as chitinase, protease/elastase and β-1,3 glucanase (Kapoor et al. 2012). This mechanism helps to parasitize the phytopathogen directly.

Streptomyces sp. is a promising BCA which possess cellulolytic, chitinolytic and xylanolytic activity. They are identified as plant growth promoting and disease control agents in tomato (Da et al. 2008). Bacillus subtilis, B. cereus and B. thuringensis were reported to produce hydrolytic enzymes for the biocontrol of phytopathogen F. oxysporum. They produced swelling and curling in the hyphae which further caused the hyphal tip to burst (Jadhav and Sayyed 2016). Chitinase, β-1,3 glucanase and β-1,4 glucanase produced by Pseudomonas fluorescens and Bacillus subtilis were found to inhibit pathogenic fungi causing root rot disease in tomato crop (El-Gamal et al. 2016). Prasanna et al. (2013) reported that B. subtilis produced hydrolytic enzymes β-1,4 glucanase and chitosanase which were fungicidal to FOL. Evaluation of extracellular lytic enzymes viz. chitinase, β-1,3 glucanase, protease and cellulase from indigenous Bacillus sp. isolated from tomato rhizosphere provided potential bioresource for the benefit of the agricultural industry (Praveen et al. 2012). Seed bacterization and soil application of B. atrophaeus S2BC-2 reduced disease incidence in plants challenged with FOL and AS. Maximum induction of chitinase and β-1,3 glucanase were found in the leaf and root sample analysis (Shanmugam and Kanoujia 2011).

Application of PGPR has extended to remediate the contaminated soil enabling the plant to survive such stress conditions. The metal resistant PGPB have also been reported to produce enzymes that lyse the cell of the fungal pathogen (Ma et al. 2010). Besides the above-mentioned biocontrol mechanisms of several rhizobacterial strains, the effectiveness of these strains depends upon the host plant and soil characteristics. Moreover, their inherent capacities and rhizospheric competence also plays a major role in exhibiting their biocontrol traits (Gamalero et al. 2010).

HCN production

Biogenic cyanogenesis (HCN) has been found in rhizobacteria, by de novo synthesis (Rijavec and Lapanje 2017). This volatile antimicrobial compound is known for its role in disease suppression (Jain and Das 2016). HCN is likely to inhibit electron transport chain and energy supply to the cell eventually leading to cell death. It is also known to inhibit the action of cytochrome oxidase (Heydari and Mohammad 2010). This deleterious property allows PGPR to gain a competitive advantage over fungal pathogens and it can be further exploited in biocontrol of plant diseases (Ramette et al. 2003; Hayat et al. 2010). Sehrawat and Sindhu (2019) reviewed that rhizosphere inhabiting bacteria such as Bacillus and Pseudomonas produces HCN as their secondary metabolite. Furthermore, members of the genus Chromobacterium, Burkholderia, certain Rhizobia and Cyanobacteria were also reported to show bacterial cyanogenesis (Ahemad and Kibret 2014). However, fluorescent Pseudomonas is predominantly reported as HCN producer (Mishra and Arora 2018). Most studies shows the activity of HCN producing bacteria towards fungal pathogens (Siddiqui and Shaukat 2002; Ramette et al. 2006). The study of Islam et al. (2019) reported 44.99% disease inhibition of Fusarium wilt disease treated with Brevundimonas olei Prd2 which showed HCN production in vitro. Additionally, Lachisa and Dabassa (2016) reported that the growth reduction of FOL is due to the production of HCN by the isolate Pseudomonas sp. RhB-12. Furthermore, Someya et al. (2006) confirmed that the HCN-producing Pseudomonas fluorescens strain LRB3W1 played a key role in the inhibition of disease development by FOL.

Siderophore production

Iron is an essential micronutrient for all forms of life and is present in the soil in the form of Fe³⁺ or ferric ion predominantly, which is sparingly soluble. Hence, it is not readily assimilated by plants (Colombo et al. 2014). Plants can use siderophores produced by microorganisms for iron uptake (Shirley et al. 2011). Rhizobacteria produces siderophores that are low molecular weight iron-chelating compounds with great affinity and selectivity to bind and form a complex Fe(III) (Ferreira et al. 2019). It acts like a ligand that facilitates the sequestration and transportation of iron into the cell. This particular trait has drawn attention in the recent years and the identification of such siderophore producing PGPR along with its in vivo testing has been reported (Ghavami et al. 2017; Liu et al. 2017; Sabate et al. 2017). Siderophores are stable complexes and different kinds of siderophores are reported including hydroxamates, phenolcatecholates and carboxylates. (Kundan et al. 2015). Siderophore mediated iron transfer system is better studied in gram-negative PGPR transport systems rather than gram-positive transport systems. Among 500 different types of siderophores known, 270 have been structurally characterized (Hider and Kong 2010). Siderophores have been suggested to be an eco-friendly alternative to harmful pesticides (Schenk et al. 2012).

Because siderophores produced by PGPR show greater affinity for iron as compared to fungal pathogens, they have a competitive advantage for efficiently suppressing phytopathogen proliferation (Schippers et al. 1987). Eventually, the fungal pathogen under iron scarcity are unable to proliferate and are excluded from the ecological niche. Hence, siderophore production is a desirable characteristic of PGPR as a biocontrol agent. Among the various bacterial siderophores, those produced by Pseudomonas are known to be with higher affinity (Beneduzi et al. 2012). There are various reports on biocontrol efficiency of siderophore producing PGPR. Arya et al. (2018) reported that siderophore producing Pseudomonas strains SPs9 and SPs20 suppressed Fusarium wilt of tomato under field conditions. Streptomyces strain SNL2 with siderophore producing ability was also reported which reduced wilt disease incidence by 88.5% (Goudjal et al. 2016). Segarra et al. (2010) also reported that Trichoderma asperellum producing siderophores restrict FOL. Similarly, Pseudomonas aeruginosa strains JO and JO7, capable of producing siderophore inhibited AS and FOL (Paramanandham et al. 2017). Bacillus subtilis SBMP4, Lysinibacillus fusiformis NBRC 15717 and Achromobacter xylosoxidans NBRC15126 produced hydroxamate siderophore which had a vital role in suppression of early blight in tomato (Attia et al. 2020).

Consortium of BCA

Inconsistent performance of BCA is the primary barrier for its commercialization. A single organism may fail during adverse environmental conditions, so a combination of more than one BCA is appreciated. There is a chance for increased, neutral and decreased biocontrol efficiency when more than one BCA is used together. Moreover, they can easily colonize the rhizosphere. It is reported that, consortium of BCA helps to reduce disease incidence through synergistic action. Kannan and Sureendar (2009) proved the efficiency of consortial treatment in growth promotion and wilt resistance of tomato. Unfortunately, the interactions involved were not clearly determined and hence they need further clarification. A synergistic study among biocontrol agents Bacillus subtilis and Pseudomonas fluorescens displayed increased plant growth promotion more than its biocontrol activity on early blight disease (Suleiman et al. 2017). A thorough understanding of biocontrol mechanisms is therefore essential for employing this method in plant disease control.

These drawbacks have led to a slow progress in the successful development and marketing of bio-formulations. However, the use of a mixture of BCA for biocontrol were highly encouraged in the recent decades because it helped to defeat the efficacy problems. Thilagavathi et al. (2007) reported that a combination of BCA Pseudomonas fluorescens pf1 and Trichoderma viride tv1 improves the management of dry root rot in green gram. The activity of defence enzymes was significantly greater in treated plants receiving consortium treatments.

Commercialisation of BCAs

Commercialization of BCA is a multistep process that involves isolation and screening of potential antagonistic bacteria from natural ecosystems, testing the efficiency of the isolate in the field, mass production, formulation, toxicity studies, delivery, compatibility, registration and release (Junaid et al. 2013). Recent reports claims that bioformulations were prepared from BCAs such as Bacillus cereus, Pseudomonas rhodesiae, Pseudomonas chlororaphis, Pseudomonas fluorescens, Bacillus coagulans which acts as both nutrient and growth enhancer to selected crops (Kalita et al. 2015; Jorjani et al. 2011). Bioformulations are defined as the preparation of microorganism(s) that may be a partial or complete substitute for chemical fertilization/ pesticides (Arora et al. 2010). In this approach, the degree of success depends upon the consistent broad-spectrum action, economical and viable market demand, safety, stability, longer shelf life, low capital costs and easy availability of carrier materials. Bioformulations consists of an active ingredient i.e. a viable organism which may be a microbe/spore and an inert carrier material that supports the active ingredient/cells (Mishra and Naveen 2016). Selection of a superior carrier material is essential as it is expected to meet the prerequisites, such as high water holding capacity, high water retention capacity, no heat production while wetting condition prevails, sterility, chemically and physically uniform in nature, biodegradable, non-polluting and nearly neutral pH that supports bacterial viability (Singh et al. 2015). Available carrier materials are talc, sawdust, fuller’s earth, rice husk, sugar cane, bagasse, charcoal and wheat bran (Singh et al. 2014).

Before developing a biocontrol agent into a commercial product, an intensive knowledge on several factors such as phytopathogen species, type of hosts it attacks, epidemiology of the disease, resistance of phytopathogen and environmental conditions under which the BCA will be used must be known (Carmona-Hernandez et al. 2019). Talc based formulation of B. subtilis PSIRB2 and P. aeruginosa 2apa were found to significantly exhibit disease protection traits against fusarium wilt and early blight diseases of tomato (Gowtham et al. 2017). Similarly, talc-based formulation of P. fluorescens delivered through farmyard manure and vermicompost were tested against Fusarium oxysporum and Alternaria solani (Kaur et al. 2016).

Unfortunately, the successful establishment of such biologicals in agriculture is hampered by the inadequate knowledge about the plant–microbe interactions, though there were some progress in the past decade (Ravensberg 2015). For a fruitful PGPR inoculum, the chosen strain ought to colonize the plant roots, should be able to persevere in the rhizosphere and ought not to be a potential hazard for the environment and human wellbeing. Certain bacterial strains display promising impacts in advancing plant development in lab conditions yet fail in field trials because of their insufficiency in colonizing the rhizosphere and plant roots. These strains are unable to adjust with the plant microenvironment and consequently, incapable to rival with the current local bacterial network for foundation and perseverance in the soil.

Henceforth, investigating the components of PGPB would uncover new experiences to structure systems for improving the efficacy of biocontrol agents.

Conclusion

The present review indicates that plant growth-promoting rhizobacteria (PGPR) not only triggers different biological promotional effects on tomato plant growth parameters, but also helps in protecting the plant from several pathogens by acting as biocontrol agents. To replace chemical pesticides with the system of a biopesticide, it is ought to be progressively more effective and economical. Before commercialization, molecular analysis can result in stabilizing the effects of PGPR in biological control and possible risk assessments. Effective usage of PGPR for disease reduction or crop protection within the future will demand a rational selection of organism as well as technical enhancements in upscaling and formulation techniques. Genetic engineering of PGPR may intensify the expression of plant growth and health-promoting genomic products. Therefore, a single bacterial strain or a consortium with variable attributes will mitigate the pathogen assault and promote plant growth to encourage the producers. It has become clear that PGPR strains employ several mechanisms to act as an effective biocontrol agent, although studies ought to be centered on the relative contribution of every mechanism responsible for its significant biocontrol activity. A thorough understanding of the plant–microbe interactions and processes as well as exploiting the microbial ecology in the soil and rhizosphere would help us reveal the multiple facets of disease suppression by these biocontrol agents. Moreover, carefully controlled field trials of tomato plants inoculated with PGPR inoculants is obligatory for maximum commercial exploitation of these strains. In conclusion, the success of microbial inoculant-producing industries, notably those utilizing PGPRs, will depend on measures including product marketing and extensive research. In addition, for better fermentation and formulation processes, the optimization of PGPR strains will be required to introduce them in the agriculture industry.

Author contributions

SK and SV conceptualized and designed the manuscript; MSJ reviewed and approved the manuscript.

Funding

The first author is very much thankful to the University Grants Commission, Government of India for the financial support in the form of SRF, Vide Sr. No.2061530793.

Compliance with ethical standards

Conflict of interest

The authors declare that there are no conflicts of interest regarding the publication of this manuscript.