Introduction

Common bean (Phaseolus vulgaris L.) is one of the most important pulse crops having a great human nutritional importance for their high seed protein content (Celmeli et al. 2018) and was reported as the second source of calories after corn worldwide (Broughton et al. 2003). Therefore, common bean (CB) is regarded as a critical component to combat malnutrition for hundreds of millions of smallholder farmers and people especially in developing countries (Meziadi et al. 2016). Despite this importance, CB production is severely affected by various diseases throughout the plant cycle mainly by those caused by fungi (Meziadi et al. 2016; Martins et al. 2018). It was reported that fungal diseases cause severe losses (20–100%) to yield and quality of CB worldwide depending on the occurrence and severity of the individual and collective diseases occurring in the same field, production systems, environmental conditions, and management practices used (Singh and Schwartz 2010). For the time being, the most harmful fungal disease in CB plantation is root rot (Paparu et al. 2018). The CB root rot (RR) disease is responsible for losses estimated at 221.000 metric tons per year in sub-Saharan Africa (Paparu et al. 2018) and is mainly caused by fungal species as Fusarium sp., Pythium sp., Macrophomina sp., and Alternaria sp. (Singh and Schwartz 2010; Vural and Soylu 2012; Paparu et al. 2018). These phytopathogenic fungi are also reported as serious foliar and seedborne pathogens in CB (Singh and Schwartz 2010; Vural and Soylu 2012; Marcenaro and Valkonen 2016). A recent research investigation conducted in Tunisia showed that CB-RR is a major widespread disease affecting this grain legume (Sendi et al. 2019). The study attributed the RR disease mainly to the genera Fusarium, Macrophomina, and Alternaria, and their aggressiveness was confirmed (Sendi et al. 2019). In Tunisia, CB is a favorite pulse crop for the majority of people. However, this grain legume is cultivated only in limited areas in sub-humid regions located in the north of the country and its production is limited and fluctuates strongly (Mrabet et al. 2005; Sendi et al. 2019). Fungal diseases are among the main limiting factors that drastically reduce the CB production in Tunisia (Sendi et al. 2019). Thus, effective strategies to control such fungal pathogens are urgently needed. Notoriously, chemical pesticides may provide effective protection against fungal diseases affecting various crops; however, their excessive and/or improper use has an adverse environmental impact and raises health concerns for humans and animals (Nicolopoulou-Stamati et al. 2016). Therefore, the development and implementation of biological control methods, based on using antagonistic microorganisms against plant pathogens, are gaining a growing interest as an eco-friendly alternative for providing important long-term protection to agricultural crops. Among biocontrol agents, bacteria are considered as the most prospective group of microorganisms demonstrating promising features to be considered in plant bioprotection strategies (Gond et al. 2015; Mrabet et al. 2015; Torres et al. 2017; Vurukonda et al. 2018). The biocontrol activity against plant pathogens is prompted by several mechanisms exhibiting antifungal activity such as production of hydrogen cyanide (HCN), hydrolytic enzymes as chitinase, siderophore, cyclic lipopeptides by some bacterial species (Gond et al. 2015; Keshavarz-Tohid et al. 2017; Bahroun et al. 2018), or improving plant fitness and growth as by indole-3-acetic acid (IAA) production and phosphate solubilization (Van Lenteren et al. 2018). Those bacterial properties are nowadays regarded as interesting traits of performance in the strain selection scheme.

Regarding the severity of the RR disease in CB caused by Fusarium sp., Macrophomina sp., and Alternaria sp. phytopathogenic fungi (Sendi et al. 2019), this study is conceived to search for potential biocontrol agents among the CB endophyte and rhizospheric bacteria. Additional traits of performance as siderophore and IAA production, phosphate solubilization, chitinase and xylanase activity, and the detection of cyclic lipopeptide biosynthetic genes were analyzed. Obviously, the present study represents the first investigation on the biocontrol of RR fungal disease in CB using the whole CB microbiome and targeting three major fungal pathogens threatening almost various crops as highly phytopathogenic strains of Fusarium sp., Macrophomina sp., and Alternaria sp.

Materials and methods

Fungal strains and growth conditions

Fusarium sp. strain PVF26 (NCBI GenBank accession KU831515), Macrophomina sp. strain PVF32 (NCBI GenBank accession KU831521), and Alternaria sp. strain PVF1 (NCBI GenBank accession KU831490) are used in this study. The fungal strains had been previously isolated from field-grown and infected CB plants from Tunisia and reported to get severe aggressiveness on host plants (Sendi et al. 2019). The fungal strains were grown on potato dextrose agar medium (Biolife Italia, ref. 4019352) at 24 °C, stored at 4 °C, and monthly transplanted onto PDA medium.

Bacterial strains and growth conditions

Healthy CB plant samples were harvested at flowering stage from a field in Boucharray region (northeast of Tunisia) and used to isolate root endophytic and rhizospheric bacterial strains. Collected plants represented three different points from the field, and from each one, 3 whole plants were sampled.

Isolation of bacteria from roots

The isolation of endophytic root bacteria was performed according to the protocol of Kelemu et al. (2011). Briefly, healthy CB roots from various plants were cut into small pieces of 1 cm long and then disinfected with 1% sodium hypochlorite solution for 2 min, then with 70% ethanol for 1 min, and 3–4 times washed with sterile distilled water. Each root fragment was then crushed in 1 ml sterile distilled water using sterile glass rod. A volume of 100 μl were taken from each dilution suspension (10−1 to 10−5), spread on Petri dishes containing Luria–Bertani (LB) agar medium (Miller 1972), and incubated at 28 °C for growing colonies. Forty-five pure bacterial colonies representing the various morphologies observed from various root fragment samples were transplanted separately and purified.

Isolation of rhizospheric bacteria

The rhizosphere linked to roots of healthy CB plants—representing the three sampling sites—was racked up separately using sterile scalpel and put into flasks containing autoclaved LB broth and allowed to incubate in a shaking incubator at 28 °C for 2–3 h. Subsequently, dilutions (10−1 to 10−5) were made in sterile distilled water and 100 µl of the bacterial suspension was plated on LB agar medium. Plates were, then, incubated at 28 °C and time-checked for colony growth. Forty-five bacterial colonies, representing the morphological variability from various isolating samples, were purified separately and kept in LB medium.

Screening of CB root microbiome for antagonism

The bacterial collection was screened in a dual culture method with the fungal strains, in order to search for the most antagonistic bacterial strains. A fungal plug disk (7 mm of diam.) was deposited in the center of PDA Petri dishes using a sterile punch. Then, a pure culture of each bacterial isolate was plated on a continuous streak of 1.5 cm from the right periphery of the Petri dish. A second streak of the same bacteria was plated in the same way on the left side of the plate. Three replicates were considered for each bacterial strain, and the percentage of inhibition was calculated using the following formula (Mrabet et al. 2015):

$${\text{Growth}}\;{\text{inhibition}}\,\left( \% \right) = \left[ {A - B/A} \right] \times 100;$$

where A is the diameter of fungal growth in the control and B is the distance of fungal growth in front of each of the two bacterial streaks.

Molecular identification of bacterial strains

DNA was extracted from TSB fresh culture of each bacterial isolate after incubation for 24 h at 28 °C in orbital shaking at 150 rpm. The total genomic bacterial DNA was extracted using the DNA extraction Qiagen Kit (DNeasy UltraClean Microbial Kit), and the amplification of the 16S rDNA genes from 12 antagonist bacterial isolates was performed using primers fD1 (5′-GGA GAG TTA GAT CTT GGC TC-3′) and rD1 (5′-AAG GAG GTG ATC CAG CCGC-3′) (Weisburg et al. 1991). The amplification program was based on an initial denaturation at 94 °C for 5 min, then 30 cycles for 1 min of denaturation at 94 °C, 1 min of annealing at 55 °C and extension of 2 min at 72 °C, and a final extension at 72 °C for 7 min. The PCR amplifiers were migrated in agarose gel (1%) in TAE migration buffer for 30 min at 100 volts, and then, the gel was immersed in an ethidium bromide solution at 10 mg/l. The DNA bands were visualized under UV and photographed using an UV transilluminator imager (UVITEC N° 092586). The amplified fragments were cut and purified from agarose gel (1%) using a PCR purification kit (Biobasic Inc. EZ-10 spin column DNA Extraction Kit) and sent to Macrogen Europe (https://dna.macrogen.com/eng/) for sequencing step. Then, the DNA sequences were blasted, bacterial strains were identified (https://blast.ncbi.nlm.nih.gov/) and deposited in the Genbank database, and accession numbers were attributed.

Research for PGPR activities in selected bacterial strains

Screening for indole-3-acetic acid production (IAA)

The production of IAA by bacterial strains was carried out according to Bano and Musarrat (2003). Briefly, a single colony from an overnight bacterial culture was streaked onto LB agar broth containing 2 mg/ml l-trytophan. These cultures were incubated at 30 °C with shaking at 125 rpm for 3 days and then harvested by centrifugation at 12,000×g for 15 min at 4 °C. One ml of the supernatant was mixed with 2 ml of Salkowski reagent (2% 0.5 M FeCl3 solution in 35% perchloric acid), and the appearance of a pink color indicated IAA production.

Siderophore production

The siderophore production was assessed using the chromeazurol (CAS) agar assay, as described by Schwyn and Neilands (1987). Wells were made on the CAS medium, and 100 μl of each bacterial suspension was incubated in the dark for 2 days. Positive results were indicated by the formation of a light halo around the colonies, showing a visual change in color from dark blue to yellow. Each test was performed in triplicate.

HCN production

Bacterial strains were screened for HCN production using the method of Feigl and Anger (1966). The bacterial isolates were streaked on Luria–Bertani medium (LB). A Whatman filter paper was placed at the top of the plate. The plates were sealed with parafilm and incubated for 4 days at 30 °C. Production of HCN was indicated by the development of blue color.

Phosphate-solubilizing activity

To assess the phosphate-solubilizing activity by bacterial strains, 10 ml of NBRIP (National Botanical Research Institute Phosphate) broth medium which contained the following ingredients (g/l): glucose, 10.0; tricalcium phosphate (TCP), 10.0; MgCl2.6H2O, 5.0; MgSO4.7H2O, .25; KCl, 0.2; (NH4)2SO4, 0.1—was added to 100 μl of bacterial suspensions (108 CFU/ml). Then, the suspension was kept in a shaking incubator (150 rpm at 30 °C) for 7 days. Finally, the volume was centrifuged at 12.000 rpm for 10 min, and the supernatant was recovered. The amount of solublization of phosphate was determined by the vanadomolybdate method (Murphy and Riley 1962).

PCR detection of the lipopeptide biosynthetic genes in the antagonistic bacterial strains

The presence of lipopeptide biosynthetic genes, including the genes of surfactin, iturin A, fengycin, and bacillomycin D, has been investigated for 12 selected antagonistic bacterial strains. The bacterial strains were grown, and the total DNA was extracted as previously described. The PCR amplification of the lipopeptide genes was performed using initial denaturation for 3 min at 94 °C followed by denaturation of 35 cycles (1 min at 94 °C), annealing (30 s at 60 °C), extension (1 min 45 s to 72 °C), and a final extension at 72 °C for 6 min. Five primers were used for lipopeptide genes (Gond et al. 2015).

Biocontrol potential of selected bacterial strains against Fusarium sp., Macrophomina sp., and Alternaria sp. under greenhouse conditions

Common bean seed disinfection and germination

CB cv. Coco blanc seeds were surface-disinfected with mercury chloride solution (HgCl2 0.2%), 5 times washed with sterile distilled water, then soaked with a bacterial suspension (108 cfu/ml) for 15 min, and incubated overnight at 25 °C. Then, the CB seeds were sown in a mix of sand/peat (1:2).

Preparation of the fungal inoculums

Inoculum of the fungal strains was prepared in sorghum grains according to the protocol of Scandiani et al. (2011). From a PDA fresh fungal culture, 10 disks (0.7 cm diam.) were mixed in a 1-l Erlenmeyer flask containing 100 g of autoclaved sorghum grains and 50 ml of water. Cultures were incubated in complete darkness for 1 week at 25 °C.

Experimental design of the biocontrol assay

The experiment consisted of 4 treatments with three replicates for each one as follows: (1) plants inoculated with each fungal strain, (2) plants inoculated with fungal strains and fungicide, (3) plants co-inoculated with each fungal strain and one bacterial strain, and (4) control non-inoculated and non-treated plants. The fungal strains were used in the biocontrol assay; Fusarium sp. strain PVF26, Macrophomina sp. strain PVF32, and Alternaria sp. strain PVF1. Each Fungal inoculum produced in sorghum grains was mixed with sterile sand/peat mixture (1:2) in order of 15 g of each sorghum fungal inoculum per 1 kg of sand/peat mixture. To obtain homogenous inoculation for each fungal strain, the sand/peat mixture was treated with fungal inoculum in the same recipient, and then, plastic pots of 1 l were filled aseptically. The CB plantlets were grown in the plastic pots in order of 1 plant per pot and were irrigated with sterile water as needed. This experiment was conducted under controlled conditions in greenhouse at 25 °C, with a photoperiod 16 h/8 h. The CB plants were harvested after 30 days post-plantation, and root rotting level was recorded with a three scored scale in which “0” means no rotting symptoms, “1” moderate rotting symptoms, and “2” severe rotting symptoms. Shoot dry weight was measured and analyzed.

Statistical analysis

For each parameter, statistical analyses of mean values and variance were performed using SPSS software (version 21.0).

Results

Screening for antifungal activity among CB root microbiome

Antibiosis was checked for 90 endophytic and rhizospheric bacterial isolates against Fusarium sp. strain PVF26, Macrophomina sp. PVF32, and Alternaria sp. strain PVF1 in dual cultures on PDA medium. Among this bacterial collection, 35 isolates showed a weak (INH < 20%) or absence of antagonistic activity, 43 isolates exhibited a moderate antifungal activity (20% < INH < 40%), and 12 bacterial isolates were able to inhibit at least one among the three fungal strains at more than a percentage of 40%. The 12 antagonistic bacterial isolates were retained for molecular identification and for further studies. In Fig. 1, an illustration of the inhibition of the Fusarium sp. strain PVF26 by the bacterial isolates PVB17 is shown.

Fig. 1
figure 1

Inhibition of Fusarium sp. (PVF26) by B. amyloliquefaciens (PVB17). aFusarium sp. strain PVF26, bFusarium sp. strain PVF26 in a dual culture with B. amyloliquefaciens strain PVB17

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Molecular identification of isolated bacteria

Molecular identification using 16S rDNA sequence of the highly antagonistic bacterial isolates indicated that the majority of the bacterial strains belong to the genus Bacillus (58.33%), including Bacillus velezensis (B.vel) PVB18, Bacillus amyloliquefaciens (B.amy) PVB17, Bacillus halotolerans (B.hal) PVB10 and PVB16, Bacillus mojavensis (B.moj) PVB15, Bacillus methylotrophicus (B.met) PVB14, Bacillus subtilus (B.sub) PVB12. One isolate from the following species: Pseudomonas frederiksbergensis (P.fre) PVB9, Pseudomonas lini (P.lin) PVB19, Agrobacterium fabrum (A.fab) PVB8 and two isolates of Glutamicibacter halophytocola (G.hal) PVB11 and PVB13 were detected (Table 1).

Table 1 Identification of the antagonistic bacterial strains by sequencing of the 16S rDNA region. The NCBI accession number was attributed for each bacterial strain
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Antifungal activity of the identified bacterial strains

The percentage of inhibition of fungal strains by bacterial ones is given in Table 2. Results showed that 5 bacterial strains (B.hal PVB16 and PVB10, B.met PVB14, B.amy PVB17, and B.vel PVB18) are able to inhibit Fusarium sp. strain PVF26, Macrophomina sp. strain PVF32, and Alternaria sp. strain PVF1 at more than 50% of their control growth. Bacterial strains B.sub PVB12 and B.moj PVB15 are able to inhibit at more than 50% only of Macrophomina sp. PVF32 and Alternaria sp. PVF1. However, their inhibition of Fusarium sp. PVF26 is of 29% and 41%, respectively (Table 2).

Table 2 Percentages of the in vitro growth inhibition of Fusarium sp. strain PVF26, Macrophomina sp. strain PVF32, Alternaria sp. strain PVF1 using 12 preselected common bean endophytic and rhizospheric bacterial strains
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Possible plant growth promotion activity in selected antagonistic bacterial strains

Siderophores production, phosphate-solubilizing activity, HCN and IAA production, and presence of xylanase and chitinase in 12 bacterial strains are given in Table 3. Results showed that bacterial strains have a positive result for the production of siderophores with a high production noticed in B.amy PVB17 and B.sub PVB12. Phosphate-solubilizing activity ranged from 186 µg/ml for B.vel PVB18 to 399 µg/ml for B.met PVB14.

Table 3 Biochemical characterization of bacterial strains showing antagonistic activities toward phytopathogenic fungi
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For HCN production, only P.fre strain PVB9 and P.lin strain PVB19 showed a positive result. Among the tested bacterial collection, the xylanase was produced by B.hal PVB10, B.met PVB14, B.moj PVB15, B. hal PVB16, B.amy PVB17 and B.vel PVB18. The IAA is produced by A.fab PVB8, P.fre PVB9, G.hal PVB11, B.sub PVB12, B.moj PVB15, B.amy PVB17 and B.vel PVB18. Chitinase was produced by 41% of the bacterial strains as B.sub PVB12, B.met PVB14, B.moj PVB15, B.amy PVB17 and B.vel PVB18 strains (Table 3).

Biocontrol of Fusarium sp., Macrophomina sp., and Alternaria sp. on common bean plants

The biocontrol assay was performed considering three fungal strains while inoculating with 12 bacterial strains, demonstrating the strongest inhibitory effect. The growth and diseases parameters of CB plants were studied after 4 weeks of culture under greenhouse conditions. The disease parameter consists on scoring the root rotting level in a scale of three scores as previously described. Results showed that when inoculating Fusarium sp. PVF26, Macrophomina sp. PVF32, and Alternaria sp. PVF1, the whole developed roots presented high rotting score (2) (data not shown). However, plants co-inoculated with each of the fungal and antagonistic bacterial strains showed reduced root rotting level to score “1” for bacterial strains PVB12, PVB13, and PVB15 and to score “0” (complete absence of root rot) for the remaining antagonistic bacterial strains (data not shown). Figure 2b illustrates the negative effect of Fusarium sp. strain PVF26 on CB plants and the plant growth improvement associated with the biocontrol bacterial strain B.amy PVB17 (Fig. 2a). The measurement of shoot dry weight of CB plants in the biocontrol assay using the three fungal strains and the 12 bacterial strains is shown in Figs. 3, 4 and 5. Results revealed that the inoculation of Fusarium sp. strain PVF26 causes a decrease of 44% in the shoot dry weight of CB plants compared to the control. Interestingly, the inoculation of CB plants with bacterial strains re-established the plant growth and even enhanced the shoot dry weight up to 217% for B.hal strain PVB10 against Alternaria sp. strain PVF1, up to 194% for B.vel strain PVB18 against Fusarium sp. strain PVF26, and up to 182% for G.hal strain PVB11 against Macrophomina sp. strain PVF32 in comparison with the control plant growth.

Fig. 2
figure 2

Common bean cv. Coco blanc growth in the biocontrol assay of Fusarium sp. strain PVB26 using the antagonistic B. amyloliquefaciens strain PVB17. aFusarium sp. + B. amyloliquefaciens PVB17, bFusarium sp., cFusarium sp. + fungicide and d control

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Fig. 3
figure 3

Effect of bacterial strains on the biocontrol of Fusarium sp. strain PVF26 in common bean (shoot dry weight). For each column, the values followed by the same letter are not significantly different according to the Tukey HSD test at p = 0.05

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Fig. 4
figure 4

Effect of bacterial strains on the biocontrol of Macrophomina sp. strain PVF32 in common bean (shoots dry weight). For each column, the values followed by the same letter are not significantly different according to the Tukey HSD test at p = 0.05

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Fig. 5
figure 5

Effect of bacterial strains on the biocontrol of Alternaria sp. strain PVF1 in common bean (shoots dry weight). For each column, the values followed by the same letter are not significantly different according to the Tukey HSD test at p = 0.05

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Detection of the lipopeptide biosynthetic genes in the antagonistic bacterial strains

Among the 12 antagonistic bacterial strains yet selected, 6 strains were able to carry out the genes encoding cyclic lipopeptides including fengycin, bacillomycin, iturin, and surfactin (Table 4). These bacteria can produce at least one or more lipopeptides that may be involved in the biocontrol activity. B. halotolerans strain PVB16 carried out genes responsible for iturin and fungycin production. In the B. velezensis strain PVB18, only genes encoding surfactin and iturin production were detected. The B. amyloliquefaciens strain PVB17 and B. methylotrophicus strain PVB14 carried the genes encoding bacillomycin, iturin, and surfactin production.

Table 4 PCR detection of lipopeptides biosynthetic genes in the selected antagonistic bacterial strains
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Discussion

In this study, pathogenic strains of Fusarium sp., Macrophomina sp., and Alternaria sp. demonstrating aggressiveness on CB roots in a previous study (Sendi et al. 2019) were used. The objective was to search for potential biocontrol agents from CB root microbiome to fight against those soilborne phytopathogens. Among a bacterial collection of 90 endophytic and rhizospheric strains, 12 strains exhibited a potential antagonistic activity against those pathogenic fungi in vitro. Results showed that these bacterial strains belong to the genera Bacillus, Pseudomonas, Agrobacterium, and Glutamicibacter. The level of inhibition reached a percentage of 71% in comparison with the control fungal growth. Results showed that all Bacillus spp. strains are able to inhibit the three fungal species with, generally, more than 50% of their control growth. Previous studies reported the efficient antifungal activity of Bacillus spp. strains against diverse phytopathogenic fungi (Durairaj et al. 2018; Fuentes et al. 2018; Khan et al. 2018). Nevertheless, the use of various Bacillus species in this study against the three pathogenic fungi causing CB root rot is a significant enrichment to the previous reports. Pseudomonas spp. strains were able to inhibit at least one of the three fungal strains used in this study; however, the percentage of inhibition is not exceeding the value of 43%. The antifungal activity of Pseudomonas spp. strains was previously reported and attributed to the ability to produce various bioactive metabolites inhibiting the growth of pathogenic fungi (Mrabet et al. 2015; Srinivasa et al. 2015; Durairaj et al. 2018). Interestingly, we showed that strains of the genera Glutamicibacter and Agrobacterium exhibited a strong antifungal activity on the three pathogenic fungal strains. According to bibliographic reports, no bacterium of the genus Glutamicibacter and Agrobacterium has been reported to have an antagonistic activity against pathogenic fungi of CB so far. The biochemical characterization of the bacterial strains based on hydrolytic enzymes as chitinase and xylanase showed that strains of the genus Bacillus are able to produce these enzymes. This finding is in agreement with those of Saber et al. (2015), reporting their key role in degrading the walls of phytopathogenic fungi and in plant bioprotection. On the other hand, we revealed that the antifungal of Pseudomonas sp. strains is possibly due to the production of HCN and siderophores. These two components are known to be involved in bacterial antifungal activity as previously reported (Beneduzi et al. 2012). However, Negi et al. (2017) reported that some strains of Pseudomonas are able to synthesize chitinases playing a key role in fungal cell wall lysis. Thus, hydrolytic enzymes production may be a strain dependant property. The strain of A. fabrum PVB8 producing high amounts of IAA was associated with an increase in the plant growth. Such finding corroborates with previous data on the role of IAA production in the plant growth property of plant growth rhizobacteria (Mohite 2013). B. amyloliquefaciens strain PVB17 produced the highest amount of IAA among all bacterial strains. Taking into account different results of CB-associated bacteria, we showed that Bacillus spp. strains manifested superiority in exhibiting various plant growth promoting activities. In our study, we have shown that B. amyloliquefaciens PVB17, B. halotolerans PVB10, and B. velezensis PVB18 are among the bacteria with high biocontrol potential. This is in concordance with previous results reporting the effectiveness of Bacillus species in the biocontrol of fungal diseases in different plants (Torres et al. 2017; Durairaj et al. 2018). This biocontrol effectiveness was associated with the detection of the antifungal cyclic lioppeptide genes responsible for the production of fengycin, iturin, bacillomycin, and surfactin playing key roles in controlling fungal growth and infection of host plants as previously reported (El Arbi et al. 2016). Recent investigation demonstrated the effectiveness of B. amyloliquefaciens strains to control CB root rot diseases caused by Rhizoctonia solani (Martins et al. 2018). However, this study remains the first investigation reporting the effectiveness of Bacillus species to control Fussarium sp., Alternaria sp., and Macrophomina sp. in CB plants.

Conclusion

This study represents the first investigation on the role of CB root microbiome in the biocontrol of RR disease and to act as plant growth promoters. Among the bacterial collection used, 13% exhibited potential antifungal and biocontrol activities of Fusarium sp., Macrophomina sp., and Alternaria sp., reducing fungal disease incidence and enhancing plant growth. The most efficient bacterial strains are assigned to Bacillus spp., Pseudomonas spp., Glutamicibacter spp., and Agrobacterium spp. The bacterial strains displayed of considerable PGPR activities, such as phosphate solubilization, siderophore, IAA and HCN production. Considering various analyzed traits, the study proved the superiority of Bacillus species among various bacterial species in expressing both biocontrol and plant growth promoting activities. More challenges will arise as attempts are made to change from the use of chemicals to sustainable agricultural practices. Hence, the CB root microbiome selected bacterial strains will be the core of this perspective.