The horticultural sector improves land use for food and promotes crop diversification, employment generation and poverty alleviation. Among the horticultural crops, fruits and vegetables are the most numerous crops; however, there are also flowers, aromatic plants, spices, and plantation crops. There are many examples of different crops that improved their yield or quality after the application of a biological control agent, including vegetable, fruit, and ornamental plants [4].

One of the most important aspects of achieving the good quality and yield of horticultural crop production is the availability of nutrients in the soil. For this reason, over the years, chemical fertilizers have played the main role in increasing the productivity of crops. This practice has led to several problems, such as environmental pollution and therefore impacts on human health. The best green alternative has been the development of biofertilizers, which are supported by microorganisms that are nitrogen fixers, solubilizers of phosphates, and phytohormones and growth promoters. All of them use different strategies to facilitate plant growth. Biofertilizers have been evaluated in a wide variety of crops, including rice, cucumber, wheat, sugarcane, and corn, among others [5]. The application of biofertilizers in horticulture implies the improvement of the yield and quality of crops. Beneficial microorganisms improve the rhizospheric region, making nutrients available for plants or producing phytohormones.

Bacillus spp. use direct and indirect mechanisms that can act simultaneously in plant growth. The direct mechanisms include achievement of nutrient supplies and modulation of plant hormone levels. The indirect mechanisms include the secretion of chemical compounds to act against phytopathogens or the induction of pathogen resistance [6].

There are several examples of the role of Bacillus as a biofertilizer. Among vegetables, some examples are included. The yield of mustard and tomato was increased after applying Bacillus- or Trichoderma-based fertilizers [7,8]. By applying individual inoculants of Bacillus, Brevibacillus, and Rhizobium, the macro- and micronutrient content in broccoli was improved [9]. Bacillus and Pseudomonas improved the biomass of lettuce seedlings [10]. Similarly, other crops such as spinach and flax, also exhibited improvements after treatment with Azotobacter, Bacillus, or AMF [11,12]. B. subtilis was applied as a biofertilizer to increase cotton yield [13]. Treatment with B. subtilis and B. megaterium resulted in growth and yield increasement, and improved seed quality of maize [14].

Bacillus strains have been intensively used against Fusarium [15,16,17,18,19] and Aspergillus [20,21,22] species. Also, Bacillus-based biocontrol has been used to decrease mycotoxin contamination in crops [23,24,25]. The studies devoted to lower mycotoxin content in GM-Bt plants (maize) [26,27,28] should also be mentioned.

Generally, fruit crops have received more attention than vegetables and ornamental crops. The application of Bacillus strains has reduced the crop maturation days of strawberry plants [29]. The inoculation with the commercial product Rhizocell C containing B. amyloliquefaciens improved the photosynthetic capacity of strawberry plants, increasing the fruit yield and biomass compared to other commercialized products [30]. The inoculation with B. amyloliquefaciens has improved the yield of banana, infested with the fungal disease, under field conditions [31]. A liquid B. subtilis commercial microbial fertilizer was applied to citrus groves of the Tarocco blood orange (Citrus sinensis), exerting positive effects on fruit quality [32]. Bacillus spp. was applied as a biofertilizer to treat nutmeg seeds, showing an improvement in the growth of nutmeg seedlings [33].

Bacillus species also use indirect mechanisms to inhibit plant pathogens. The genus Bacillus spp. secretes several secondary metabolites that act against phytopathogens causing plant diseases, promoting plant growth [34,35,36,37]. In addition, these bacteria induce systemic resistance in plants [38]. There are some mechanisms to control pathogens causing plant diseases. Some of these mechanisms include (a) competition; (b) antibiosis; (c) predation or parasitism; and (d) induction of host plant resistance [39].

Biofungicides have several advantages in use against the crop pests compared with chemical pesticides. The first is that they have a strong selectivity, being safe for humans and animals. Second, they are safe for the environment since they are derived from natural ecosystems. Moreover, they are easily decomposed by sunlight, plants, or various soil microorganisms, completing a natural life cycle. This guarantees that these products do not persist long in the environment, which reduces the risk to non-target organisms [37]. Bacillus-based biopesticides control crop pests, improving soil quality and health, and the growth, yield, and quality of crops [40].

B. thuringiensis (Bt) has been the most used and commercialized biopesticide [41]. It has been widely used in agriculture since it is eco-friendly and safe for non-target organisms, but it is effective and highly specific against insect pests affecting crops belonging to the Lepidopteran, Dipteran, and Coleopteran insect orders [41]. Many commercial products of Bt bioinsecticides have been developed over the decades and are available on the market [42]. This biopesticide capacity is due to the production of crystalline proteins called Cry proteins along with spores during the sporulation stage, which are toxic to different insect orders. This capacity of Bt is important to the application of this bacterium as a green biopesticide against crop pests.

Genetic engineering is a method of making changes to the genetic material of an organism using scientific techniques. Genetic engineering has become an intervention in the field of agricultural and industrial biotechnology including different types of plants, animals, and microorganisms [43]. In agriculture, these techniques have been applied to achieve modified crops by integrating sequences of DNA into the germplasm of crop plants to obtain new crops with better characteristics than wild-type crops, such as appearance, yield, size, and resistance to pests. The integrated DNA sequences encode insecticidal proteins in transgenic plants to resist insect pests [44].

To understand how B. thuringiensis was genetically modified for introduction into several crops for pest control, it is necessary to know how this bacterium acts against several pests through its insecticidal proteins derived from toxin genes. The mechanism of action of insecticidal toxins is basically described in Figure 1. Briefly, the insecticidal toxins of B. thuringiensis need to be ingested by the insect larvae to be effective [45]. After ingestion, the toxins are solubilized by the alkaline conditions and then are converted into toxic core fragments, which bind to the receptors of epithelial midgut cells. Then, the toxin adopts a specific conformation allowing its insertion into the cell membrane and forming transmembrane pores, which cause an osmotic imbalance causing cell rupture. This leads to insect death caused by bacteremia [46].

These insecticidal toxins are derived from cry genes [47], which have been classified and organized in a systematic nomenclature. Cry toxins have been effective for the control of several insect pests affecting important crops. Naturally occurring cry genes and several mutations show varied specificity and novel/improved toxicity against a specific insect group. However, some insects can acquire resistance to the cry gene product [46]. Traits of Bt, such as pest resistance and herbicide properties, are most extensively used in plant genetic engineering. Bt toxin genes have been used in genetic engineering for application to many crops to act against specific pests [48]. For several years, the development of new toxin genes in new Bt strains was the main aim of researchers on this topic. After the toxin mechanism of action was studied and elucidated, research centered on altering the amino acids of the main domains of toxin. In this way, new proteins could be created.

Bt biopesticides have some advantages, such as specificity and their environmental safety and they are cheap and easily formulated [49]. However, they can have some disadvantages, such as their instability under field conditions due to sunlight; therefore, frequent applications are necessary, making their use more expensive. As has been seen, short persistence and low residual activity are two factors limiting the wide use of Bt products. Different formulations and strategies have been developed to protect Bt biopesticides from sunlight [50].

Another problem is their restricted field application since they have been applied mainly to the aerial parts of the plant. To solve this problem, genetically modified crops have been employed to allow the plant to express the toxin throughout the plant. These transgenic Bt crops are protected from insect attack by expressing Bt toxins in plant tissues. During decades of improvement of B. thuringiensis strains as biopesticides, the main issue has been their application to crops. For this reason, cry genes were manipulated to achieve genes with a wider target spectrum or higher toxicity than wild-type strains [47,51,52]. Therefore, several genetic tools were developed.

The first genetic exchange system available in B. thuringiensis was generalized transduction [53]. The second important advance in genetic exchange was the discovery of a conjugation-like process involving plasmid transfer. This tool permitted the development of strains with crystal protein gene combinations that are active against some insect species. The transfer of recombinant plasmids was possible from one strain to another. However, this technique has some limitations such as plasmid incompatibility, location of cry genes on non-transmissible plasmids, the presence of undesirable genetic material, and eventual plasmid loss [54]. Using the molecular method of in vivo homologous recombination, this structural instability or loss of plasmids can be avoided. Homologous recombination utilizes integrational vectors and thermosensitive plasmids along with chromosome fragments. These fragments are homologous to the B. thuringiensis chromosome and are introduced into the integrative plasmids to realize recombination with the chromosome. When the transformation does not occur naturally, alternative methods such as electroporation and biolistic bombardment have been effectively used on Bt transgenic crops (Figure 2). Plant expression systems such as cauliflower mosaic virus 35S promoter, maize promoter, or chloroplast promoter, were the key to expressing Bt genes in plants [55,56]. Effective promoters and expression cassettes probably could improve gene expression instead of “transformation” methods.

The best option to avoid plant toxicity is to transform truncated toxin genes. For this reason, truncated cry1A genes have been used to achieve transgenic tomato, tobacco, and cotton. Several companies, such as Monsanto or Mycogen, have made several probes changing the promoters, antibiotic resistance genes, transformation-tissue culture systems, and developing novel insecticidal proteins [57]. In this way, some genetically modified products were sold by several companies, such as Ecogen. New Leaf was the variety of potato expressing the cry3A toxin gene. This was the first commercially available product of its kind, manufactured in 1995 by an affiliate of Monsanto (NatureMark) [57]. After this, other transgenic Bt crops were commercialized, including maize and cotton [58,59]. Some crops like potato, tomato, tobacco, rice, maize, and broccoli have been genetically modified to express cry genes to kill the pests causing damage to the plant. This caused great controversy about their safety for human health [60].

Similarly, genetically modified organisms, generated via transfection of B. thuringiensis subspecies genes, produce biotechnological products that have various applications. B. thuringiensis var. kurstaki (Btk) is a bacterium, which protects crops from insect pathogens and is available as a registered formulation in the marketplace (DiPel and Forey). These two formulations are applied by spraying crops in agriculture, horticulture, and woodland plants. Moreover, the insect and fungal pathogen, B. thuringiensis subsp. israelensis (Bti), is a biologically active strain that acts against mosquito species but is harmless to humans [60]. Therefore, Bti is employed for the effective treatment of stagnant ditches, ponds, lakes, and wastewater settling tanks.

Corn expressing Cry1Ab and cotton expressing Cry1Ac are other genetically modified crops [61]. Transgenic crop cultivation expressing the insecticidal cry gene derived from B. thuringiensis, the most successful bioinsecticide, is now a common practice worldwide [62]. These transgenic plants include cotton, cauliflower, tomato, corn, chilli, and eggplants, products famous for their resistance against insects [63]. Two toxins, Cry1Ac and Cry2Ab, have been commercialized for the cotton crop with the name of Bollgard II, protecting against lepidopteran pests [64]. Another strategy was to produce GM crops with several different genes active against different target insect pests such as Monsanto’s YieldGard Plus maize expressing cry1Ab1, which is active against lepidopteran insects, and the cry3Bb1 gene, active against the coleopteran corn borer pest [65]. Another modification has been the expression of Vip3 proteins, which are vegetative insecticidal proteins active against lepidopteran insects, along with Cry proteins [66,67,68]. Using double stranded RNA (dsRNA), a transgenic cotton has been developed against H. armigera [69]. A generalized strategy that is followed to clone Bt genes into plant genome is schematized in Figure 3.