Pepper bacterial wilt is caused by the bacterial pathogen, Ralstonia solanacearum. It is the most destructive disease of many Solanaceous crops such as potatoes, tobacco, pepper, tomatoes, and eggplant and is a significant source of crop loss worldwide. Physical, cultural and chemical controls have been employed to combat this destructive disease. However, none of these strategies has been able to control the disease completely due to the broad host range and genetic diversity of the pathogen, its prolonged survival in the soil and survival on vegetation as a latent infection. Owing to co‐management strategies, biological control is the best approach for human health and environmental friendly motivations. It makes use of various antagonistic rhizobacteria and epiphytic species such as Bacillus cereus, Pseudomonas putida, Bacillus subtilis, Paenibacillus macerans, Serratia marcescens, Bacillus pumilus and Pseudomonas fluorescens, which compete with and ultimately inhibit the growth of the pathogen. The possible mechanisms of bio‐control by these species involve multifaceted interactions between the host, pathogen and the antagonists. These can involve competition for nutrients and space, plant‐mediated systemic resistance, siderophore production, and production of extracellular cell wall degrading enzymes to inhibit or suppress the growth of the bacterial wilt agent.

Postharvest decay of vegetables and fruits presents a significant threat confronting sustainable food production worldwide, and in the recent times, applying synthetic fungicides has become the most popular technique of managing postharvest losses. However, there are concerns and reported proofs of hazardous impacts on consumers’ health and the environment, traceable to the application of chemical treatments as preservatives on fresh produce. Physical methods, on the other hand, cause damage to fresh produce, exposing it to even more infections. Therefore, healthier and more environmentally friendly alternatives to existing methods for managing postharvest decays of fresh produce should be advocated. There is increasing consensus that utilization of biological control agents (BCAs), mainly fungi, represents a more sustainable and effective strategy for controlling postharvest losses compared to physical and chemical treatments. Secretion of antifungal compounds, parasitism, as well as competition for nutrients and space are the most common antagonistic mechanisms employed by these BCAs. This article provides an overview of (i) the methods currently used for management of postharvest diseases of fresh produce, highlighting their limitations, and (ii) the use of biocontrol agents as an alternative strategy for control of such diseases, with emphasis on fungal antagonists, their mode of action, and, more importantly, their advantages when compared to other methods commonly used. We therefore hypothesize that the use of fungal antagonists for prevention of postharvest loss of fresh produce is more effective compared to physical and chemical methods. Finally, particular attention is given to the gaps observed in establishing beneficial microbes as BCAs and factors that hamper their development, particularly in terms of shelf life, efficacy, commercialization, and legislation procedures.

Fresh produce vegetables are colonized by different bacterial species, some of which are antagonistic to microbes that cause postharvest losses. However, no comprehensive assessment of the diversity and composition of bacteria inhabiting surfaces of fresh pepper plants grown under different conditions has been conducted. In this study, 16S rRNA amplicon sequencing was used to reveal bacterial communities inhabiting the surfaces of red and green pepper (fungicides-treated and non-fungicides-treated) grown under hydroponic and open field conditions. Results revealed that pepper fruit surfaces were dominated by bacterial phylum Proteobacteria, Firmicutes, Actinobacteria, and, Bacteroidetes. The majority of the bacterial operation taxonomic units (97% similarity cut-off) were shared between the two habitats, two treatments, and the two pepper types. Phenotypic predictions (at phylum level) detected a high abundance of potentially pathogenic, biofilm-forming, and stress-tolerant bacteria on samples grown on open soils than those from hydroponic systems. Furthermore, bacterial species of genera mostly classified as fungal antagonists including; Acinetobacter, Agrobacterium, and Burkholderia were the most abundant on the surfaces. These results suggest that peppers accommodate substantially different bacterial communities with antagonistic activities on their surfaces, independent of employed agronomic strategies and that the beneficial bacterial strains maybe more important for peppers established on open fields, which seems to be more vulnerable to abiotic and biotic stresses.

Biological control of plant pathogens, particularly using microbial antagonists, is posited as the most effective, environmentally-safe, and sustainable strategy to manage plant diseases. However, the roles of antagonists in controlling bacterial wilt, a disease caused by the most devastating and widely distributed pathogen of sweet peppers (i.e., R. solanacearum), are poorly understood. Here, amplicon sequencing and several microbial function assays were used to depict the identities and the potential antagonistic functions of bacteria isolated from 80 red and green sweet pepper fruit samples, grown under hydroponic and open soil conditions, with some plants, fungicide-treated while others were untreated. Amplicon sequencing revealed the following bacterial strains: Bacillus cereus strain HRT7.7, Enterobacter hormaechei strain SRU4.4, Paenibacillus polymyxa strain SRT9.1, and Serratia marcescens strain SGT5.3, as potential antagonists of R. solanacearum. Optimization studies with different carbon and nitrogen sources revealed that maximum inhibition of the pathogen was produced at 3% (w/v) starch and 2,5% (w/v) tryptone at pH 7 and 30 °C. The mode of action exhibited by the antagonistic isolates includes the production of lytic enzymes (i.e., cellulase and protease enzymes) and siderophores, as well as solubilization of phosphate. Overall, the results demonstrated that the maximum antimicrobial activity of bacterial antagonists could only be achieved under specific environmental conditions (e.g., available carbon and nitrogen sources, pH, and temperature levels), and that bacterial antagonists can also indirectly promote crop growth and development through nutrient cycling and siderophore production.

Post-harvest decay of fresh agricultural produce is a major threat to food security globally. Synthetic fungicides, commonly used in practice for managing the post-harvest losses, have negative impacts on consumers' health. Studies have reported the effectiveness of fungal isolates from plants as biocontrol agents of post-harvest diseases, although this is still poorly established in tomatoes (Solanum lycopersicum L. cv. Jasmine). In this study, 800 endophytic fungi were isolated from mature green and ripe untreated and fungicide-treated tomato fruits grown in open soil and hydroponics systems. Of these, five isolates (Aureobasidium pullulans SUG4.1, Coprinellus micaceus SUG4.3, Epicoccum nigrum SGT8.6, Fusarium oxysporum HTR8.4, Preussia africana SUG3.1) showed antagonistic properties against selected post-harvest pathogens of tomatoes (Alternaria alternata, Fusarium solani, Fusarium oxysporum, Geotrichum candidum, Rhizopus stolonifera, Rhizoctonia solani), with Lactiplantibacillus plantarum as a positive control. P. africana SUG3.1 and C. micaceus SUG4.3 significantly inhibited growth of all the pathogens, with antagonistic capabilities comparable to that exhibited by L. plantarum. Furthermore, the isolates produced an array of enzymes, including among others, amylase, cellulose and protease; and were able to utilize several carbohydrates (glucose, lactose, maltose, mannitol, sucrose). In conclusion, P. africana SUG3.1 and C. micaceus SUG4.3 may complement L. plantarum as biocontrol agents against post-harvest pathogens of tomatoes.

Tomato (Solanum lycopersicum) is an essential crop worldwide, yet it remains highly vulnerable to severe fungal and bacterial diseases. Traditional chemical-based disease management strategies, aimed at controlling these diseases face increasing scrutiny, due to concerns regarding pathogen resistance, environmental degradation, and potential health risks to humans. This has catalyzed the exploration of sustainable alternatives, with biological control emerging as a viable and promising strategy. Endophytic and epiphytic microorganisms are pivotal as biocontrol agents (BCAs), employing diverse strategies, such as generating antimicrobial substances, enzymes, and volatile organic compounds (VOCs), to suppress pathogen growth and enhance plant health. The efficacy of these antagonistic microorganisms is influenced by the cultivation systems employed, with significant variations observed between soil and hydroponic environments. Factors such as nutrient dynamics and microbial interactions play crucial roles in determining the success of BCAs in these different settings. The advent of metagenomic tools has transformed the landscape of microbial community research, facilitating the identification of functional genes associated with antagonistic activities and the adaptation of these microorganisms to diverse environmental conditions. This review aims to elucidate the potential of endophytic and epiphytic microorganisms in biological control, examining their mechanisms of action, the impact of cultivation systems on their effectiveness, and the application of metagenomics to optimize their use in sustainable disease management strategies for tomato crops.