Food safety risks and biocontrol in controlled environment agriculture: Evaluating plant growth-promoting bacteria against Listeria monocytogenes and Salmonella Typhimurium

As the global population is expected to surpass 9 billion by 2050, traditional agriculture must produce more food with fewer resources. Controlled environment agriculture (CEA) systems offer sustainable means of food production by optimizing water and land use, reducing the use of chemical inputs, and enabling year-round production. However, these systems also have unique food safety concerns that must be addressed. Some of the features that make CEA systems great for plant growth and yields create an ideal environment for pathogen persistence and dissemination. The closed nature, absence of soil, close plant spacing, and warm, humid, and nutrient-rich conditions for most system types support the contamination, survival, and dissemination of pathogens, including foodborne pathogens. The food safety concern in CEA systems is substantiated by the fact that most of the CEA-grown produce is consumed raw with no terminal ‘kill’ step, increasing incidence of fresh produce-associated foodborne illnesses, and documented survival of pathogens such as Salmonella spp. and Listeria monocytogenes in these systems, both of which have been implicated in severe produce-associated outbreaks. Furthermore, most of the existing research and interventions focus on postharvest pathogen control, with preharvest food safety strategies remaining limited and often unsuitable for integration into live production systems. To safely expand CEA, this research investigated food safety risks in commercial herb production operations and assessed plant growth-promoting rhizobacteria (PGPR) as biocontrol agents to inhibit Listeria monocytogenes and Salmonella Typhimurium in hydroponics. In order to assess food safety management practices and risk factors, a multiple case comparative design was utilized in the in-depth assessment of six U.S. CEA commercial herb producers (three containerized live-produce and three fresh-cut operations). Data were obtained through the use of harmonized self-assessments and in-depth interviews. Containerized operations primarily produced live potted herbs in soil or inert substrates, utilizing overhead or flood irrigation methods. These operations prioritized plant health over food safety, with minimal processing and handling. Fresh-cut operations, on the other hand, utilized highly formalized food safety management systems, which were frequently backed by industry certifications such as SQF. Nonetheless, fresh-cut facilities posed the greatest overall food safety risk, stemming from harvesting and postharvest handling due to tissue cutting, human contact, equipment use, and inadequate sanitation. Containerized systems exhibited a greater risk primarily in the input stage due to the use of unapproved seeds and substrates for food safety risks; however, their slight processing reduced the risk post-growth. The implications of these results emphasize that equally applying conventional produce safety frameworks to all CEA systems overlooks operation-specific risks and realities. The second study identified the microbial risks associated with hydroponics by examining the survival of Listeria monocytogenes and Salmonella enterica serovar Typhimurium in basil grown under deep-water culture (DWC) and nutrient film technique (NFT) systems over a 28-day production cycle. The systems were both inoculated with the pathogens, and samples taken at intervals along the production cycle from the nutrient solution, the roots, and the leaves, and subjected to enumeration. Both pathogens showed a biphasic decrease but persisted throughout the cycle, with persistence influenced by the system used, particularly in roots (p < 0.05), and no contamination on edible leaves was detectable under the study conditions. DWC generally resulted in greater survival than NFT, particularly in the latter half of the cycle. The greatest decrease in nutrient solutions occurred over the first six days, but thereafter, these concentrations were below the limit of quantification and showed no significant difference by system type for both pathogens. In roots, however, the pathogens persisted for a longer period. L. monocytogenes showed generally more persistence in both systems than S. Typhimurium. By harvest, L. monocytogenes fell below quantifiable limits on roots in NFT (64% decline) but remained quantifiable in DWC (36% decline). Conversely, by harvest, S. Typhimurium fell below quantifiable limits on roots in both systems (92.3% and 81.7% in NFT and DWC, respectively). These results demonstrate that system type is a key factor in determining the food safety risk in hydroponic systems, emphasizing the need for system-specific risk assessments and targeted management strategies. This study lays the groundwork for future research on the influence of system design on food safety risks, as well as provides guidelines for food safety in hydroponics. The last study evaluated the effects of three commercial bioinoculants, Terragrow™ (a Bacillus-trichoderma harzianum consortium), Bacillus subtilis QST 713 (Serenade™), and Streptomyces lydicus WYEC 108 (Actinovate™) on Listeria monocytogenes- and Salmonella enterica serovar Typhimurium survival in basil grown in DWC and NFT hydroponic systems. The survival patterns of the pathogens were influenced by the type of bioinoculant, system type, and pathogen type. For Listeria, the NFT system showed greater pathogen reduction than DWC, with complete elimination observed for TerragrowTM. In nutrient solutions, reductions ranged from 85.9% to 94.7% (DWC) and 88.5% to 100% (NFT), representing 4.2-5.4 Log reduction, generally higher than those observed on the roots (35.9% to 74.7%). All bioinoculants significantly reduced L. monocytogenes to levels lower than those in the controls in both systems. For Salmonella, all PGPR treatments except TerragrowTM facilitated longer pathogen persistence than the control. The impact of the hydroponic system on PGPR efficacy varied by bioinoculant. Contrary to other bioinoculants, TerragrowTM was more effective in DWC than in NFT, achieving complete elimination in the DWC nutrient solution (100% reduction; 4.62-log decrease). These findings demonstrate that PGPR significantly reduced L. monocytogenes but not S. Typhimurium, with effectiveness dependent on the bioinoculant type, system, and time (the stage of the production cycle). Thus, while PGPR bio-inoculants offer some promise for increasing the microbial safety of hydroponic products, successful integration constitutes a challenge. Careful selection of the bioinoculant is key, and for growers using PGPR bioinoculants for their growth promotion benefits, they need to implement the necessary preventative food safety measures, such as sanitation, cleaning, and water treatment, as a means to prevent pathogen introduction into the system, as the effect on food safety may be negative. The study provides novel insights into the potential of PGPR bioinoculants for biocontrol of foodborne pathogens in hydroponic production. The evidence presented here demonstrates that CEA offers a sustainable solution for meeting future food needs; however, it also raises new challenges with its proposed solutions. The findings from the commercial herb production study indicate that CEA systems are inherently diverse, and risk profiles differ by operation type between potted and fresh-cut operations, thus suggesting that CEA requires specific food safety approaches compared to a ‘one-size-fits-all’ approach. The pathogen survival study confirmed that both Listeria monocytogenes and Salmonella Typhimurium can persist throughout production cycles, and system design significantly influences pathogen persistence, with DWC being more favorable for survival than NFT systems. Importantly, the work also indicates that PGPR-based biocontrol shows strong but context-dependent promise, shaped by the interaction between bioinoculant type, hydroponic system design, and production duration. Certain bio-inoculants, such as those based on multi-Bacillus-Trichoderma bioinoculants, can significantly reduce pathogen survival, yet some like the Streptomyces lydicus-based, allow greater pathogen persistence. These results, when taken together, provide key insights into the microbial risks inherent to CEA and offer insight into the possibility of using PGPR as sustainable, system-dependent biocontrol agents. In the future, the incorporation of PGPR into hydroponic management methods, together with the formulation of risk-based food safety approaches, will be critical for ensuring microbial safety and resilience of CEA systems as they expand to meet the global needs of a growing population.