Cascading effects of composts and cover crops on soil chemistry, bacterial communities and the survival of foodborne pathogens

Optimizing Agroecological Measures for Climate-Resilient Olive Farming in the Mediterranean

In order to evaluate the potential of climate change mitigation measures on soil physiochemical properties, an experiment based on the application of five agroecological practices such as the addition of composted olive-mill wastes, recycling pruning residue, cover crops, organic insect manure, and reduced soil tillage, solely or combined, was conducted over two years (2020 to 2022) in a 48-year-old olive plantation. The results showed significant increases in soil water content during the spring and summer periods for the combined treatment (compost + pruning residue + cover crops) (ALL) compared to the control (CONT) by 41.6% and 51.3%, respectively. Also, ALL expressed the highest soil organic matter (4.33%) compared to CONT (1.65%) at 0-10 cm soil depth. When comparing soil nutrient contents, ALL (37.86 mg kg-1) and cover crops (COVER) (37.21 mg kg-1) had significant increases in soil nitrate compared to CONT (22.90 mg kg-1), the lowest one. Concerning exchangeable potassium, ALL (169.7 mg kg-1) and compost (COMP) (168.7 mg kg-1) were higher than CONT (117.93 mg kg-1) at the 0-10 cm soil depth and had, respectively an increase of 100.9% and 60.7% in calcium content compared to CONT. Over the experimental period, the implementation of the five agroecological management practices resulted in enhanced soil fertility. In a long-term Mediterranean context, this study suggests that these sustainable practices would significantly benefit farmers by improving agroecosystem services, reducing reliance on synthetic fertilizers, optimizing irrigation water use, and ultimately contributing towards a circular economy.

Biocontrol of Escherichia coli O157:H7 by Enterobacter asburiae AEB30 on intact cantaloupe melons

Escherichia coli O157:H7 causes >73,000 foodborne illnesses in the United States annually, many of which have been associated with fresh ready-to-eat produce including cantaloupe melons. In this study, we created a produce-associated bacterial (PAB) library containing >7500 isolates and screened them for the ability to inhibit the growth of E. coli O157:H7 using an in vitro fluorescence-based growth assay. One isolate, identified by 16S and whole-genome sequence analysis as Enterobacter asburiae, was able to inhibit the growth of E. coli by ~30-fold in vitro and produced zones of inhibition between 13 and 21 mm against 12 E. coli outbreak strains in an agar spot assay. We demonstrated that E. asburiae AEB30 was able to grow, persist and inhibit the growth of E. coli on cantaloupe melons under simulated pre- and post-harvest conditions. Analysis of the E. asburiae AEB30 genome revealed an operon encoding a contact-dependent growth inhibition (CDI) system that when mutated resulted in the loss of E. coli growth inhibition. These data suggest that E. asburiae AEB30 is a potential biocontrol agent to prevent E. coli contamination of cantaloupe melons in both pre- and post-harvest environments and that its mode of action is via a CDI system.

Effect of on-farm poultry litter composting processes on physicochemical, biological, and toxicological parameters and reduction of antibiotics and antibiotic-resistant Escherichia coli

Poultry litter is a valuable source of nutrients for crop production, but its use in agriculture can lead to environmental and public health concerns due to the presence of pollutants, antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs). We compared the effect of different on-farm poultry litter composting processes on physicochemical, biological, and toxicological parameters, as well as on the occurrence of antibiotics and resistant Escherichia coli. The composting treatments consisted of passively-aerated piles C:N = 19 (PAC19), mechanically-aerated piles C:N = 19 (MAC19), and mechanically-aerated piles C:N = 30 (MAC30). Poultry litter composting led to a significant reduction of antibiotic residues, enteroparasites and antibiotic resistant E. coli. The conditions of the process, such as extra C source and mechanical aeration influence the quality of the final product. MAC19 is a low-cost effective method to reduce the potential risks associated with poultry litter use in agriculture and produce good quality compost.

Medium-term storage of calf beddings affects bacterial community and effectiveness to inactivate zoonotic bacteria

Land-spreading of animal faecal wastes -such as animal beddings- can introduce zoonotic enteropathogens into the food system environment. The study evaluated the effectiveness of animal beddings naturally contaminated by calf manure to reduce E. coli O157:H7 or Salmonella enterica. The two pathogens were introduced separately as a four strains-cocktail and at high (>6.5 Log10 g-1) concentration into bedding materials, and their inactivation over a 10 weeks-period was monitored by using a Most Probable Number (MPN) enumeration method. Inactivation of E. coli O157:H7 was more effective in the bedding inoculated immediately after collection from calf pens than in the beddings inoculated after a 2 months-pre-storage period: E. coli O157:H7 levels were reduced by 6.6 Log10 g-1 in unstored bedding (0.5 Log10 g-1 recovered; 95%CI: 0.0-1.2), and by 4.9 Log10 g-1 in pre-stored bedding (2.2 Log10 g-1 recovered; 95%CI: 1.5-2.8) with a significant (p<0.05) difference between unstored and pre-stored. S. enterica was inactivated less effectively as counts were reduced by one order of magnitude, with no significant difference in inactivation between unstored and pre-stored beddings. Low levels of naturally occurring E. coli O157 and Salmonella spp. were detected in the non-inoculated beddings, as well as in the straw prior to use in the animal facility. To better understand the possible biological processes involved, the bacterial community present in the beddings was characterised by short-read 16S rRNA sequencing. Pre-storage of the bedding affected the composition but not the diversity of the bacterial community. Analyses of the key bacterial phyla suggested that the presence of a diverse and stable bacterial community might facilitate inactivation of the introduced pathogens, and a possible role of bacterial orders associated with lignocellulolytic resources. Overall, the study contributed to the understanding of the fate of zoonotic bacteria introduced in animal beddings during storage and identified bedding storage practices pre-and post-use in animal facilities that could be important to prevent the risk of zoonosis dissemination to the environment or to the dairy herds.

Prevalence and molecular characterization of Salmonella isolated from wild birds in fresh produce environments

Wild birds pose a difficult food safety risk to manage because they can avoid traditional wildlife mitigation strategies, such as fences. Birds often use agricultural fields and structures as foraging and nesting areas, which can lead to defecation on crops and subsequent transfer of foodborne pathogens. To assess the food safety risk associated with these events, wild bird feces were collected from produce fields across the southeastern United States during the 2021 and 2022 growing seasons. In total 773 fecal samples were collected from 45 farms across Florida, Georgia, South Carolina, and Tennessee, and 2.1% (n = 16) of samples were Salmonella-positive. Importantly, 75% of Salmonella were isolated from moist feces, showing reduced Salmonella viability when feces dry out. 16S microbiome analysis showed that presence of culturable Salmonella in moist feces correlated to a higher proportion of the Enterobacteriaceae family. From the Salmonella-positive samples, 62.5% (10/16) contained multi-serovar Salmonella populations. Overall, 13 serovars were detected, including six most commonly attributed to human illness (Enteriditis, Newport, Typhimurium, Infantis, Saintpaul, and Muenchen). PCR screening identified an additional 59 Salmonella-positive fecal samples, which were distributed across moist (n = 44) and dried feces (n = 15). On-farm point counts and molecular identification from fecal samples identified 57 bird species, including for 10 Salmonella-positive fecal samples. Overall, there was a low prevalence of Salmonella in fecal samples, especially in dried feces, and we found no evidence of Salmonella transmission to proximal foliage or produce. Fecal samples collected in farms close together shared highly related isolates by whole genome sequencing and also had highly similar Salmonella populations with comparable relative frequencies of the same serovars, suggesting the birds acquired Salmonella from a common source.

Use of Pantoea agglomerans ASB05 as a biocontrol agent to inhibit the growth of Salmonella enterica on intact cantaloupe melons

AIMS

To identify biocontrol agents to prevent the growth of Salmonella serotype Enterica on cantaloupe melons during the pre- and postharvest periods.

METHODS AND RESULTS

We created a produce-associated bacterial library containing 8736 isolates and screened it using an in-vitro fluorescence inhibition assay to identify bacteria that inhibit the growth of S. Enterica. One isolate, Pantoea agglomerans ASB05, was able to grow, persist, and inhibit the growth of S. Enterica on intact cantaloupe melons under simulated pre- and postharvest conditions. We also demonstrated that the growth inhibition of S. Enterica by P. agglomerans ASB05 was due to the production of a phenazine type antibiotic.

CONCLUSIONS

Pantoea agglomerans ASB05 is an effective biocontrol agent for the prevention of S. Enterica growth on intact cantaloupe melons in both the pre- and postharvest environments.

A longitudinal study to examine the influence of farming practices and environmental factors on pathogen prevalence using structural equation modeling

The contamination of fresh produce with foodborne pathogens has been an on-going concern with outbreaks linked to these commodities. Evaluation of farm practices, such as use of manure, irrigation water source, and other factors that could influence pathogen prevalence in the farming environment could lead to improved mitigation strategies to reduce the potential for contamination events. Soil, water, manure, and compost were sampled from farms in Ohio and Georgia to identify the prevalence of Salmonella, Listeria monocytogenes (Lm), Campylobacter, and Shiga-toxin-producing Escherichia coli (STEC), as well as Arcobacter, an emerging human pathogen. This study investigated agricultural practices to determine which influenced pathogen prevalence, i.e., the percent positive samples. These efforts identified a low prevalence of Salmonella, STEC, and Campylobacter in soil and water (< 10%), preventing statistical modeling of these pathogens. However, Lm and Arcobacter were found in soil (13 and 7%, respectively), manure (49 and 32%, respectively), and water samples (18 and 39%, respectively) at a comparatively higher prevalence, suggesting different dynamics are involved in their survival in the farm environment. Lm and Arcobacter prevalence data, soil chemical characteristics, as well as farm practices and weather, were analyzed using structural equation modeling to identify which factors play a role, directly or indirectly, on the prevalence of these pathogens. These analyses identified an association between pathogen prevalence and weather, as well as biological soil amendments of animal origin. Increasing air temperature increased Arcobacter and decreased Lm. Lm prevalence was found to be inversely correlated with the use of surface water for irrigation, despite a high Lm prevalence in surface water suggesting other factors may play a role. Furthermore, Lm prevalence increased when the microbiome's Simpson's Diversity Index decreased, which occurred as soil fertility increased, leading to an indirect positive effect for soil fertility on Lm prevalence. These results suggest that pathogen, environment, and farm management practices, in addition to produce commodities, all need to be considered when developing mitigation strategies. The prevalence of Arcobacter and Lm versus the other pathogens suggests that multiple mitigation strategies may need to be employed to control these pathogens.

Hermetia illucens L. larvae-associated intestinal microbes reduce the transmission risk of zoonotic pathogens in pig manure

Black soldier fly (BSF) larvae are considered a promising biological reactor to convert organic waste and reduce the impact of zoonotic pathogens on the environment. We analysed the effects of BSF larvae on Staphylococcus aureus and Salmonella spp. populations in pig manure (PM), which showed that BSF larvae can significantly reduce the counts of the associated S. aureus and Salmonella spp. Then, using a sterile BSF larval system, we validated the function of BSF larval intestinal microbiota in vivo to suppress pathogens, and lastly, we isolated eight bacterial strains from the BSF larval gut that inhibit S. aureus. Results indicated that functional microbes are essential for BSF larvae to antagonise S. aureus. Moreover, the analysis results of the relationship between the intestinal microbiota and S. aureus and Salmonella spp. showed that Myroides, Tissierella, Oblitimonas, Paenalcalignes, Terrisporobacter, Clostridium, Fastidiosipila, Pseudomonas, Ignatzschineria, Savagea, Moheibacter and Sphingobacterium were negatively correlated with S. aureus and Salmonella. Overall, these results suggested that the potential ability of BSF larvae to inhibit S. aureus and Salmonella spp. present in PM is accomplished primarily by gut‐associated microorganisms.

Interactions between Microbial Food Safety and Environmental Sustainability in the Fresh Produce Supply Chain

Improving the environmental sustainability of the food supply chain will help to achieve the United Nations Sustainable Development Goals (SDGs). This environmental sustainability is related to different SDGs, but mainly to SDG 2 (Zero Hunger), SDG 12 (Responsible Production and Consumption), SDG 13 (Climate Action), and SDG 15 (Life on Land). The strategies and measures used to improve this aspect of the food supply chain must remain in balance with other sustainability aspects (economic and social). In this framework, the interactions and possible conflicts between food supply chain safety and sustainability need to be assessed. Although priority must be given to safety aspects, food safety policies should be calibrated in order to avoid unnecessary deleterious effects on the environment. In the present review, a number of potential tensions and/or disagreements between the microbial safety and environmental sustainability of the fresh produce supply chain are identified and discussed. The addressed issues are spread throughout the food supply chain, from primary production to the end-of-life of the products, and also include the handling and processing industry, retailers, and consumers. Interactions of fresh produce microbial safety with topics such as food waste, supply chain structure, climate change, and use of resources have been covered. Finally, approaches and strategies that will prove useful to solve or mitigate the potential contradictions between fresh produce safety and sustainability are described and discussed. Upon analyzing the interplay between microbial safety and the environmental sustainability of the fresh produce supply chain, it becomes clear that decisions that are taken to ensure fresh produce safety must consider the possible effects on environmental, economic, and social sustainability aspects. To manage these interactions, a global approach considering the interconnections between human activities, animals, and the environment will be required.