Bacterial communities associated with surfaces of leafy greens: shift in composition and decrease in richness over time

Isolation and Identification of the Antibacterial Compounds Produced by Maillard Reaction of Xylose with Phenylalanine or Proline

Maillard reaction products (MRPs) of xylose with phenylalanine and xylose with proline exhibit high antibacterial activity. However, the active antibacterial compounds in MRPs have not yet been identified or isolated. This study aimed to isolate the active compounds in the two antibacterial MRPs. The organic layer of the MRP solution was separated and purified using silica gel chromatography and high-performance liquid chromatography. The chemical structures of the isolated compounds were determined by mass spectrometry and nuclear magnetic resonance spectroscopy. The compounds inhibited the growth of Bacillus cereus and Salmonella Typhimurium at 25 °C for 7 days at a concentration of 0.25 mM. Furthermore, the isolated compounds inhibited the growth of naturally occurring microflora of lettuce and chicken thighs at 25 °C for 2 days at a concentration of 0.5-1.0 mM. The antibacterial compounds found in MRPs demonstrated a wide range of effectiveness and indicated their potential as alternative preservatives.

Transfer of Salmonella, Escherichia coli O157:H7 and Listeria monocytogenes from contaminated soilless substrate and seeds to microgreens

Microgreens can be contaminated by various preharvest sources including soilless substrate, plant nutrition solution, water and seeds. The aim of this study was to determine the transfer level of Salmonella, Shiga toxin-producing Escherichia coli O157:H7, and Listeria monocytogenes to the edible part of various type of microgreens from plant nutrient solution-soaked perlite as soilless substrate or seeds. Ampicillin resistant 3-strain cocktails of Salmonella and E. coli O157:H7 and non-resistant L. monocytogenes were independently inoculated into plant nutrient solution-soaked perlite and seeds in low (102-103 CFU/g) and high (105-106 CFU/g) populations. Twenty types of microgreens were grown in inoculated perlite. The seed inoculation was performed on five types of microgreens. Correlations between pathogen transfer levels with seed characteristics and harvest time were assessed. Pathogen populations (1.6 ± 0.2 to 7.7 ± 0.1 log CFU/g) transferred to microgreens were dependent on type of pathogen and microgreen but not affected by contamination source and inoculation level. The level of pathogen transferred to microgreens had a moderate to high negative correlations (R2) with seed surface area (-0.551 to -0.781), seed weight (-0.735 to -0.818), and harvest time (-0.332 to -0.919) when grown in Salmonella and E. coli O157:H7 inoculated perlite. This study suggests a high risk of pathogen population transferring to microgreens in case of seed or soilless substrate contamination when pathogen growth or survival is supported in plant nutrient solution.

Microbiome-based classification models for fresh produce safety and quality evaluation

Small sample sizes and loss of sequencing reads during the microbiome data preprocessing can limit the statistical power of differentiating fresh produce phenotypes and prevent the detection of important bacterial species associated with produce contamination or quality reduction. Here, we explored a machine learning-based k-mer hash analysis strategy to identify DNA signatures predictive of produce safety (PS) and produce quality (PQ) and compared it against the amplicon sequence variant (ASV) strategy that uses a typical denoising step and ASV-based taxonomy strategy. Random forest-based classifiers for PS and PQ using 7-mer hash data sets had significantly higher classification accuracy than those using the ASV data sets. We also demonstrated that the proposed combination of integrating multiple data sets and leveraging a 7-mer hash strategy leads to better classification performance for PS and PQ compared to the ASV method but presents lower PS classification accuracy compared to the feature-selected ASV-based taxonomy strategy. Due to the current limitation of generating taxonomy using the 7-mer hash strategy, the ASV-based taxonomy strategy with remarkably less computing time and memory usage is more efficient for PS and PQ classification and applicable for important taxa identification. Results generated from this study lay the foundation for future studies that wish and need to incorporate and/or compare different microbiome sequencing data sets for the application of machine learning in the area of microbial safety and quality of food.

IMPORTANCE

Identification of generalizable indicators for produce safety (PS) and produce quality (PQ) improves the detection of produce contamination and quality decline. However, effective sequencing read loss during microbiome data preprocessing and the limited sample size of individual studies restrain statistical power to identify important features contributing to differentiating PS and PQ phenotypes. We applied machine learning-based models using individual and integrated k-mer hash and amplicon sequence variant (ASV) data sets for PS and PQ classification and evaluated their classification performance and found that random forest (RF)-based models using integrated 7-mer hash data sets achieved significantly higher PS and PQ classification accuracy. Due to the limitation of taxonomic analysis for the 7-mer hash, we also developed RF-based models using feature-selected ASV-based taxonomic data sets, which performed better PS classification than those using the integrated 7-mer hash data set. The RF feature selection method identified 480 PS indicators and 263 PQ indicators with a positive contribution to the PS and PQ classification.

Effect of dietary living microbe intake on depression symptom in American adult: An opinion from NHANES study

BACKGROUND

Daily diet represents a potentially modifiable factor in the development of depression. However, to date, no studies have investigated the impact of dietary active microorganisms on depressive symptoms. The aim of this study is to explore the relationship between these two factors.

METHODS

Population data from NHANES 2005-2018 indicated that the exposure variable was dietary intake of active microbes, while the outcome variable was depression as defined by a 9-item Patient Health Questionnaire (PHQ-9) score. A multivariate logistic regression model was employed to assess the impact of dietary living microbe intake on depression symptoms.

RESULTS

A total of 19,169 American adults with a mean age of 46.89 years (SD = 16.97) were included in this cross-sectional analysis; among them, 53.84 % were male and 8.11 % (n = 1555) met the criteria for depression symptoms. In the fully adjusted model, patients with medium and high dietary living microbe intake exhibited a significant reduction in depression symptoms prevalence by 28 % (OR, 0.72; 95 % CI: 0.64-0.81) and 26 % (OR, 0.74; 95 % CI: 0.63-0.85), respectively, compared to those with low dietary living microbe intake. Subgroup analyse indicate that no significant interaction was observed between dietary living microbe intake group and subgroups.

CONCLUSION

Higher intake of active microbes in the diet was found to have a negative correlation with depression.

Effect of pre-harvest sanitizer treatments on Listeria survival, sensory quality and bacterial community dynamics on leafy green vegetables grown under commercial conditions

Leafy green vegetables (LGVs) have large surface areas and can be colonized by various microorganisms including pathogens. In this study, we investigated the effect of pre-harvest sanitizer treatments on the survival of inoculated proxy pathogen Listeria innocua ATCC 33090 and the natural microbial community of mizuna, rocket (arugula), red chard and spinach grown under commercial conditions. Electrolyzed water (e-water), peracetic acid (PAA), and 1-bromo-3-chloro-5-dimethylhydantoin (BCDMH) were tested against water controls. We also observed the subsequent sensorial changes of harvested, bagged LGV leaves over a period of 12 days within chill storage alongside the growth, diversity and structure of bacterial populations determined using 16S rRNA gene amplicon sequencing and total viable counts (TVC). Treatment with PAA resulted in the highest reductions of L. innocua (2.4-5.5 log units) compared to the other treatments (0.25-2.5 log units). On day 0 (24 h after sanitizer application), the TVC on sanitizer treated LGVs were significantly reduced compared to water controls, except for rocket. During storage at 4.5 (±0.5)°C sanitisers only hindered microbial growth on LGVs initially and did not influence final bacterial population levels, growth rates or changes in LGV sample colour, decay, odour and texture compared to water controls. Shelf-life was not extended nor was it reduced. The community structure on LGV types differed though a core set of bacterial amplicon sequence variants (ASV) were present across all samples. No significant differences were observed in bacterial diversity between sanitizer treatments, however sanitizer treated LGV samples had initially reduced diversity compared to water treated samples. The bacterial compositions observed at the end point of storage considerably differed from what was observed at initial point owing to the increase in abundance of specific bacterial taxa, mainly Pseudomonas spp., the abundance and growth responses differing between LGV types studied. This study provides a better understanding on the microbiology and sensory impact of pre-harvest applied sanitiser treatments on different LGVs destined for commercial food use.

Weather factors, soil microbiome, and bacteria-fungi interactions as drivers of the epiphytic phyllosphere communities of romaine lettuce

Lettuce is associated with seasonal outbreaks of Shiga toxin-producing Escherichia coli (STEC) infections. Little is known about how various biotic and abiotic factors affect the lettuce microbiome, which in turn impacts STEC colonization. We characterized the lettuce phyllosphere and surface soil bacterial, fungal, and oomycete communities at harvest in late-spring and -fall in California using metagenomics. Harvest season and field type, but not cultivar, significantly influenced the microbiome composition of leaves and surface soil near plants. Phyllosphere and soil microbiome compositions were correlated with specific weather factors. The relative abundance of Enterobacteriaceae, but not E. coli, was enriched on leaves (5.2%) compared to soil (0.4%) and correlated positively with minimum air temperature and wind speed. Co-occurrence networks revealed seasonal trends in fungi-bacteria interactions on leaves. These associations represented 39%-44% of the correlations between species. All significant E. coli co-occurrences with fungi were positive, while all negative associations were with bacteria. A large proportion of the leaf bacterial species was shared with those in soil, indicating microbiome transmission from the soil surface to the canopy. Our findings provide new insight into factors that shape lettuce microbial communities and the microbial context of foodborne pathogen immigration events in the lettuce phyllosphere.

Composition and variability of core phyllosphere fungal mycobiota on field-grown broccoli

BACKGROUND

Fresh vegetables harbor an assemblage of different microorganisms on their surfaces. The phyllosphere microbiota is important for maintaining plant health and managing crop quality before and after harvest. However, the diversity and ecology of fungal communities are largely unexplored in fresh vegetables. This study investigated the phyllosphere mycobiota of field-grown broccoli florets (n = 66) collected from 22 farms across four regions in Korea, using culturing, amplicon sequencing of the internal transcribed spacer region, and microbial network analysis.

RESULTS

Microbial network analysis identified core genera (Purpureocillium, Filobasidium, Cystofilobasidium, Papiliotrema, Aureobasidium, and unclassified genera of Capnodiales) specific to the broccoli phyllosphere. The composition and network complexity of core and unique populations varied among farming regions, and was associated with local agro-meteorological conditions. The complexity of microbial associations was higher in mature communities than in immature communities, but complexity was lost upon development of plant pathogenic disease. Broccoli mycobiota were classified according to the dominance of Purpurecillium. While Purpurecillium-type microbiota were prevalent in normal samples, Filobasidium-type microbiota were frequently observed in immature, damaged, or postharvest samples.

CONCLUSIONS

Together, fungal communities were important components of phyllosphere microbiota on fresh vegetables, and have substantial potential for exploitation to enhance and stabilize plant health and growth.

Opportunities and Challenges of Understanding Community Assembly in Spontaneous Food Fermentation

Spontaneous fermentations that do not rely on backslopping or industrial starter cultures were especially important to the early development of society and are still practiced around the world today. While current literature on spontaneous fermentations is observational and descriptive, it is important to understand the underlying mechanism of microbial community assembly and how this correlates with changes observed in microbial succession, composition, interaction, and metabolite production. Spontaneous food and beverage fermentations are home to autochthonous bacteria and fungi that are naturally inoculated from raw materials, environment, and equipment. This review discusses the factors that play an important role in microbial community assembly, particularly focusing on commonly reported yeasts and bacteria isolated from spontaneously fermenting food and beverages, and how this affects the fermentation dynamics. A wide range of studies have been conducted in spontaneously fermented foods that highlight some of the mechanisms that are involved in microbial interactions, niche adaptation, and lifestyle of these microorganisms. Moreover, we will also highlight how controlled culture experiments provide greater insight into understanding microbial interactions, a modest attempt in decoding the complexity of spontaneous fermentations. Further research using specific in vitro microbial models to understand the role of core microbiota are needed to fill the knowledge gap that currently exists in understanding how the phenotypic and genotypic expression of these microorganisms aid in their successful adaptation and shape fermentation outcomes. Furthermore, there is still a vast opportunity to understand strain level implications on community assembly. Translating these findings will also help in improving other fermentation systems to help gain more control over the fermentation process and maintain consistent and superior product quality.

Fungal Communities of Spring Barley from Seedling Emergence to Harvest During a Severe Puccinia hordei Epidemic

All plant tissues from leaves, stems, and roots are hosting a wide diversity of fungal species. Our understanding of the assembly of this diversity of fungi during the plant growth cycle is limited. Here, we characterized the mycobiome of three spring barley cultivars grown in Zealand, Denmark, at weekly intervals during a growth season from seedling emergence to senescence and seed maturity. A notable proportion of members of the fungal communities were shared among different plant organs, but community dynamics were tissue-specific. A severe attack of Puccinia hordei occurring during the vegetative stage had profound effects on the mycobiome, and P. hordei biomass displaced that of other taxa. Plant tissue type was the most important factor determining the mycobiome, but also plant age was contributing significantly. Using a random forest model, we found that specific members of the mycobiome were responding differently to plant age, for instance, Olpidium and Articulospora in roots, Dioszegia and Sporobolomyces in leaves, Pyrenophora in stems, and Epicoccum in heads. A co-occurrence network analysis revealed complex interactions among fungal OTUs, and network connectivity was changing as per plant growth stage and plant tissue type. This study contributes to the understanding of assembly of fungal communities in cereals by providing a detailed description of fungal communities associated with barley. This knowledge will be vital for microbiome assisted plant health management and our study will serve as an important baseline for future efforts to harness microbiota in cereal health.

The mature phyllosphere microbiome of grapevine is associated with resistance against Plasmopara viticola

Phyllosphere microbiota represents a substantial but hardly explored reservoir for disease resistance mechanisms. The goal of our study was to understand the link between grapevine cultivars susceptibility to Plasmopara viticola, one of the most devastating leaf pathogens in viticulture, and the phyllosphere microbiota. Therefore, we analyzed a 16S rRNA gene library for the dominant phyllosphere bacterial phyla Alphaproteobacteria of seven Vitis genotypes at different developmental stages, i.e., flowering and harvesting, via amplicon sequencing. Young leaves had significantly higher Alphaproteobacterial richness and diversity without significant host-specificity. In contrast, the microbial communities of mature leaves were structurally distinct in accordance with P. viticola resistance levels. This statistically significant link between mature bacterial phyllosphere communities and resistant phenotypes was corroborated by beta diversity metrics and network analysis. Beyond direct host-driven effects via the provision of microhabitats, we found evidence that plants recruit for specific bacterial taxa that were likely playing a fundamental role in mediating microbe-microbe interactions and structuring clusters within mature communities. Our results on grape-microbiota interaction provide insights for targeted biocontrol and breeding strategies.

A Classification System for Defining and Estimating Dietary Intake of Live Microbes in US Adults and Children

BACKGROUND

Consuming live microbes in foods may benefit human health. Live microbe estimates have not previously been associated with individual foods in dietary databases.

OBJECTIVES

We aimed to estimate intake of live microbes in US children (aged 2-18 y) and adults (≥19 y) (n = 74,466; 51.2% female).

METHODS

Using cross-sectional data from the NHANES (2001-2018), experts assigned foods an estimated level of live microbes per gram [low (Lo), <104 CFU/g; medium (Med), 104-107 CFU/g; or high (Hi), >107 CFU/g]. Probiotic dietary supplements were also assessed. The mean intake of each live microbe category and the percentages of subjects who ate from each live microbe category were determined. Nutrients from foods with live microbes were also determined using the population ratio method. Because the Hi category comprised primarily fermented dairy foods, we also looked at aggregated data for Med or Hi (MedHi), which included an expanded range of live microbe-containing foods, including fruits and vegetables.

RESULTS

Our analysis showed that 52%, 20%, and 59% of children/adolescents, and 61%, 26%, and 67% of adults, consumed Med, Hi, or MedHi foods, respectively. Per capita intake of Med, Hi, and MedHi foods was 69, 16, and 85 g/d for children/adolescents, and 106, 21, and 127 g/d for adults, respectively. The proportion of subjects who consumed live microbes and overall per capita intake increased significantly over the 9 cycles/18-y study period (0.9-3.1 g/d per cycle in children across categories and 1.4 g/d per cycle in adults for the Med category).

CONCLUSIONS

This study indicated that children, adolescents, and adults in the United States steadily increased their consumption of foods with live microbes between the earliest (2001-2002) and latest (2017-2018) survey cycles. Additional research is needed to determine the relations between exposure to live microbes in foods and specific health outcomes or biomarkers.

The live bacterial load and microbiota composition of prepacked "ready-to-eat" leafy greens during household conditions, with special reference to E. coli

Ready-to-eat (RTE) leafy greens are popular products that unfortunately have been associated with numerous foodborne illness outbreaks. Since the influence of consumer practices is essential for their quality and safety, the objective of this study was to analyze the microbiota of RTE products throughout shelf life during simulated household conditions. Products from different companies were analyzed in terms of plate counts, and resealed and unopened packages were compared. High bacterial loads were found, up to a total plate count of 9.6 log₁₀ CFU/g, and Enterobacteriaceae plate counts up to 6.0 CFU/g on the expiration date. The effect of consumer practice varied, thus no conclusions regarding resealed or unopened bags could be drawn. The tested products contained opportunistic pathogens, such as Enterobacter homaechei, Hafnia paralvei and Pantoea agglomerans. Amplicon sequencing revealed that the relative abundance of major taxonomic groups changed during shelf life; Pseudomonadaceae and Xanthomonadaceae decreased, while Flavobacteriaceae and Marinomonadaceae inceased. Inoculation with E. coli CCUG 29300^T showed that the relative abundance of Escherichia-Shigella was lower on rocket than on other tested leafy greens. Inoculation with E. coli strain 921 indicate growth at the beginning of shelf-life time, while E. coli 731 increases at the end, seemingly able to adapt to cold storage conditions. The high levels of live microorganisms, the detection of opportunistic pathogens, and the ability of E. coli strains to grow at refrigeration temperature raise concerns and indicate that the shelf life may be shortened to achieve a safer product. Due to variations between products, further studies are needed to define how long the shelf-life of these products should be, to ensure a safe product even at the end of the shelf-life period.

Investigation on the Microbial Diversity of Fresh-Cut Lettuce during Processing and Storage Using High Throughput Sequencing and Their Relationship with Quality

Microbial community distribution in vegetables can affect their quality. This study analyzed the distribution of the microbial community at various stages during processing and storage with the microbial diversity analysis, and evaluated the correlation between the dominant bacteria and sensory quality of lettuce using correspondence analysis with multiple regression analysis. Results showed that the process of washing, cutting, then disinfection and dewatering could change the community distribution and dominant bacteria in lettuce, and maintain better texture, morphology, aroma, color qualities of lettuce. The total number of colonies and relative abundance of Xanthomonas in fresh-cut lettuce decreased, while Afipia and Ralstonia increased during processing and pre-storage (storage for 6 h, 12 h and 1 d). After storage for 3 d, the total number of colonies in lettuce increased (more than 5 log CFU/g), especially the relative abundance of Pseudomonas, which led to the obvious deterioration of the sensory quality of lettuce. Throughout the process, the number of Bacillus cereus, Staphylococcus aureus, and E. coli was less than 100 CFU/g and 3 MPN/g. The number of typical pathogenic bacteria, Salmonella, Listeria monocytogenes and E. coli O157:H7, was below the detection limit. Overall, the prevention and control of psychrotrophic Pseudomonas in lettuce was still necessary. These results will provide useful information for the fresh-cut lettuce industry.

Bacterial Succession and Community Dynamics of the Emerging Leaf Phyllosphere in Spring

Every year, deciduous trees shed their leaves, and when new leaves emerge next spring, they establish a characteristic bacterial leaf community. In this exploratory study, we assessed the bacterial phyllosphere (aboveground plant surfaces) of eight London plane trees (Platanus × acerifolia) in Antwerp and Milan by sampling weekly during leaf emergence and expansion. We sampled the surfaces of different tree compartments: leaves, leaf buds, branches, and trunk, for up to 6 weeks. Phyllosphere community composition was most strongly determined by tree compartment. Only the communities on the emerging leaves showed changing dynamics over time. The rate of change in the leaf phyllosphere composition, expressed as the beta dissimilarity between consecutive time points, was very high following leaf emergence, with decreasing speed over time, indicating that these communities stabilize over time. We also identified cooccurring groups of bacteria associated with potential stages of ecological succession on the leaves and accordingly named them general cluster, early cluster, middle cluster, and late cluster. Taxa of the general cluster were not only more abundant than the others on leaves, but they were also widespread on other tree compartments. The late cluster was most pronounced in trees surrounded by trafficked urban land use. This study mainly generates hypotheses on the ecological succession on the emerging leaves of deciduous trees in urban environments and contributes to understanding the development of the tree leaf phyllosphere in spring. IMPORTANCE Improving our understanding of phyllosphere ecology is key in successfully applying bacterial biological agents or modulating the leaf microbiome in order to achieve valuable ecosystem services, such as plant protection, plant growth, air purification, and developing a healthy human immune system. Modulation of the phyllosphere microbiome in the field works only with variable success. To improve the impact of our applications in the field, a better understanding of the ecological principles governing phyllosphere dynamics is required. This exploratory study demonstrates how the combination of different analyses of a chronosequence of bacterial communities can provide new ecological insights. With a limited number of sampled trees, we demonstrated different indications of ecological succession of bacterial communities in the leaves and observed a potential impact of intensely trafficked land use becoming apparent in the leaf bacterial communities approximately 3 weeks after leaf emergence, consisting of a separate stage in community development.

Persistence of Escherichia coli in the microbiomes of red Romaine lettuce (Lactuca sativa cv. 'Outredgeous') and mizuna mustard (Brassica rapa var. japonica) - does seed sanitization matter?

BACKGROUND

Seed sanitization via chemical processes removes/reduces microbes from the external surfaces of the seed and thereby could have an impact on the plants' health or productivity. To determine the impact of seed sanitization on the plants' microbiome and pathogen persistence, sanitized and unsanitized seeds from two leafy green crops, red Romaine lettuce (Lactuca sativa cv. 'Outredgeous') and mizuna mustard (Brassica rapa var. japonica) were exposed to Escherichia coli and grown in controlled environment growth chambers simulating environmental conditions aboard the International Space Station. Plants were harvested at four intervals from 7 days post-germination to maturity. The bacterial communities of leaf and root were investigated using the 16S rRNA sequencing while quantitative polymerase chain reaction (qPCR) and heterotrophic plate counts were used to reveal the persistence of E. coli.

RESULT

E. coli was detectable for longer periods of time in plants from sanitized versus unsanitized seeds and was identified in root tissue more frequently than in leaf tissue. 16S rRNA sequencing showed dynamic changes in the abundance of members of the phylum Proteobacteria, Firmicutes, and Bacteroidetes in leaf and root samples of both leafy crops. We observed minimal changes in the microbial diversity of lettuce or mizuna leaf tissue with time or between sanitized and unsanitized seeds. Beta-diversity showed that time had more of an influence on all samples versus the E. coli treatment.

CONCLUSION

Our results indicated that the seed surface sanitization, a current requirement for sending seeds to space, could influence the microbiome. Insight into the changes in the crop microbiomes could lead to healthier plants and safer food supplementation.

A Comparative Analysis of the Microbiome of Kiwifruit at Harvest Under Open-Field and Rain-Shelter Cultivation Systems

The composition of microbial communities can directly affect fruit quality, health status, and storability. The present study characterized the epiphytes and endophytes of “Hongyang” and “Cuiyu” kiwifruit at harvest under grown under open-field (OF) and rain-shelter (RS) cultivation systems. Disease incidence in kiwifruit was significantly lower (p < 0.05) under the RS system than it was under the OF system. High-throughput sequencing [16S V3-V4 ribosomal region and the fungal internal transcribed spacer (ITS2)] was conducted to compare the composition of the epiphytic and endophytic microbial community of kiwifruit under the two cultivation systems. Results indicated that the abundance of Actinobacteria, Bacteroidetes, Enterobacteriales, Acetobacterales, Sphingomonas, Pseudomonas, and Sphingobacterium was higher under the RS system, relative to the OF system, while the abundance of Capnodiales, Hypocreales, Vishniacozyma, and Plectosphaerella was also higher under the RS system. Some of these bacterial and fungal taxa have been reported to as act as biocontrol agents and reduce disease incidence. Notably, the α-diversity of the epiphytic bacterial and fungal communities on kiwifruit was higher under RS cultivation. In summary, RS cultivation reduced natural disease incidence in kiwifruit, which may be partially attributed to differences in the structure and composition of the microbial community present in and on kiwifruit.

Spatial Characterization of Microbial Communities on Multi-Species Leafy Greens Grown Simultaneously in the Vegetable Production Systems on the International Space Station

The establishment of steady-state continuous crop production during long-term deep space missions is critical for providing consistent nutritional and psychological benefits for the crew, potentially improving their health and performance. Three technology demonstrations were completed achieving simultaneous multi-species plant growth and the concurrent use of two Veggie units on the International Space Station (ISS). Microbiological characterization using molecular and culture-based methods was performed on leaves and roots from two harvests of three leafy greens, red romaine lettuce (Lactuca sativa cv. ‘Outredgeous’); mizuna mustard, (Brassica rapa var japonica); and green leaf lettuce, (Lactuca sativa cv. Waldmann’s) and associated rooting pillow components and Veggie chamber surfaces. Culture based enumeration and pathogen screening indicated the leafy greens were safe for consumption. Surface samples of the Veggie facility and plant pillows revealed low counts of bacteria and fungi and are commonly isolated on ISS. Community analysis was completed with 16S rRNA amplicon sequencing. Comparisons between pillow components, and plant tissue types from VEG-03D, E, and F revealed higher diversity in roots and rooting substrate than the leaves and wick. This work provides valuable information for food production-related research on the ISS and the impact of the plant microbiome on this unique closed environment.

Metagenomic Survey of the Highly Polyphagous Anastrepha ludens Developing in Ancestral and Exotic Hosts Reveals the Lack of a Stable Microbiota in Larvae and the Strong Influence of Metamorphosis on Adult Gut Microbiota

We studied the microbiota of a highly polyphagous insect, Anastrepha ludens (Diptera: Tephritidae), developing in six of its hosts, including two ancestral (Casimiroa edulis and C. greggii), three exotic (Mangifera indica cv. Ataulfo, Prunus persica cv. Criollo, and Citrus x aurantium) and one occasional host (Capsicum pubescens cv. Manzano), that is only used when extreme drought conditions limit fruiting by the common hosts. One of the exotic hosts (“criollo” peach) is rife with polyphenols and the occasional host with capsaicinoids exerting high fitness costs on the larvae. We pursued the following questions: (1) How is the microbial composition of the larval food related to the composition of the larval and adult microbiota, and what does this tell us about transience and stability of this species’ gut microbiota? (2) How does metamorphosis affect the adult microbiota? We surveyed the microbiota of the pulp of each host fruit, as well as the gut microbiota of larvae and adult flies and found that the gut of A. ludens larvae lacks a stable microbiota, since it was invariably associated with the composition of the pulp microbiota of the host plant species studied and was also different from the microbiota of adult flies indicating that metamorphosis filters out much of the microbiota present in larvae. The microbiota of adult males and females was similar between them, independent of host plant and was dominated by bacteria within the Enterobacteriaceae. We found that in the case of the “toxic” occasional host C. pubescens the microbiota is enriched in potentially deleterious genera that were much less abundant in the other hosts. In contrast, the pulp of the ancestral host C. edulis is enriched in several bacterial groups that can be beneficial for larval development. We also report for the first time the presence of bacteria within the Arcobacteraceae family in the gut microbiota of A. ludens stemming from C. edulis. Based on our findings, we conclude that changes in the food-associated microbiota dictate major changes in the larval microbiota, suggesting that most larval gut microbiota is originated from the food.

Genomic analysis of high copy-number sequences for the targeted detection of Listeria species using a flow-through surveillance system

The bacterial foodborne pathogen Listeria monocytogenes has been implicated in fresh produce outbreaks with a significant economic impact. Given that L. monocytogenes is widespread in the environment, food production facilities constantly monitor for the presence of Listeria species. To develop a surveillance platform for food processing facilities, this study conducted a comparative genomic analysis for the identification of conserved high copy sequences in the ribosomal RNA of Listeria species. Simulated folding was performed to assess RNA accessibility in the identified genomic regions targeted for detection, and the developed singleplex assay accurately detected cell amounts lower than 5 cells, while no signals were detected for non-targeted bacteria. The singleplex assay was subsequently tested with a flow-through system, consisting of a DNA aptamer-capture step, followed by sample concentration and mechanical lysis for the detection of Listeria species. Validation experiments indicated the continuous flow-through system accurately detected Listeria species at low cell concentrations.

Evolution of fungal community associated with ready-to-eat pineapple during storage under different temperature conditions

The international market of fresh-cut products has witnessed dramatic growth in recent years, stimulated by consumer's demand for healthy, nutritious and convenient foods. One of the main challenging issues for the quality and safety of these products is the potential microbial spoilage that can significantly reduce their shelf-life. The complete identification of fresh-cut product microbiota together with the evaluation of environmental factors impact on microbial composition is of primary importance. We therefore assessed the fungal communities associated with the spoilage of ready-to-eat (RTE) pineapple using a metagenetic amplicon sequencing approach, based on the ITS2 region. Our results revealed a significant variability on fungal species composition between the different batches of RTE pineapple. The initial microbiota composition was the main influencing factor and determined the progress of spoilage. Temperature and storage time were the secondary factors influencing spoilage and their impact was depending on the initial prevalent fungal species, which showed different responses to the various modifications. Our results strongly suggest that further large-scale sampling of RTE pineapple production should be conducted in order to assess the full biodiversity range of fungal community involved in the spoilage process and for unravelling the impact of important environmental factors shaping the initial microbiota.

Canopy Position Has a Stronger Effect than Tree Species Identity on Phyllosphere Bacterial Diversity in a Floodplain Hardwood Forest

The phyllosphere is a challenging microbial habitat in which microorganisms can flourish on organic carbon released by plant leaves but are also exposed to harsh environmental conditions. Here, we assessed the relative importance of canopy position-top, mid, and bottom at a height between 31 and 20 m-and tree species identity for shaping the phyllosphere microbiome in a floodplain hardwood forest. Leaf material was sampled from three tree species-maple (Acer pseudoplatanus L.), oak (Quercus robur L.), and linden (Tilia cordata MILL.)-at the Leipzig canopy crane facility (Germany). Estimated bacterial species richness (Chao1) and bacterial abundances approximated by quantitative PCR of 16S rRNA genes exhibited clear vertical trends with a strong increase from the top to the mid and bottom position of the canopy. Thirty operational taxonomic units (OTUs) formed the core microbiome, which accounted for 77% of all sequence reads. These core OTUs showed contrasting trends in their vertical distribution within the canopy, pointing to different ecological preferences and tolerance to presumably more extreme conditions at the top position of the canopy. Co-occurrence analysis revealed distinct tree species-specific OTU networks, and 55-57% of the OTUs were unique to each tree species. Overall, the phyllosphere microbiome harbored surprisingly high fractions of Actinobacteria of up to 66%. Our results clearly demonstrate strong effects of the position in the canopy on phyllosphere bacterial communities in a floodplain hardwood forest and-in contrast to other temperate or tropical forests-a strong predominance of Actinobacteria.

Should There Be a Recommended Daily Intake of Microbes?

The collective findings from human microbiome research, randomized controlled trials on specific microbes (i.e., probiotics), and associative studies of fermented dairy consumption provide evidence for the beneficial effects of the regular consumption of safe live microbes. To test the hypothesis that the inclusion of safe, live microbes in the diet supports and improves health, we propose assessment of the types and evidentiary quality of the data available on microbe intake, including the assembly and evaluation of evidence available from dietary databases. Such an analysis would help to identify gaps in the evidence needed to test this hypothesis, which can then be used to formulate and direct initiatives focused on prospective and randomized controlled trials on live microbe consumption. Outcomes will establish whether or not the evidence exists, or can be generated, to support the establishment of dietary recommendations for live microbes.

Commercial wash of leafy vegetables do not significantly decrease bacterial load but leads to shifts in bacterial species composition

Production of leafy vegetables for the "Ready-to-eat"-market has vastly increased the last 20 years, and consumption of these minimally processed vegetables has led to outbreaks of food-borne diseases. Contamination of leafy vegetables can occur throughout the production chain, and therefore washing of the produce has become a standard in commercial processing. This study explores the bacterial communities of spinach (Spinacia oleracea) and rocket (Diplotaxis tenuifolia) in a commercial setting in order to identify potential contamination events, and to investigate effects on bacterial load by commercial processing. Samples were taken in field, after washing of the produce and at the end of shelf-life. This study found that the bacterial community composition and diversity changed significantly from the first harvest to the end of shelf-life, where the core microbiome from the first to the last sampling constituted <2% of all OTUs. While washing of the produce had no reducing effect on bacterial load compared to unwashed, washing led to a change in species composition. As the leaves entered the cold chain after harvest, a rise was seen in the relative abundance of spoilage bacteria. E. coli was detected after the washing indicating issues of cross-contamination in the wash water.

Understanding Phytomicrobiome: A Potential Reservoir for Better Crop Management

Recent crop production studies have aimed at an increase in the biotic and abiotic tolerance of plant communities, along with increased nutrient availability and crop yields. This can be achieved in various ways, but one of the emerging approaches is to understand the phytomicrobiome structure and associated chemical communications. The phytomicrobiome was characterized with the advent of high-throughput techniques. Its composition and chemical signaling phenomena have been revealed, leading the way for “rhizosphere engineering”. In addition to the above, phytomicrobiome studies have paved the way to best tackling soil contamination with various anthropogenic activities. Agricultural lands have been found to be unbalanced for crop production. Due to the intense application of agricultural chemicals such as herbicides, fungicides, insecticides, fertilizers, etc., which can only be rejuvenated efficiently through detailed studies on the phytomicrobiome component, the phytomicrobiome has recently emerged as a primary plant trait that affects crop production. The phytomicrobiome also acts as an essential modifying factor in plant root exudation and vice versa, resulting in better plant health and crop yield both in terms of quantity and quality. Not only supporting better plant growth, phytomicrobiome members are involved in the degradation of toxic materials, alleviating the stress conditions that adversely affect plant development. Thus, the present review compiles the progress in understanding phytomicrobiome relationships and their application in achieving the goal of sustainable agriculture.

Enantioselective effects of imazethapyr residues on Arabidopsis thaliana metabolic profile and phyllosphere microbial communities

Imazethapyr (IM) is a widely used acetolactate synthase-inhibiting chiral herbicide. It has long-term residuals that may be absorbed by the human body through the edible parts of plants, such as vegetable leaves or fruits. Here, we selected a model plant, Arabidopsis thaliana, to determine the effects of R-IM and S-IM on its leaf structure, photosynthetic efficiency, and metabolites, as well as the structures of microorganisms in the phyllosphere, after 7 days of exposure. Our results indicated enantiomeric differences in plant growth between R-IM and S-IM; 133 µg/kg R-IM showed heavier inhibition of photosynthetic efficiency and greater changes to subcellular structure than S-IM. R-IM and S-IM also had different effects on metabolism and leaf microorganisms. S-IM mainly increased lipid compounds and decreased amino acids, while R-IM increased sugar accumulation. The relative abundance of Moraxellaceae human pathogenic bacteria was increased by R-IM treatment, indicating that R-IM treatment may increase leaf surface pathogenic bacteria. Our research provides a new perspective for evaluating the harmfulness of pesticide residues in soil, phyllosphere microbiome changes via the regulation of plant metabolism, and induced pathogenic bacterial accumulation risks.

Phyllosphere bacterial assembly in citrus crop under conventional and ecological management

Divergences between agricultural management can result in different types of biological interactions between plants and microorganisms, which may affect food quality and productivity. Conventional practices are well-established in the agroindustry as very efficient and lucrative; however, the increasing demand for sustainable alternatives has turned attention towards agroecological approaches. Here we intend to explore microbial dynamics according to the agricultural management used, based on the composition and structure of these bacterial communities on the most environmentally exposed habitat, the phyllosphere. Leaf samples were collected from a Citrus crop (cultivated Orange) in Mogi-Guaçu (SP, Brazil), where either conventional or ecological management systems were properly applied in two different areas. NGS sequencing analysis and quantitative PCR allowed us to comprehend the phyllosphere behavior and µ-XRF (micro X-ray fluorescence) could provide an insight on agrochemical persistence on foliar tissues. Our results demonstrate that there is considerable variation in the phyllosphere community due to the management practices used in the citrus orchard, and it was possible to quantify most of this variation. Equally, high copper concentrations may have influenced bacterial abundance, having a relevant impact on the differences observed. Moreover, we highlight the intricate relationship microorganisms have with crop production, and presumably with crop yield as well.

Industrial development as a key factor explaining variances in soil and grass phyllosphere microbiomes in urban green spaces

Microbiota in urban green spaces underpin ecosystem services that are essential to environmental health and human wellbeing. However, the factors shaping the microbial communities in urban green spaces, especially those associated with turf grass phyllosphere, remain poorly understood. The lack of this knowledge greatly limits our ability to assess ecological, social and recreational benefits of urban green spaces in the context of global urbanization. In this study, we used amplicon sequencing to characterize soil and grass phyllosphere bacterial communities in 40 urban green spaces and three minimally disturbed national parks in Victoria, Australia. The results indicated that urbanization might have shown different impacts on soil and grass phyllosphere microbial communities. The bacterial diversity in soil but not in grass phyllosphere was significantly higher in urban green spaces than in national parks. Principal coordinate analysis revealed significant differences in the overall patterns of bacterial community composition between urban green spaces and national parks for both soil and grass phyllosphere. Industrial development, as represented by the number of industries in the region, was identified as a key driver shaping the bacterial community profiles in urban green spaces. Variation partitioning analysis suggested that industrial factors together with their interaction with other factors explained 20% and 28% of the variances in soil and grass phyllosphere bacterial communities, respectively. The findings highlight the importance of industrial development in driving the spatial patterns of urban microbiomes, and have important implication for the management of microbiomes in urban green spaces.

Effect of Bacteria and Bacterial Constituents on Recovery and Resistance of Tulane Virus

Noroviruses encounter numerous and diverse bacterial populations in the host and environment, but the impact of bacteria on norovirus transmission, infection, detection, and inactivation are not well understood. Tulane virus (TV), a human norovirus surrogate, was exposed to viable bacteria, bacterial metabolic products, and bacterial cell constituents and was evaluated for impact on viral recovery, propagation, and inactivation resistance, respectively. TV was incubated with common soil, intestinal, skin, and phyllosphere bacteria, and unbound viruses were recovered by centrifugation and filtration. TV recovery from various bacterial suspensions was not impeded, which suggests a lack of direct, stable binding between viruses and bacteria. The cell-free supernatant (CFS) of Bifidobacterium bifidum 35914, a bacterium that produces glycan-modifying enzymes, was evaluated for effect on the propagation of TV in LLC-MK2 cells. CFS did not limit TV propagation relative to TV absent of CFS. The impact of Escherichia coli O111:B4 lipopolysaccharide (LPS) and Bacillus subtilis peptidoglycan (PEP) on TV thermal and chlorine inactivation resistance was evaluated. PEP increased TV thermal and chlorine inactivation resistance compared with control TV in phosphate-buffered saline (PBS). TV suspended in PBS and LPS was reduced by more than 3.7 log at 60°C, whereas in PEP, TV reduction was approximately 2 log. Chlorine treatment (200 ppm) rendered TV undetectable (>3-log reduction) in PBS and LPS; however, TV was still detected in PEP, reduced by 2.9 log. Virus inactivation studies and food processing practices should account for potential impact of bacteria on viral resistance.

Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications

The phyllosphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communities on the leaf surface. The microbiome of phyllosphere is rich in diversity of bacteria, fungi, actinomycetes, cyanobacteria, and viruses. The diversity, dispersal, and community development on the leaf surface are based on the physiochemistry, environment, and also the immunity of the host plant. A colonization process is an important event where both the microbe and the host plant have been benefited. Microbes commonly established either epiphytic or endophytic mode of life cycle on phyllosphere environment, which helps the host plant and functional communication with the surrounding environment. To the scientific advancement, several molecular techniques like metagenomics and metaproteomics have been used to study and understand the physiology and functional relationship of microbes to the host and its environment. Based on the available information, this chapter describes the basic understanding of microbiome in leaf structure and physiology, microbial interactions, especially bacteria, fungi, and actinomycetes, and their adaptation in the phyllosphere environment. Further, the detailed information related to the importance of the microbiome in phyllosphere to the host plant and their environment has been analyzed. Besides, biopotentials of the phyllosphere microbiome have been reviewed.

Microbiological and Nutritional Analysis of Lettuce Crops Grown on the International Space Station

The ability to grow safe, fresh food to supplement packaged foods of astronauts in space has been an important goal for NASA. Food crops grown in space experience different environmental conditions than plants grown on Earth (e.g., reduced gravity, elevated radiation levels). To study the effects of space conditions, red romaine lettuce, Lactuca sativa cv 'Outredgeous,' plants were grown in Veggie plant growth chambers on the International Space Station (ISS) and compared with ground-grown plants. Multiple plantings were grown on ISS and harvested using either a single, final harvest, or sequential harvests in which several mature leaves were removed from the plants at weekly intervals. Ground controls were grown simultaneously with a 24-72 h delay using ISS environmental data. Food safety of the plants was determined by heterotrophic plate counts for bacteria and fungi, as well as isolate identification using samples taken from the leaves and roots. Molecular characterization was conducted using Next Generation Sequencing (NGS) to provide taxonomic composition and phylogenetic structure of the community. Leaves were also analyzed for elemental composition, as well as levels of phenolics, anthocyanins, and Oxygen Radical Absorbance Capacity (ORAC). Comparison of flight and ground tissues showed some differences in total counts for bacteria and yeast/molds (2.14 - 4.86 log10 CFU/g), while screening for select human pathogens yielded negative results. Bacterial and fungal isolate identification and community characterization indicated variation in the diversity of genera between leaf and root tissue with diversity being higher in root tissue, and included differences in the dominant genera. The only difference between ground and flight experiments was seen in the third experiment, VEG-03A, with significant differences in the genera from leaf tissue. Flight and ground tissue showed differences in Fe, K, Na, P, S, and Zn content and total phenolic levels, but no differences in anthocyanin and ORAC levels. This study indicated that leafy vegetable crops can produce safe, edible, fresh food to supplement to the astronauts' diet, and provide baseline data for continual operation of the Veggie plant growth units on ISS.

Effects of imazethapyr spraying on plant growth and leaf surface microbial communities in Arabidopsis thaliana

Imazethapyr (IM) is an acetolactate synthase (ALS)-inhibiting herbicide that has been widely used in recent years. However, IM spraying can lead to the accumulation of herbicide residues in leaves. Here, we determined the effects of IM spraying on the plant growth and leaf surface microbial communities of Arabidopsis thaliana after 7 and 14 days of exposure. The results suggested that IM spraying inhibited plant growth. Fresh weight decreased to 48% and 26% of the control value after 7 and 14 days, respectively, of 0.035 kg/ha IM exposure. In addition, anthocyanin content increased 9.2-fold and 37.2-fold relative to the control content after 7 and 14 days of treatment, respectively. Furthermore, IM spraying destroyed the cell structures of the leaves, as evidenced by increases in the number of starch granules and the stomatal closure rate. Reductions in photosynthetic efficiency and antioxidant enzyme activity were observed after IM spraying, especially after 14 days of exposure. The diversity and evenness of the leaf microbiota were not affected by IM treatment, but the composition of community structure at the genus level was altered by IM spraying. Imazethapyr application increased the abundance of Pseudomonas, a genus that includes species pathogenic to plants and humans, indicating that IM potentially increased the abundance of pathogenic bacteria on leaves. Our findings increase our understanding of the relationships between herbicide application and the microbial community structures on plant leaves, and they provide a new perspective for studying the ecological safety of herbicide usage.

Leaf mineral content govern microbial community structure in the phyllosphere of spinach (Spinacia oleracea) and rocket (Diplotaxis tenuifolia)

The plant microbiome is an important factor for plant health and productivity. While the impact of nitrogen (N) availability for plant growth and development is well established, its influence on the microbial phyllosphere community structure is unknown. We hypothesize that nitrogen impacts the growth and abundance of several microorganisms on the leaf surface. The bacterial and fungal communities of baby leaf spinach (Spinacia oleracea), and rocket (Diplotaxis tenuifolia) were investigated in a field trial for two years in a commercial setting. Nitrogen fertilizer was tested in four doses (basic nitrogen, basic + suboptimal, basic + commercial, basic + excess) with six replicates in each. Culture-independent (Illumina sequencing) and culture-dependent (viable count and identification of bacterial isolates) community studies were combined with monitoring of plant physiology and site weather conditions. This study found that alpha diversity of bacterial communities decreased in response to increasing nitrogen fertilizer dose, whereas viable counts showed no differences. Correspondingly, fungal communities of the spinach phyllosphere showed a decreasing pattern, whereas the decreasing diversity of fungal communities of rocket was not significant. Plant species and effects of annual variations on microbiome structure were observed for bacterial and fungal communities on both spinach and rocket. This study provides novel insights on the impact of nitrogen fertilizer regime on a nutrient scarce habitat, the phyllosphere.

Dynamics of bacterial communities in alfalfa and mung bean sprouts during refrigerated conditions

Sprouts are considered a healthy ready-to-eat food and has gained popularity in recent years. The objective of the present study was to determine the dynamics of sprouts' microbiome during cold storage to the end of their shelf-life at home. The microbiological quality of fresh alfalfa (Medicago sativa) and mung bean (Vigna radiata) sprouts from two commercial brands was tested and the number of APC ranges from 5.0 to 8.7 log CFU/g in alfalfa and 6.7 to 9.3 log CFU/g in mung bean sprouts. In the case of alfalfa, but not mung beans, there were differences in the mean numbers of APC between the two brands. The number of coliform bacteria ranges from 4.3 to 7.7 log CFU/g in alfalfa and 4.1 to 8.1 log CFU/g in mung bean sprouts. Four independent batches of sprouts were used for DNA preparation and were sampled immediately after purchase and once a week during subsequent storage in refrigerator until the end of their shelf-life. Microbial population of the sprouts was determined using next generation sequencing of 16S rRNA amplicons. Alfalfa sprouts were dominated by Pseudomonas throughout the storage time with relative abundance of >60% at 3 weeks. Fresh mung bean sprouts were dominated by both Pseudomonas and Pantoea, but Pantoea became the dominant taxa after 2 weeks of storage, with >46% of relative abundance. The bacterial communities associated with sprouts were largely dependent on the sprout type, and less dependent on the brand. The species richness and diversity declined during storage and the development of spoilage. Among the 160 genera identified on sprouts, 23 were reported to contain known spoilage-associated species and 30 genera comprise potential human pathogenic species. This study provides new insight into the microbiome dynamics of alfalfa and mung bean sprouts during cold storage.

Establishment Limitation Constrains the Abundance of Lactic Acid Bacteria in the Napa Cabbage Phyllosphere

Patterns of phyllosphere diversity have become increasingly clear with high-throughput sequencing surveys, but the processes that control phyllosphere diversity are still emerging. Through a combination of lab and field experiments using Napa cabbage and lactic acid bacteria (LAB), we examined how dispersal and establishment processes shape the ecological distributions of phyllosphere bacteria. We first determined the abundance and diversity of LAB on Napa cabbage grown at three sites using both culture-based approaches and 16S rRNA gene amplicon sequencing. Across all sites, LAB made up less than 0.9% of the total bacterial community abundance. To assess whether LAB were low in abundance in the Napa cabbage phyllosphere due to a limited abundance in local species pools (source limitation), we quantified LAB in leaf and soil samples across 51 vegetable farms and gardens throughout the northeastern United States. Across all sites, LAB comprised less than 3.2% of the soil bacterial communities and less than 1.6% of phyllosphere bacterial communities. To assess whether LAB are unable to grow in the phyllosphere even if they dispersed at high rates (establishment limitation), we used a gnotobiotic Napa cabbage system in the lab with experimental communities mimicking various dispersal rates of LAB. Even at high dispersal rates, LAB became rare or completely undetectable in experimental communities, suggesting that they are also establishment limited. Collectively, our data demonstrate that the low abundance of LAB in phyllosphere communities may be explained by establishment limitation.IMPORTANCE The quality and safety of vegetable fermentations are dependent on the activities of LAB naturally present in the phyllosphere. Despite their critical role in determining the success of fermentation, the processes that determine the abundance and diversity of LAB in vegetables used for fermentation are poorly characterized. Our work demonstrates that the limited ability of LAB to grow in the cabbage phyllosphere environment may constrain their abundance on cabbage leaves. These results suggest that commercial fermentation of Napa cabbage proceeds despite low and variable abundances of LAB across different growing regions. Propagule limitation may also explain ecological distributions of other rare members of phyllosphere microbes.

Plant species affects establishment of Escherichia coli O157:H7 gfp+ on leafy vegetables

AIMS

Greenhouse trials were conducted with different cultivars of baby leaf spinach, rocket and Swiss chard and inoculation of Escherichia coli O157:H7 gfp+, to determine whether plant species and cultivar have an impact on the establishment of this strain.

METHODS AND RESULTS

Three cultivars each of spinach, rocket and Swiss chard were spray inoculated with E. coli O157:H7 gfp+ at doses of log 7 CFU per ml. Due to the different lengths of growing period spinach and Swiss chard were spray inoculated three times and rocket five times, with final inoculation performed 3 days prior to harvest. After a growing period of 26-33 days, E. coli O157:H7 gfp+ was recovered from the leaf surface in mean populations between log 1 and 6 CFU per gram. The lowest occurrence of E. coli O157:H7 gfp+ was found on rocket leaves and the highest on spinach. There was no significant difference in the establishment of E. coli O157:H7 gfp+ between cultivars, but there were differences between plant species. Indigenous phyllosphere bacteria were pure cultured and identified with 16S rRNA gene sequencing.

CONCLUSIONS

Despite the same high inoculation dose of E. coli O157:H7 gfp+ on leaves, the establishment rate differed between plant species. However, plant cultivar did not affect establishment. Pantoea agglomerans dominated the identified bacterial isolates.

SIGNIFICANCE AND IMPACT OF THE STUDY

As previous studies are inconclusive on choice of model plant species and cultivar, we studied whether plant species or cultivar determines the fate of E. coli O157:H7 gfp+ on leafy vegetables. The findings indicate that plant species is a key determinant in the establishment of E. coli O157:H7 gfp+.

Euonymus japonicus phyllosphere microbiome is significantly changed by powdery mildew

Euonymus japonicus Thunb. is a woody and ornamental plant popular in China, Europe and North America. Powdery mildew is one of the most serious diseases that affect E. japonicus growth. In this study, the diseased and apparently healthy leaves were collected from E. japonicus planted in a greenbelt in Beijing, and the effect of powdery mildew on the epiphytic microbial community was investigated by using Illumina sequencing. The results showed that the healthy leaves (HL) harbored greater bacterial and fungal diversity than diseased leaves (DL). Furthermore, both bacterial and fungal communities in DL exhibited significantly different structures from those in HL. The relative abundance of several bacterial phyla (Proteobacteria and Firmicutes) and fungal phyla (Ascomycota and Basidiomycota) were altered by powdery mildew. At the genus level, most genera decreased as powdery mildew pathogen Erysiphe increased, while the genera Kocuria and Exiguobacterium markedly increased. Leaf properties, especially protein content was found to significantly affect beta-diversity of the bacterial and fungal community. Network analysis revealed that positive bacterial interactions in DL were stronger than those in HL samples. Insights into the underlying the indigenous microbial phyllosphere populations of E. japonicus response to powdery mildew will help in the development of methods for controlling plant diseases.

Gamma Irradiation Influences the Survival and Regrowth of Antibiotic-Resistant Bacteria and Antibiotic-Resistance Genes on Romaine Lettuce

Contamination of romaine lettuce with human pathogens, antibiotic-resistant bacteria (ARB), and antibiotic resistance genes (ARGs) occurs during production. Post-harvest interventions are emplaced to mitigate pathogens, but could also mitigate ARB and ARGs on vegetables. The objective of this research was to determine changes to lettuce phyllosphere microbiota, inoculated ARB, and the resistome (profile of ARGs) following washing with a sanitizer, gamma irradiation, and cold storage. To simulate potential sources of pre-harvest contamination, romaine lettuce leaves were inoculated with compost slurry containing antibiotic-resistant strains of pathogenic (Escherichia coli O157:H7) and representative of spoilage bacteria (Pseudomonas aeruginosa). Various combinations of washing with sodium hypochlorite (50 ppm free chlorine), packaging under modified atmosphere (98% nitrogen), irradiating (1.0 kGy) and storing at 4°C for 1 day versus 14 days were compared. Effects of post-harvest treatments on the resistome were profiled by shotgun metagenomic sequencing. Bacterial 16S rRNA gene amplicon sequencing was performed to determine changes to the phyllosphere microbiota. Survival and regrowth of inoculated ARB were evaluated by enumeration on selective media. Washing lettuce in water containing sanitizer was associated with reduced abundance of ARG classes that confer resistance to glycopeptides, β-lactams, phenicols, and sulfonamides (Wilcoxon, p < 0.05). Washing followed by irradiation resulted in a different resistome chiefly due to reductions in multidrug, triclosan, polymyxin, β-lactam, and quinolone ARG classes (Wilcoxon, p < 0.05). Irradiation followed by storage at 4°C for 14 days led to distinct changes to the β-diversity of the host bacteria of ARGs compared to 1 day after treatment (ANOSIM, R = 0.331; p = 0.003). Storage of washed and irradiated lettuce at 4°C for 14 days increased the relative abundance of Pseudomonadaceae and Carnobacteriaceae (Wilcoxon, p < 0.05), two groups whose presence correlated with detection of 10 ARG classes on the lettuce phyllosphere (p < 0.05). Irradiation resulted in a significant reduction (∼3.5 log CFU/g) of inoculated strains of E. coli O157:H7 and P. aeruginosa (ANOVA, p < 0.05). Results indicate that washing, irradiation and storage of modified atmosphere packaged lettuce at 4°C are effective strategies to reduce antibiotic-resistant E. coli O157:H7 and P. aeruginosa and relative abundance of various ARG classes.

Metagenomic Characterization of Bacterial Communities on Ready-to-Eat Vegetables and Effects of Household Washing on their Diversity and Composition

Ready-to-eat (RTE) leafy salad vegetables are considered foods that can be consumed immediately at the point of sale without further treatment. The aim of the study was to investigate the bacterial community composition of RTE salads at the point of consumption and the changes in bacterial diversity and composition associated with different household washing treatments. The bacterial microbiomes of rocket and spinach leaves were examined by means of 16S rRNA gene high-throughput sequencing. Overall, 886 Operational Taxonomic Units (OTUs) were detected in the salads’ leaves. Proteobacteria was the most diverse high-level taxonomic group followed by Bacteroidetes and Firmicutes. Although they were processed at the same production facilities, rocket showed different bacterial community composition than spinach salads, mainly attributed to the different contributions of Proteobacteria and Bacteroidetes to the total OTU number. The tested household decontamination treatments proved inefficient in changing the bacterial community composition in both RTE salads. Furthermore, storage duration of the salads at refrigeration temperatures affected the microbiome, by decreasing the bacterial richness and promoting the dominance of psychrotropic bacteria. Finally, both salads were found to be a reservoir of opportunistic human pathogens, while washing methods usually applied at home proved to be inefficient in their removal.

Endophytic bacterial communities in peels and pulp of five root vegetables

Plants contain endophytic bacteria, whose communities both influence plant growth and can be an important source of probiotics. Here we used deep sequencing of a 16S rRNA gene fragment and bacterial cultivation to independently characterize the microbiomes of five plant species from divergent taxonomic orders—potato (Solanum tuberosum), carrot (Daucus sativus), beet (Beta vulgaris), neep (Brassica napus spp. napobrassica), and topinambur (Helianthus tuberosus). We found that both species richness and diversity tend to be higher in the peel, where Alphaproteobacteria and Actinobacteria dominate, while Gammaproteobacteria and Firmicutes dominate in the pulp. A statistical analysis revealed that the main characteristic features of the microbiomes of plant species originate from the peel microbiomes. Topinambur pulp displayed an interesting characteristic feature: it contained up to 10⁸ CFUs of lactic acid bacteria, suggesting its use as a source of probiotic bacteria. We also detected Listeria sp., in topinambur pulps, however, the 16S rRNA gene fragment is unable to distinguish between pathogenic versus non-pathogenic species, so the evaluation of this potential health risk is left to a future study.

Long-term organic fertilization increased antibiotic resistome in phyllosphere of maize

Phyllosphere contains various microorganisms that may harbor diverse antibiotic resistance genes (ARGs). However, we know little about the composition of antibiotic resistome and the factors influencing the diversity and abundance of ARGs in the phyllosphere. In this study, 16S rRNA gene amplicon sequencing and high-throughput quantitative PCR approaches were employed to investigate the effects of long-term (over 10 years) organic fertilization on the phyllosphere bacterial communities and antibiotic resistome. Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes dominated in the phyllosphere bacterial communities. Long-term application of sewage sludge and chicken manure altered the phyllosphere bacterial community composition, with a remarkable decrease in bacterial alpha-diversity. A total of 124 unique ARGs were detected in the phyllosphere. The application of sewage sludge and chicken manure significantly increased the abundance of ARGs, with a maximum 2638-fold enrichment. Variation partitioning analysis (VPA) together with network analysis indicated that the profile of ARGs is strongly correlated with bacterial community compositions. These results improve the knowledge about the diversity of plant-associated antibiotic resistome and factors influencing the profile of ARGs in the phyllosphere.

Impact of weather conditions, leaf age and irrigation water disinfection on the major epiphytic bacterial genera of baby spinach grown in an open field

The effects of factors such as weather conditions, leaf age and irrigation water disinfection on the main bacterial genera (total bacterial, Enterobacteriaceae and Pseudomonas) of baby spinach were studied. Culture-dependent and independent quantification techniques were compared. Cultivation was carried out over two consecutive trials in commercial open field divided in two plots: 1) baby spinach irrigated with untreated surface water and 2) baby spinach irrigated with chlorine dioxide (ClO₂) treated water. In all the cases, higher concentrations of bacteria were detected using molecular quantification in comparison with culture dependent techniques. Based on the obtained results, wind speed, solar radiation and relative humidity seem to have an impact on the levels of total bacterial, Enterobacteriaceae and Pseudomonas during cultivation of baby spinach. However, further studies would be needed to confirm this tendency. Water disinfection treatments (ClO₂), when applied to irrigation water, impacted differently the bacterial genera evaluated in the present study. Thus, although no significant effects were observed in total bacterial enumerations of baby spinach irrigated with ClO₂ treated water; significant reductions were detected in Enterobacteriaceae (19%) and Pseudomonas spp. (14%) levels. These results were also confirmed using specific culture-dependent methods. On the other hand, leaf age did not influence the levels of the main bacterial genera of baby spinach. Considering that, a large proportion of foodborne and pathogenic bacteria associated to fresh produce belong to the Enterobacteriaceae family and Pseudomonas genera, reductions in these bacterial groups could be beneficial. However, these groups are very diverse, making difficult to link the measurement of Enterobacteriaceae and Pseudomonas levels with the presence/abundance of potential pathogenic and spoilage microorganisms.

Plant Microbiome and Its Link to Plant Health: Host Species, Organs and Pseudomonas syringae pv. actinidiae Infection Shaping Bacterial Phyllosphere Communities of Kiwifruit Plants

Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of the bacterial canker, the most devastating disease of kiwifruit vines. Before entering the host tissues, this pathogen has an epiphytic growth phase on kiwifruit flowers and leaves, thus the ecological interactions within epiphytic bacterial community may greatly influence the onset of the infection process. The bacterial community associated to the two most important cultivated kiwifruit species, Actinidia chinensis and Actinidia deliciosa, was described both on flowers and leaves using Illumina massive parallel sequencing of the V3 and V4 variable regions of the 16S rRNA gene. In addition, the effect of plant infection by Psa on the epiphytic bacterial community structure and biodiversity was investigated. Psa infection affected the phyllosphere microbiome structures in both species, however, its impact was more pronounced on A. deliciosa leaves, where a drastic drop in microbial biodiversity was observed. Furthermore, we also showed that Psa was always present in syndemic association with Pseudomonas syringae pv. syringae and Pseudomonas viridiflava, two other kiwifruit pathogens, suggesting the establishment of a pathogenic consortium leading to a higher pathogenesis capacity. Finally, the analyses of the dynamics of bacterial populations provided useful information for the screening and selection of potential biocontrol agents against Psa.

Evaluation of post-contamination survival and persistence of applied attenuated E. coli O157:H7 and naturally-contaminating E. coli O157:H7 on spinach under field conditions and following postharvest handling

This study determined the variability in population uniformity of an applied mixture of attenuated E. coli O157:H7 (attEcO157) on spinach leaves as impacted by sampling mass and detection technique over spatial and temporal conditions. Opportunistically, the survival and distribution of naturally contaminating pathogenic E. coli O157:H7 (EcO157), in a single packaged lot following commercial postharvest handling and washing, was also evaluated. From the main study outcomes, differences in the applied inoculum dose of 100-fold, resulted in indistinguishable population densities of approximately Log 1.1 CFU g^-1 by 14 days post-inoculation (DPI). Composite leaf samples of 150 g and the inclusion of the spinach petiole resulted in the greatest numerical sensitivity of detection of attEcO157 when compared to 25 and 150 g samples without petioles (P < 0.05). Differences in population density and protected-site survival and potential leaf internalization were observed between growing seasons and locations in California (P < 0.05). A Double Weibull model best described and identified two distinct populations with different inactivation rates of the inoculated attEcO157. Linear die-off rates varied between 0.14 and 0.29 Log/Day irrespective of location. Detection of EcO157- stx1-negative and stx2-positive, resulting from a natural contamination event, was observed in 11 of 26 quarantined commercial units of washed spinach by applying the 150 g sample mass protocol. The capacity to detect EcO157 varied between commercial test kits and non-commercial qPCR. Our findings suggest the need for modifications to routine pathogen sampling protocols employed for lot acceptance of spinach and other leafy greens.

Impact of chlorine dioxide disinfection of irrigation water on the epiphytic bacterial community of baby spinach and underlying soil

The contamination of pathogenic bacteria through irrigation water is a recognized risk factor for fresh produce. Irrigation water disinfection is an intervention strategy that could be applied to reduce the probability of microbiological contamination of crops. Disinfection treatments should be applied ensuring minimum effective doses, which are efficient in inhibiting the microbial contamination while avoiding formation and accumulation of chemical residues. Among disinfection technologies available for growers, chlorine dioxide (ClO₂) represents, after sodium hypochlorite, an alternative disinfection treatment, which is commercially applied by growers in the USA and Spain. However, in most of the cases, the suitability of this treatment has been tested against pathogenic bacteria and low attention have been given to the impact of chemical residues on the bacterial community of the vegetable tissue. The aim of this study was to (i) to evaluate the continual application of chlorine dioxide (ClO₂) as a water disinfection treatment of irrigation water during baby spinach growth in commercial production open fields, and (ii) to determine the subsequent impact of these treatments on the bacterial communities in water, soil, and baby spinach. To gain insight into the changes in the bacterial community elicited by ClO₂, samples of treated and untreated irrigation water as well as the irrigated soil and baby spinach were analyzed using Miseq® Illumina sequencing platform. Next generation sequencing and multivariate statistical analysis revealed that ClO₂ treatment of irrigation water did not affect the diversity of the bacterial community of water, soil and crop, but significant differences were observed in the relative abundance of specific bacterial genera. This demonstrates the different susceptibility of the bacteria genera to the ClO₂ treatment. Based on the obtained results it can be concluded that the phyllosphere bacterial community of baby spinach was more influenced by the soil bacteria community rather than that of irrigation water. In the case of baby spinach, the use of low residual ClO₂ concentrations (approx. 0.25 mg/L) to treat irrigation water decreased the relative abundance of Pseudomonaceae (2.28-fold) and Enterobacteriaceae (2.5-fold) when comparing treated versus untreated baby spinach. Members of these two bacterial families are responsible for food spoilage and foodborne illnesses. Therefore, a reduction of these bacterial families might be beneficial for the crop and for food safety. In general it can be concluded that the constant application of ClO₂ as a disinfection treatment for irrigation water only caused changes in two bacterial families of the baby spinach and soil microbiota, without affecting the major phyla and classes. The significance of these changes in the bacterial community should be further evaluated.

Screening of microbial communities associated with endive lettuce during postharvest processing on industrial scale

In this study, the composition of the microbial community on endive lettuce (Cichorium endivia) was evaluated during different postharvest processing steps. Microbial community structure was characterized by culture-dependent and culture-independent methods. Endive lettuce was sampled exemplarily at four different stages of processing (raw material, cut endive lettuce, washed endive lettuce, and spin-dried (ready to pack) endive lettuce) and analysed by plate count analysis using non-selective and selective agar plates with subsequent identification of bacteria colonies by matrix-assisted laser desorption/ionization time-of light mass spectrometry (MALDI-TOF MS). Additionally, terminal-restriction fragment length polymorphism (TRFLP) analysis and 16S rRNA gene nucleotide sequence analysis were conducted.

The results revealed structural differences in the lettuce microbiomes during the different processing steps. The most predominant bacteria on endive lettuce were detected by almost all methods. Bacterial species belonging to the families Pseudomonadaceae, Enterobacteriaceae, Xanthomonadaceae, and Moraxellaceae were detected in most of the examined samples including some unexpected potentially human pathogenic bacteria, especially those with the potential to build resistance to antibiotics (e.g., Stenotrophomonas maltophilia (0.9 % in cut sample, 0.4 % in spin-dried sample), Acinetobacter sp. (0.6 % in raw material, 0.9 % in cut sample, 0.9 % in washed sample, 0.4 % in spin-dried sample), Morganella morganii (0.2 % in cut sample, 3 % in washed sample)) revealing the potential health risk for consumers.

However, more seldom occurring bacterial species were detected in varying range by the different methods. In conclusion, the applied methods allow the determination of the microbiome's structure and its dynamic changes during postharvest processing in detail. Such a combined approach enables the implementation of tailored control strategies including hygienic design, innovative decontamination techniques, and appropriate storage conditions for improved product safety.

Characterization of Milkisin, a Novel Lipopeptide With Antimicrobial Properties Produced By Pseudomonas sp. UCMA 17988 Isolated From Bovine Raw Milk

Biosurfactants such as lipopeptides are amphiphilic compounds produced by microorganisms such as bacteria of the genera of Pseudomonas and Bacillus. Some of these molecules proved to have interesting antimicrobial, antiviral, insecticide, and/or tensioactive properties that are potentially useful for the agricultural, chemical, food, and pharmaceutical industries. Raw milk provides a physicochemical environment that is favorable to the multiplication of a broad spectrum of microorganisms. Among them, psychrotrophic bacterial species, especially members of the genus Pseudomonas, are predominant and colonize milk during cold storage and/or processing. We isolated the strain Pseudomonas sp. UCMA 17988 from raw cow milk, with antagonistic activity against Listeria monocytogenes, Staphylococcus aureus, and Salmonella enterica Newport. Antimicrobial molecules involved in the antagonistic activity of this strain were characterized. A mass spectrometry analysis highlighted the presence of four lipopeptides isoforms. The major isoform (1409 m/z), composed of 10 carbons in the lipidic chain, was named milkisin C. The three other isoforms detected at 1381, 1395, and 1423 m/z, that are concomitantly produced, were named milkisin A, B, and D, respectively. The structure of milkisin, as confirmed by nuclear magnetic resonance analyses, is closely related to amphisin family. Indeed, the peptidic chain was composed of 11 amino acids, 6 of which are conserved among the family. In conclusion, Pseudomonas sp. UCMA 17988 produces new members of the amphisin family which are responsible for the antagonistic activity of this strain.