Microbiota Analysis and Microbiological Hazard Assessment in Chinese Chive (Allium tuberosum Rottler) Depending on Retail Types.

Chinese chive (Allium tuberosum Rottler) has potential risks associated with pathogenic bacterial contamination as it is usually consumed raw. In this study, we investigated the microbiota of Chinese chives purchased from traditional markets and grocery stores in March (Spring) and June (Summer) 2017. Differences in bacterial diversity were observed, and the microbial composition varied across sampling times and sites. In June, potential pathogenic genera, such as Escherichia, Enterobacter, and Pantoea, accounted for a high proportion of the microbiota in samples purchased from the traditional market. A large number of pathogenic bacteria (Acinetobacter lwoffii, Bacillus cereus, Klebsiella pneumoniae, and Serratia marcescens) were detected in the June samples at a relatively high rate. In addition, the influence of the washing treatment on Chinese chive microbiota was analyzed. After storage at 26°C, the washing treatment accelerated the growth of enterohemorrhagic Escherichia coli (EHEC) because it caused dynamic shifts in Chinese chive indigenous microbiota. These results expand our knowledge of the microbiota in Chinese chives and provide data for the prediction and prevention of food-borne illnesses.

Study on the Diversity of Fungal and Bacterial Communities in Continuous Cropping Fields of Chinese Chives (Allium tuberosum).

In this study, high-throughput sequencing technology was used to analyse the diversity and composition of fungal and bacterial communities in continuous cropping soil of Chinese chives. The soil nutrient was also measured to explore the rationality of current fertilization management. These results can provide a basis for the prevention and control of the continuous cropping obstacles of Chinese chives and further scientific management. Soil samples from fields continuously cropped with Chinese chives for one year, three years, and five years were collected and analysed. The results showed that the nutrient content of TP, AP, AK and TK increased significantly with increasing continuous cropping years. Short-term continuous cropping soil nutrients have not deteriorated. Alpha-diversity analysis showed that significant differences were not found in the diversity of the fungal and bacterial community among different years. Ascomycota, Basidiomycota and Mortierellomycota were the three most dominant fungal phyla. Proteobacteria, Actinobacteria, Chloroflexi and Acidobacteria were the dominant bacterial phyla. Continuous cropping makes Fusarium increase, and the beneficial bacteria Pseudomonas decreased significantly. According to the correlation heat map analysis of environmental factors, excessive phosphorus may lead to the increase of Fusarium, potassium may promote the proliferation of beneficial bacteria in the continuous cropping process, and it is necessary to regulate the application of phosphate and potassium fertilizer.

Control of Panama disease of banana by intercropping with Chinese chive (Allium tuberosum Rottler): cultivar differences.

Panama disease (Fusarium wilt disease) caused by Fusarium oxysporum f. sp. cubense race 4 (FOC) severely threatens banana (Musa spp.) production worldwide. Intercropping of banana with Allium plants has shown a potential to reduce Panama disease. In this study, six cultivars of Chinese chive (Allium tuberosum Rottler) were selected to compare their differences in antifungal activity and active compounds. Three cultivars Duokang Fujiu 11, Fujiuhuang 2, and Duokang Sijiqing with higher levels of antifungal compounds were further used for intercropping with banana in the pots and field to compare their effects on growth and disease incidence of banana.The six cultivars showed significant differences in antifungal activity against FOC mycelia growth in both leaf volatiles and aqueous leachates. The aqueous leachates displayed stronger antifungal activity than the volatiles. FJH cultivar showed the best inhibitory effect among all six cultivars. Contents of three main antifungal compounds dipropyl trisulfide (DPT), dimethyl trisulfide (DMT), and 2-methyl-2-pentenal (MP) in volatiles and aqueous leachates varied considerably among cultivars. Pot and field experiments showed that intercropping with three selected Chinese chive cultivars significantly improved banana vegetative growth, increased photosynthetic characteristics and yield but decreased disease incidence of Panama disease.Our results indicate that intercropping with Chinese chive shows potential to reduce banana Panama disease and selection of appropriate cultivars is vital for effective disease control.

The variability of bacterial communities in both the endosphere and ectosphere of different niches in Chinese chives (Allium tuberosum).

Deciphering the various types of interactions between plants and their microbiomes is a hot topic for research in ecology as well as in plant sciences and agronomy. To analyse and compare the differences in microbial communities in different compartments of Chinese chives, high-throughput sequencing technology was employed to amplify and sequence the V5-V6 region of the 16S rDNA of microorganisms in the leaves, phylloplanes, stems, roots and rhizospheres of Chinese chives. The sequences were clustered by operational taxonomic units (OTUs), and the community composition of bacteria between the endosphere (inner tissues) and ectosphere (outer surfaces) of Chinese chives was analysed based on the OTU. Overall, the results indicated that the endophytic bacteria in Chinese chives mainly include Proteobacteria, Actinobacteria, and Actinomycetes. Alpha diversity index analysis and OTU number analysis showed that the bacterial diversity and richness of the underground plant compartments were higher than those of the above-ground parts. PCoA based on the OTU level showed that the vertical stratification structure of plants and compartments had significant effects on the bacterial community structure. The richness of endophytic bacteria also varied greatly among the different varieties of Chinese chive. A considerable number of endophytic bacteria form symbiotic and mutually beneficial relationships with host plants, which play an important role in regulating host growth, metabolism and stress resistance. Further investigations are needed to uncover the evolution of interactions between plants and endophytes.

Di-n-butyl phthalate degrading endophytic bacterium Bacillus amyloliquefaciens subsp. strain JR20 isolated from garlic chive and its colonization in a leafy vegetable.

Di-n-butyl phthalate (DBP) is one of the primary PAEs (phthalate acid esters) pollutants. DBP can be absorbed by plants and threaten human health via the food chain. Some DBP-degrading bacteria have been successfully isolated from the environment (water, soil, etc.). However, only a few DBP-degrading plant endophytes have been isolated. In this study, an endophytic bacterium, Bacillus amyloliquefaciens subsp. strain JR20, which was found capable of degrading DBP, was isolated from garlic chive. We found that strain JR20 metabolized 89.74% of DBP at a 5 mg/L concentration within 4 d in liquid mineral salts medium (MSM). The optimized conditions for maximum removal of DBP were as follows: DBP concentration, 5 mg/L; pH, 7-8; temperature, 30-40 °C. The colonization of strain JR20 significantly improved the degradation rate of DBP in the roots, stems and leaves of leafy vegetables.

Tracing back multidrug-resistant bacteria in fresh herb production: from chive to source through the irrigation water chain.

Environmental antibiotic-resistant bacteria (ARB) can be transferred to humans through foods. Fresh produce in particular is an ideal vector due to frequent raw consumption. A major contamination source of fresh produce is irrigation water. We hypothesized that water quality significantly affects loads of ARB and their diversity on fresh produce despite various other contamination sources present under agricultural practice conditions. Chive irrigated from an open-top reservoir or sterile-filtered water (control) was examined. Heterotrophic plate counts (HPC) and ARB were determined for water and chive with emphasis on Escherichia coli and Enterococcus spp. High HPC of freshly planted chive decreased over time and were significantly lower on control- vs. reservoir-irrigated chive at harvest (1.3 log (CFU/g) lower). Ciprofloxacin- and ceftazidime-resistant bacteria were significantly lower on control-irrigated chive at harvest and end of shelf life (up to 1.8 log (CFU/g) lower). Escherichia coli and Enterococcus spp. repeatedly isolated from water and chive proved resistant to up to six or four antibiotic classes (80% or 49% multidrug-resistant, respectively). Microbial source tracking identified E. coli-ST1056 along the irrigation chain and on chive. Whole-genome sequencing revealed that E. coli-ST1056 from both environments were clonal and carried the same transmissible multidrug-resistance plasmid, proving water as source of chive contamination. These findings emphasize the urgent need for guidelines concerning ARB in irrigation water and development of affordable water disinfection technologies to diminish ARB on irrigated produce.

Host- and stage-dependent secretome of the arbuscular mycorrhizal fungus Rhizophagus irregularis.

Arbuscular mycorrhizal fungi form the most wide-spread endosymbiosis with plants. There is very little host specificity in this interaction, however host preferences as well as varying symbiotic efficiencies have been observed. We hypothesize that secreted proteins (SPs) may act as fungal effectors to control symbiotic efficiency in a host-dependent manner. Therefore, we studied whether arbuscular mycorrhizal (AM) fungi adjust their secretome in a host- and stage-dependent manner to contribute to their extremely wide host range. We investigated the expression of SP-encoding genes of Rhizophagus irregularis in three evolutionary distantly related plant species, Medicago truncatula, Nicotiana benthamiana and Allium schoenoprasum. In addition we used laser microdissection in combination with RNA-seq to study SP expression at different stages of the interaction in Medicago. Our data indicate that most expressed SPs show roughly equal expression levels in the interaction with all three host plants. In addition, a subset shows significant differential expression depending on the host plant. Furthermore, SP expression is controlled locally in the hyphal network in response to host-dependent cues. Overall, this study presents a comprehensive analysis of the R. irregularis secretome, which now offers a solid basis to direct functional studies on the role of fungal SPs in AM symbiosis.

Degradation of chlorpyrifos by an endophytic bacterium of the Sphingomonas genus (strain HJY) isolated from Chinese chives (Allium tuberosum).

The degradation of chlorpyrifos (CP) by an endophytic bacterial strain (HJY) isolated from Chinese chives (Allium tuberosum Rottl. ex Spreng) was investigated. Strain HJY was identified as Sphingomonas sp. based on morphological, physiological, and biochemical tests and a 16S rDNA sequence analysis. Approximately 96% of 20 mg L-1 CP was degraded by strain HJY over 15 days in liquid minimal salts medium (MSM). The CP degradation rate could also be increased by glucose supplementation. The optimal conditions for the removal of 20 mg L-1 CP by strain HJY in MSM were 2% inoculum density, pH 6.0, and 30-35°C. The CP degradation rate constant and half-life were 0.2136 ± 0.0063 d-1 and 3.2451 ± 0.0975 d, respectively, under these conditions, but were raised to 0.7961 ± 0.1925 d-1 and 0.8707 ± 0.3079 d with 1% glucose supplementation. The detection of metabolic products and screening for degrading genes indicated that O,O-diethyl O-3,5,6-trichloropyridinol was the major degradation product from CP, while it was likely that some functional genes were undetected and the mechanism responsible for CP degradation by strain HJY remained unknown. Strain HJY is potentially useful for the reduction of CP residues in Chinese chives and may be used for the in situ phytoremediation of CP.

Isolation, Colonization, and Chlorpyrifos Degradation Mediation of the Endophytic Bacterium Sphingomonas Strain HJY in Chinese Chives (Allium tuberosum).

The endophyte-plant interaction can benefit the host in many different ways. An endophytic bacterium strain (HJY) capable of degrading chlorpyrifos (CP) was isolated from Chinese chives (Allium tuberosum Rottl. ex Spreng). The isolated bacterium HJY classified as Sphingomonas sp. strain HJY could use CP as the sole carbon source. After being marked with the gfp gene, the colonization and distribution of strain HJY-gfp were directly observed in different tissues of Chinese chives with a confocal laser scanning microscope. The inoculation of strain HJY-gfp in Chinese chives resulted in a higher degradation of CP inside the plants than in uninoculated plants. With drench application, up to 70 and 66% of CP were removed from shoots and roots of inoculated Chinese chives, respectively. Moreover, up to 75% of CP was removed from the soil containing plants inoculated with HJY-gfp. With foliage application, the applied concentration of chlorpyrifos affected the degradation performance of strain HJY in Chinese chives. Significant differences were observed only between inoculated and uninoculated Chinese chives with the low applied concentration of CP. Together, other than natural endophyte-assisted plant protection for food safety, the interaction of HJY and plant may be also a promising strategy for in situ bioremediation of soil contaminated with CP.

Secondary Metabolites from Endophytic Fungus Penicillium pinophilum Induce ROS-Mediated Apoptosis through Mitochondrial Pathway in Pancreatic Cancer Cells.

The endophytic fungus strain MRCJ-326, isolated from Allium schoenoprasum, which is also known as Snow Mountain Garlic or Kashmiri garlic, was identified as Penicillium pinophilum on the basis of morphological characteristics and internal transcribed spacer region nucleotide sequence analysis. The endophytic fungus extract was subjected to 2D-SEPBOX bioactivity-guided fractionation and purification. The anthraquinone class of the bioactive secondary metabolites were isolated and characterized as oxyskyrin (1), skyrin (2), dicatenarin (3), and 1,6,8-trihydroxy-3-hydroxy methylanthraquinone (4) by spectral analysis. Dicatenarin and skyrin showed marked growth inhibition against the NCI60/ATCC panel of human cancer cell lines with least IC50 values of 12 µg/mL and 27 µg/mL, respectively, against the human pancreatic cancer (MIA PaCa-2) cell line. The phenolic hydroxyl group in anthraquinones plays a crucial role in the oxidative process and bioactivity. Mechanistically, these compounds, i.e., dicatenarin and skyrin, significantly induce apoptosis and transmit the apoptotic signal via intracellular reactive oxygen species generation, thereby inducing a change in the mitochondrial transmembrane potential and induction of the mitochondrial-mediated apoptotic pathway. Our data indicated that dicatenarin and skyrin induce reactive oxygen species-mediated mitochondrial permeability transition and resulted in an increased induction of caspase-3 apoptotic proteins in human pancreatic cancer (MIA PaCa-2) cells. Dicatenarin showed a more pronounced cytotoxic/proapopotic effect than skyrin due to the presence of an additional phenolic hydroxyl group at C-4, which increases oxidative reactive oxygen species generation. This is the first report from P. pinophilum secreating these cytotoxic/proapoptotic secondary metabolites.

Shoot Injury Increases the Level of Persistence of Salmonella enterica Serovar Sofia and Listeria innocua on Cos Lettuce and of Salmonella enterica Serovar Sofia on Chive.

Minor shoot injury significantly (P < 0.05) increased the level at which Salmonella enterica serovar Sofia persisted on cos lettuce in the greenhouse. Initial mean counts of the Salmonella on the injured and uninjured cos lettuce were on the order of 6 log CFU/g. After 3 days, the mean count decreased to 4.8 log CFU/g on the injured plants compared with the significantly (P < 0.05) smaller count of 3.4 log CFU/g on the uninjured plants. By the end of the 3-week experiment, the count from the injured plants was 2.9 log CFU/g compared with a count of below the level of detection from the uninjured plants. A similar pattern of bacterial persistence was observed on injured versus uninjured plants by using Listeria innocua on cos lettuce and S. enterica serovar Sofia on chive. The findings reaffirm earlier results with Escherichia coli and increase the impetus to avoid shoot injury during the production of cos lettuce and chive, if bacteria of food safety concern are present.

Comparison of the microbiological quality of environmentally friendly and conventionally grown vegetables sold at retail markets in Korea.

Fresh produce is usually eaten raw without cooking or heating, which may increase the probability of foodborne infection. The microbiological quality of 11 types of fresh, raw vegetables (romaine lettuce, sesame leaves, crown daisy, garlic chives, iceberg lettuce, cabbage, broccoli, leek, chili pepper, capsicum, and zucchini) purchased at retail markets in Iksan, Korea as affected by cultivation method (environmentally friendly vegetables [organic, pesticide-free, and low-pesticide vegetables] and conventionally grown vegetables) and harvest season was determined. Escherichia coli O157:H7 and Salmonella were not detected in all samples of vegetables tested. Aerobic mesophiles (>6 log cfu/g) were detected in environmentally friendly romaine lettuce and crown daisy and environmentally friendly and conventionally grown garlic chives, which also contained coliforms (>3 log cfu/g). Sesame leaf and crown daisy (regardless of cultivation method), as well as conventionally grown romaine lettuce and leek, contained >1 log cfu/g of E. coli. The overall microbiological quality of environmentally friendly and conventionally grown vegetables was not significantly different (P > 0.05). However, there were seasonal effects on populations of coliforms and generic E. coli on vegetables. The greatest numbers of microorganisms were isolated from environmentally friendly or conventionally grown vegetables purchased in winter. The vegetables, regardless of cultivation method or season, should be subjected to appropriate antimicrobial treatment to enhance their microbial safety.

Efficacy of different sanitizing agents and their combination on microbe population and quality of fresh-cut Chinese chives.

UNLABELLED: The objective of this study was to evaluate the efficacy of individual sanitizing agents (sodium hypochlorite, SH; peracetic acid, PA; chlorine dioxide, CD) and the combination of CD and PA on reducing the total aerobic bacteria, coliforms as well as their effects on ascorbic acid (Vc), chlorophyll, and a* value of Chinese chives. All sanitizing treatments significantly (P < 0.05) reduced microorganisms compared to the control. After treatment with single SH, PA, and CD, the reduction of the total aerobic bacteria on Chinese chives was <1.0 log CFU/g (where colony-forming units is CFU), approximately 1.68 to 2.22 log CFU/g, and approximately 0.99 to 2.85 log CFU/g, respectively. The greatest reduction of total aerobic bacteria achieved by the combination of 40 ppm CD, 150 ppm PA for 8 min, was 2.45 log CFU/g. This treatment had a slight discoloration effect as indicated by a* value and chlorophyll content; and is therefore the optimal combination for reducing microorganisms on Chinese chives. PRACTICAL APPLICATION: Fresh-cut vegetables are known to be susceptible to contamination; and subsequent growth of microorganisms result in quality concerns. Chinese chive leaves are hollow, cylindrical, and are more inclined to accumulate microbes. Currently, there is limited information on the decontamination of Chinese chives. This research focused on the evaluation of sanitation options for fresh-cut Chinese chives; and the information obtained should be applicable and useful in other fresh-cut vegetables.

Aislamiento de Conidiobolus coronatus a partir de una plaga de áfidos del cebollín (Allium schoenoprasum L. ) / Conidiobolus coronatus isolation from a pest aphids of chives (Allium schoenoprasum L. )

Conidiobolus coronatus, entomoftoral patógeno para el hombre y algunosinsectos, se aisló a partir de especímenes muertos del áfido Neotoxopteraformosana sobre hojas de Allium schoenoprasum. La presencia deC. coronatus supone el riesgo de una potencial infección para quienestrabajan en la producción de cebollín. El control fitosanitario de N. formosanapodría, además, contribuir a reducir el riesgo de infección humana conC. coronatus(AU)

Conidiobolus coronatus (Entomophthorales), a pathogen of human and someinsects, was isolated from dead specimens of the aphid Neotoxopteraformosana present on chives leaves. C. coronatus infected aphids could posea threat to growers health. Pest control strategies of N. formosana may alsocontribute to reduce the human infection risk by C. coronatus(AU)

Fates of seeded Escherichia coli O157:H7 and Salmonella on selected fresh culinary herbs during refrigerated storage.

The fates of seeded Escherichia coli O157:H7 and Salmonella on selected fresh culinary herbs were evaluated at a refrigerated temperature (4 degrees C). Fresh herbs, including cilantro, oregano, basil, chive, parsley, and rosemary, were inoculated with six-strain mixtures of E. coli O157:H7 and Salmonella, and the microbial populations were monitored at 1, 5, 11, 16, 19, and 24 days. For both pathogens, a significant decrease in the population (P < 0.0001) occurred within the first 5 days of storage (< 0.8 log). Both pathogens remained the highest on cilantro and the lowest on rosemary (P < 0.0001). Storage time had a significant effect on the survival of E. coli O157:H7; populations declined as storage time progressed. Although storage of cilantro, basil, and chive was terminated after 19 days because of deteriorated quality, significant numbers of both pathogens were recovered from the remaining fresh herbs after 24 days of storage. The results showed that both bacteria were extremely persistent on all test herbs under the test conditions. The results also reinforce the concept that, once contaminated, bacterial pathogens can persist on fresh herbs throughout a normal distribution time.