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Li WJ, Li HZ, Xu J, Gillings MR, Zhu YG. Sewage Sludge Promotes the Accumulation of Antibiotic Resistance Genes in Tomato Xylem. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:10796-10805. [PMID: 38853591 DOI: 10.1021/acs.est.4c02497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Xylem serves as a conduit linking soil to the aboveground plant parts and facilitating the upward movement of microbes into leaves and fruits. Despite this potential, the composition of the xylem microbiome and its associated risks, including antibiotic resistance, are understudied. Here, we cultivated tomatoes and analyzed their xylem sap to assess the microbiome and antibiotic resistance profiles following treatment with sewage sludge. Our findings show that xylem microbes primarily originate from soil, albeit with reduced diversity in comparison to those of their soil microbiomes. Using single-cell Raman spectroscopy coupled with D2O labeling, we detected significantly higher metabolic activity in xylem microbes than in rhizosphere soil, with 87% of xylem microbes active compared to just 36% in the soil. Additionally, xylem was pinpointed as a reservoir for antibiotic resistance genes (ARGs), with their abundance being 2.4-6.9 times higher than in rhizosphere soil. Sludge addition dramatically increased the abundance of ARGs in xylem and also increased their mobility and host pathogenicity. Xylem represents a distinct ecological niche for microbes and is a significant reservoir for ARGs. These results could be used to manage the resistome in crops and improve food safety.
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Affiliation(s)
- Wen-Jing Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hong-Zhe Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jiayang Xu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Michael R Gillings
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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Rangel LI, Leveau JHJ. Applied microbiology of the phyllosphere. Appl Microbiol Biotechnol 2024; 108:211. [PMID: 38358509 PMCID: PMC10869387 DOI: 10.1007/s00253-024-13042-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/16/2024]
Abstract
The phyllosphere, or plant leaf surface, represents a microbial ecosystem of considerable size, holding extraordinary biodiversity and enormous potential for the discovery of new products, tools, and applications in biotechnology, agriculture, medicine, and elsewhere. This mini-review highlights the applied microbiology of the phyllosphere as an original field of study concerning itself with the genes, gene products, natural compounds, and traits that underlie phyllosphere-specific adaptations and services that have commercial and economic value for current or future innovation. Examples include plant-growth-promoting and disease-suppressive phyllobacteria, probiotics and fermented foods that support human health, as well as microbials that remedy foliar contamination with airborne pollutants, residual pesticides, or plastics. Phyllosphere microbes promote plant biomass conversion into compost, renewable energy, animal feed, or fiber. They produce foodstuffs such as thickening agents and sugar substitutes, industrial-grade biosurfactants, novel antibiotics and cancer drugs, as well as enzymes used as food additives or freezing agents. Furthermore, new developments in DNA sequence-based profiling of leaf-associated microbial communities allow for surveillance approaches in the context of food safety and security, for example, to detect enteric human pathogens on leafy greens, predict plant disease outbreaks, and intercept plant pathogens and pests on internationally traded goods. KEY POINTS: • Applied phyllosphere microbiology concerns leaf-specific adaptations for economic value • Phyllobioprospecting searches the phyllosphere microbiome for product development • Phyllobiomonitoring tracks phyllosphere microbial profiles for early risk detection.
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Affiliation(s)
- Lorena I Rangel
- Cell & Molecular Sciences, The James Hutton Institute, Dundee, Scotland, UK.
- Department of Plant Pathology, University of California, Davis, CA, USA.
| | - Johan H J Leveau
- Department of Plant Pathology, University of California, Davis, CA, USA.
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3
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Winter H, Wagner R, Yao Y, Ehlbeck J, Schnabel U. Influence of plasma-treated air on surface microbial communities on freshly harvested lettuce. Curr Res Food Sci 2023; 7:100649. [PMID: 38115898 PMCID: PMC10728334 DOI: 10.1016/j.crfs.2023.100649] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/07/2023] [Accepted: 11/25/2023] [Indexed: 12/21/2023] Open
Abstract
Plant-based foods like lettuce are an important part of the human diet and worldwide industry. On a global scale, the number of food-associated illnesses increased in the last decades. Conventional lettuce sanitation methods include cleaning either with tap or chloritized water. Beside these water-consuming strategies, physical plasma is an innovative and effective possibility for food sanitation. Recent studies with plasma-treated water showed an effective reduction of the microbial load. Plasma-processed air (PPA) is another great opportunity to reduce the microbial load and save water. To test the efficiency of PPA, the surface microbiome of treated lettuce was analyzed via proliferation assays with special agars, live/dead assays and tests for respiratory activity of the microorganisms. PPA showed a reduction of the colony forming units (CFU/mL) on all tested microbial groups (Gram-negative and Gram-positive bacteria, yeasts and molds). These results were supported by the live/dead assay. For further insights, the PPA-ingredients were detected with Fourier Transformation Infrared Spectroscopy (FTIR), which revealed NO2, NO and N2O5 as the main reactive species in the PPA. In the future, PPA could be an outstanding, on-demand sanitation step for higher food safety standards, especially in situations where humidity and high temperature should be avoided.
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Affiliation(s)
- Hauke Winter
- Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Strasse 2, 17489, Greifswald, Germany
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Strasse 8, 17489, Greifswald, Germany
| | - Robert Wagner
- Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Strasse 2, 17489, Greifswald, Germany
| | - Yijiao Yao
- Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Strasse 2, 17489, Greifswald, Germany
- Department of Food & Nutritional Sciences, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | - Jörg Ehlbeck
- Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Strasse 2, 17489, Greifswald, Germany
| | - Uta Schnabel
- Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Strasse 2, 17489, Greifswald, Germany
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Pan X, Raaijmakers JM, Carrión VJ. Importance of Bacteroidetes in host-microbe interactions and ecosystem functioning. Trends Microbiol 2023; 31:959-971. [PMID: 37173204 DOI: 10.1016/j.tim.2023.03.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 05/15/2023]
Abstract
Bacteroidetes are prevalent in soil ecosystems and are associated with various eukaryotic hosts, including plants, animals, and humans. The ubiquity and diversity of Bacteroidetes exemplify their impressive versatility in niche adaptation and genomic plasticity. Over the past decade, a wealth of knowledge has been obtained on the metabolic functions of clinically relevant Bacteroidetes, but much less attention has been given to Bacteroidetes living in close association with plants. To improve our understanding of the functional roles of Bacteroidetes for plants and other hosts, we review the current knowledge of their taxonomy and ecology, in particular their roles in nutrient cycling and host fitness. We highlight their environmental distribution, stress resilience, genomic diversity, and functional importance in diverse ecosystems, including, but not limited to, plant-associated microbiomes.
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Affiliation(s)
- Xinya Pan
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands; Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain; Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Málaga, Spain.
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Shao L, Liu X, Liu Y, Shen J, Liu R, Chen P. Dissemination and characterization of Stenotrophomonas maltophilia isolates from Dairy Cows in Northeast China. Pol J Microbiol 2023; 72:319-323. [PMID: 37725894 PMCID: PMC10508971 DOI: 10.33073/pjm-2023-032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 07/14/2023] [Indexed: 09/21/2023] Open
Abstract
This work investigated the genetic relationship among Stenotrophomonas maltophilia strains in fecal samples from dairy cows in northeast China and identified the dominant β-lactamase genotype. One hundred and six samples were collected from two randomly selected cow farms in northeast China, and the isolates were identified with MALDI-TOF/MS. Whole-genome sequencing was conducted using Illumina HiSeq 4000-PE150 platform (Illumina, Inc., USA). The antimicrobial resistance genes were detected using CGE services. The phylogenetic analysis of S. maltophilia strains was performed by Roary and MEGA X. In total, 24 S. maltophilia isolates were isolated. The results of resistome analysis showed all S. maltophilia strains carrying bla L1 gene, which was the only β-lactamase genotype. In addition, the aminoglycoside resistance genes aac(6')-Iz and aph(3')-IIc were found. The phylogenetic tree indicated the clonal diversity of S. maltophilia in these two regions and the clonal relatedness of the strains from these regions. This study first investigated the dissemination and characterization of S. maltophilia isolates from dairy cows in northeast China and provided evidence of the potential transmission between two provinces. Furthermore, it indicated bla L1 was the most prevalent genotype of β-lactamase in these regions.
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Affiliation(s)
- Lanjun Shao
- Health Management Center, The Third Affiliated Hospital of Zhejiang Traditional Chinese Medical University, Hangzhou, China
| | - Xiaojing Liu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Structure and Morphology, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Yi Liu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Shen
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ruishan Liu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Structure and Morphology, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Pingnan Chen
- Department of Laboratory Medicine, Pingguo People's Hospital, Baise, China
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6
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Antimicrobial Susceptibility of Fresh Produce-Associated Enterobacteriaceae and Enterococci in Oman. Foods 2022; 11:foods11193085. [PMID: 36230161 PMCID: PMC9562674 DOI: 10.3390/foods11193085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/29/2022] [Accepted: 09/29/2022] [Indexed: 11/24/2022] Open
Abstract
Fresh produce bacteria may have phenotypic and/or genotypic antimicrobial resistance traits that may lead to various consequences on the environment and human health. This study evaluated the susceptibility of fresh produce bacteria (banana, cabbage, capsicum, carrots, cucumber, dates, lettuce, mango, papaya, pomegranate, radish, tomato and watermelon) to chlorhexidine and the antibiotic resistance of enterococci. Eighty-eight Enterobacteriaceae bacteria and 31 enterococci were screened for their susceptibility to chlorhexidine using the broth microdilution method. Susceptibility of enterococci to various antibiotics was determined using agar dilution, colorimetric, and Kirby-Bauer disc diffusion methods. Enterococci were more susceptible to chlorhexidine than Enterobacteriaceae indicated by chlorhexidine minimum inhibitory concentration (MIC) of 1 to 8 µg/mL for the former and 1 to 64 µg/mL for the latter. The IntI 1, qacEΔ1, qacE and qacG genes were distributed weakly in three, two, two, and three Enterobacteriaceae isolates, respectively. Enterococci had resistance to chloramphenicol (3%), tetracycline (19%), erythromycin (68%), ciprofloxacin (55%), and vancomycin (10%) while 19% of them were multi-drug resistant. In conclusion, this research detected a low to moderate level of antibiotic resistance in enterococci. Some Enterobacteriaceae bacteria had reduced chlorhexidine MICs that were not 10x less than the recommended concentration (100–200 µg/mL) in food production areas which might challenge the success of the disinfection processes or have clinical implications if the involved bacteria are pathogens. The prevalence of antimicrobial-resistant bacteria in fresh produce should be monitored in the future.
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Leonard SR, Simko I, Mammel MK, Richter TKS, Brandl MT. Seasonality, shelf life and storage atmosphere are main drivers of the microbiome and E. coli O157:H7 colonization of post-harvest lettuce cultivated in a major production area in California. ENVIRONMENTAL MICROBIOME 2021; 16:25. [PMID: 34930479 PMCID: PMC8686551 DOI: 10.1186/s40793-021-00393-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/30/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND Lettuce is linked to recurrent outbreaks of Shiga toxin-producing Escherichia coli (STEC) infections, the seasonality of which remains unresolved. Infections have occurred largely from processed lettuce, which undergoes substantial physiological changes during storage. We investigated the microbiome and STEC O157:H7 (EcO157) colonization of fresh-cut lettuce of two cultivars with long and short shelf life harvested in the spring and fall in California and stored in modified atmosphere packaging (MAP) at cold and warm temperatures. RESULTS Inoculated EcO157 declined significantly less on the cold-stored cultivar with short shelf life, while multiplying rapidly at 24 °C independently of cultivar. Metagenomic sequencing of the lettuce microbiome revealed that the pre-storage bacterial community was variable but dominated by species in the Erwiniaceae and Pseudomonadaceae. After cold storage, the microbiome composition differed between cultivars, with a greater relative abundance (RA) of Erwiniaceae and Yersiniaceae on the cultivar with short shelf life. Storage at 24 °C shifted the microbiome to higher RAs of Erwiniaceae and Enterobacteriaceae and lower RA of Pseudomonadaceae compared with 6 °C. Fall harvest followed by lettuce deterioration were identified by recursive partitioning as important factors associated with high EcO157 survival at 6 °C, whereas elevated package CO2 levels correlated with high EcO157 multiplication at 24 °C. EcO157 population change correlated with the lettuce microbiome during 6 °C storage, with fall microbiomes supporting the greatest EcO157 survival on both cultivars. Fall and spring microbiomes differed before and during storage at both temperatures. High representation of Pantoea agglomerans was a predictor of fall microbiomes, lettuce deterioration, and enhanced EcO157 survival at 6 °C. In contrast, higher RAs of Erwinia persicina, Rahnella aquatilis, and Serratia liquefaciens were biomarkers of spring microbiomes and lower EcO157 survival. CONCLUSIONS The microbiome of processed MAP lettuce evolves extensively during storage. Under temperature abuse, high CO2 promotes a lettuce microbiome enriched in taxa with anaerobic capability and EcO157 multiplication. In cold storage, our results strongly support a role for season and lettuce deterioration in EcO157 survival and microbiome composition, suggesting that the physiology and microbiomes of fall- and spring-harvested lettuce may contribute to the seasonality of STEC outbreaks associated with lettuce grown in coastal California.
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Affiliation(s)
- Susan R Leonard
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Ivan Simko
- Crop Improvement and Protection Research Unit, US Department of Agriculture, Agricultural Research Service, Salinas, CA, USA
| | - Mark K Mammel
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Taylor K S Richter
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Maria T Brandl
- Produce Safety and Microbiology Research Unit, US Department of Agriculture, Agricultural Research Service, Albany, CA, USA.
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Singh RK, Singh P, Guo DJ, Sharma A, Li DP, Li X, Verma KK, Malviya MK, Song XP, Lakshmanan P, Yang LT, Li YR. Root-Derived Endophytic Diazotrophic Bacteria Pantoea cypripedii AF1 and Kosakonia arachidis EF1 Promote Nitrogen Assimilation and Growth in Sugarcane. Front Microbiol 2021; 12:774707. [PMID: 34975800 PMCID: PMC8714890 DOI: 10.3389/fmicb.2021.774707] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/12/2021] [Indexed: 11/15/2022] Open
Abstract
Excessive, long-term application of chemical fertilizers in sugarcane crops disrupts soil microbial flora and causes environmental pollution and yield decline. The role of endophytic bacteria in improving crop production is now well-documented. In this study, we have isolated and identified several endophytic bacterial strains from the root tissues of five sugarcane species. Among them, eleven Gram-negative isolates were selected and screened for plant growth-promoting characteristics, i.e., production of siderophores, indole-3-acetic acid (IAA), ammonia, hydrogen cyanide (HCN), and hydrolytic enzymes, phosphorus solubilization, antifungal activity against plant pathogens, nitrogen-fixation, 1-aminocyclopropane-1-carboxylic acid deaminase activity, and improving tolerance to different abiotic stresses. These isolates had nifH (11 isolates), acdS (8 isolates), and HCN (11 isolates) genes involved in N-fixation, stress tolerance, and pathogen biocontrol, respectively. Two isolates Pantoea cypripedii AF1and Kosakonia arachidis EF1 were the most potent strains and they colonized and grew in sugarcane plants. Both strains readily colonized the leading Chinese sugarcane variety GT42 and significantly increased the activity of nitrogen assimilation enzymes (glutamine synthetase, NADH glutamate dehydrogenase, and nitrate reductase), chitinase, and endo-glucanase and the content of phytohormones gibberellic acid, indole-3-acetic acid, and abscisic acid. The gene expression analysis of GT42 inoculated with isolates of P. cypripedii AF1 or K. arachidis EF1 showed increased activity of nifH and nitrogen assimilation genes. Also, the inoculated diazotrophs significantly increased plant nitrogen content, which was corroborated by the 15N isotope dilution analysis. Collectively, these findings suggest that P. cypripedii and K. arachidis are beneficial endophytes that could be used as a biofertilizer to improve plant nitrogen nutrition and growth of sugarcane. To the best of our knowledge, this is the first report of sugarcane growth enhancement and nitrogen fixation by Gram-negative sugarcane root-associated endophytic bacteria P. cypripedii and K. arachidis. These strains have the potential to be utilized as sugarcane biofertilizers, thus reducing nitrogen fertilizer use and improving disease management.
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Affiliation(s)
- Rajesh Kumar Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Pratiksha Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, China
| | - Dao-Jun Guo
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bio Resources, College of Agriculture, Guangxi University, Nanning, China
| | - Anjney Sharma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Dong-Ping Li
- Microbiology Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiang Li
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Krishan K. Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Mukesh Kumar Malviya
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Xiu-Peng Song
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Prakash Lakshmanan
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- Interdisciplinary Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing, China
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Li-Tao Yang
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bio Resources, College of Agriculture, Guangxi University, Nanning, China
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bio Resources, College of Agriculture, Guangxi University, Nanning, China
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De Bock T, Zhao X, Jacxsens L, Devlieghere F, Rajkovic A, Spanoghe P, Höfte M, Uyttendaele M. Evaluation of B. thuringiensis-based biopesticides in the primary production of fresh produce as a food safety hazard and risk. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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10
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Richter L, du Plessis EM, Duvenage S, Korsten L. Microbiological safety of spinach throughout commercial supply chains in Gauteng Province, South Africa and characterization of isolated multidrug-resistant Escherichia coli. J Appl Microbiol 2021; 132:2389-2409. [PMID: 34767685 DOI: 10.1111/jam.15357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 09/28/2021] [Accepted: 11/02/2021] [Indexed: 01/02/2023]
Abstract
AIM To investigate the microbiological quality, potential foodborne pathogen presence, and to phenotypically (antimicrobial resistance [AMR] profiles) and genotypically (DNA fingerprints and diarrhoeagenic genes) characterize Escherichia coli isolated throughout spinach production systems from farm-to-sale. METHODS AND RESULTS Samples (n = 288) were collected from two commercial supply chains using either river or borehole irrigation water. E. coli was enumerated throughout the chain where river water was directly used for overhead irrigation at levels between 0.00 and 3.22 log colony forming unit (CFU) g-1 . Following enrichment, isolation and matrix-assisted laser desorption ionization time-of-flight mass spectrometry identification, E. coli was isolated from 22.57% (n = 65/288) of all samples. Salmonella spp. were isolated from 3% (n = 9/288) of river and irrigation water samples on one farm, and no Listeria monocytogenes was detected throughout the study. Of the 80 characterized E. coli isolates, one harboured the stx2 virulence gene, while 43.75% (n = 35) were multidrug resistant. Overall, 26.30% of the multidrug-resistant E. coli isolates were from production scenario one that used river irrigation water, and 17.50% from the second production scenario that used borehole irrigation water. A greater percentage of resistance phenotypes were from water E. coli isolates (52.50%), than isolates from spinach (37.50%). E. coli isolates from spinach and irrigation water clustered together at high similarity values (>90%) using enterobacterial repetitive intergenic consensus-polymerase chan reaction analysis. CONCLUSIONS This study reported the presence of multidrug-resistant environmental E. coli throughout spinach production from farm, during processing and up to retail. Furthermore, the similarity of multi-drug resistant E. coli isolates suggests transfer from irrigation water to spinach in both scenarios, reiterating that irrigation water for vegetables consumed raw, should comply with standardized microbiological safety guidelines. SIGNIFICANCE AND IMPACT OF STUDY Multidrug-resistant E. coli presence throughout spinach production emphasizes the necessity of increased surveillance of AMR in fresh produce and the production environment within a One Health paradigm to develop AMR mitigation strategies.
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Affiliation(s)
- Loandi Richter
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.,Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Erika M du Plessis
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.,Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Stacey Duvenage
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.,Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.,Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
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Franco-Frías E, Mercado-Guajardo V, Merino-Mascorro A, Pérez-Garza J, Heredia N, León JS, Jaykus LA, Dávila-Aviña J, García S. Analysis of Bacterial Communities by 16S rRNA Gene Sequencing in a Melon-Producing Agro-environment. MICROBIAL ECOLOGY 2021; 82:613-622. [PMID: 33570667 DOI: 10.1007/s00248-021-01709-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Cantaloupe melons, which have been responsible of an increasing number of foodborne disease outbreaks, may become contaminated with microbial pathogens during production. However, little information is available on the microbial populations in the cantaloupe farm environment. The purpose of this work was to characterize the bacterial communities present on cantaloupe farms. Fruit, soil, and harvester hand rinsates were collected from two Mexican cantaloupe farms, each visited three times. Microbiome analysis was performed by sequencing 16sRNA and analyzed using qiime2 software. Correlations were determined between sample type and microbial populations. The α and β diversity analysis identified 2777 sequences across all samples. The soil samples had the highest number and diversity of unique species (from 130 to 1329 OTUs); cantaloupe (from 112 to 205 OTUs), and hands (from 67 to 151 OTUs) had similar diversity. Collectively, Proteobacteria was the most abundant phyla (from 42 to 95%), followed by Firmicutes (1-47%), Actinobacteria (< 1 to 23%), and Bacteroidetes (< 1 to 4.8%). The most abundant genera were Acinetobacter (20-58%), Pseudomonas (14.5%), Erwinia (13%), and Exiguobacterium (6.3%). Genera with potential to be pathogenic included Bacillus (4%), Salmonella (0.85%), Escherichia-Shigella (0.38%), Staphylococcus (0.32%), Listeria (0.29%), Clostridium (0.28%), and Cronobacter (0.27%), which were found at lower frequencies. This study provides information on the cantaloupe production microbiome, which can inform future research into critical food safety issues such as antimicrobial resistance, virulence, and genomic epidemiology.
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Affiliation(s)
- Eduardo Franco-Frías
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Victor Mercado-Guajardo
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Angel Merino-Mascorro
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Janeth Pérez-Garza
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Norma Heredia
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Juan S León
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Lee-Ann Jaykus
- Department of Food Science, North Carolina State University, Raleigh, NC, USA
| | - Jorge Dávila-Aviña
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Santos García
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México.
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12
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Shen Y, Ryser ET, Li H, Zhang W. Bacterial community assembly and antibiotic resistance genes in the lettuce-soil system upon antibiotic exposure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 778:146255. [PMID: 33721642 DOI: 10.1016/j.scitotenv.2021.146255] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/17/2021] [Accepted: 02/27/2021] [Indexed: 06/12/2023]
Abstract
Bacteria and antibiotic resistance genes (ARGs) in vegetables may influence human gut microbiome and ultimately human health. However, little is known about how vegetable microbiomes and ARGs respond to exposure of anthropogenic antibiotics from crop irrigation water. This study investigated bacterial community assembly and ARG profiles in lettuce (Lactuca sativa) shoots and roots, rhizosphere soil, and bulk soil irrigated with antibiotics-containing water, using 16S rRNA amplicon sequencing and high throughput real-time qPCR, respectively. With antibiotic exposure alpha diversity values remained unchanged for the rhizosphere soil and lettuce roots, but were significantly decreased for the bulk soil and lettuce shoots (p < 0.05). Based on calculations of normalized stochastic ratio (NST), bacterial community assembly was more stochastic in the rhizosphere soil (83%-86%) and bulk soil (81%-84%) than in the lettuce roots (45%-48%). These results suggest a stronger deterministic control of plant roots in bacterial community assembly. Antibiotic exposure did not substantially change the stochasticity of the bacterial communities, despite the NST values were significantly increased by ~3% (p < 0.05) for the rhizosphere soil and lettuce roots and significantly decreased by ~3% (p < 0.05) for the bulk soil, when comparing treatments with and without antibiotics. The levels of Methylophilaceae and Beijerinckiaceae were significantly different between the antibiotic and antibiotics-free treatments. Antibiotic exposure consistently increased the abundance of mobile genetic elements (MGEs) in the rhizosphere soil, but not in other samples. No consistent changes in ARGs were observed with and without antibiotic exposure. Finally, the correlation network analysis revealed that the rhizosphere soil may be a hotspot for interactions between ARGs, MGEs, bacterial communities, and antibiotic residues.
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Affiliation(s)
- Yike Shen
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States; Environmental Science and Policy Program, Michigan State University, East Lansing, MI 48824, United States; Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, United States
| | - Elliot T Ryser
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, United States
| | - Hui Li
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States
| | - Wei Zhang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States; Environmental Science and Policy Program, Michigan State University, East Lansing, MI 48824, United States.
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13
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An overview on endophytic bacterial diversity habitat in vegetables and fruits. Folia Microbiol (Praha) 2021; 66:715-725. [PMID: 34259998 DOI: 10.1007/s12223-021-00896-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/30/2021] [Indexed: 01/02/2023]
Abstract
Nowadays, scientific research revolution is going on in many areas, and the human health is one of them. However, in the earlier studies, it was observed that most of the people health in the world affects by consumptions of contaminated food which is dangerous for human health and country economy. Recent studies showed that the fresh vegetables and fruits are the major habitat for endophytic bacterial communities. Salmonella and Escherichia coli both are the very common bacteria founds in fresh vegetables and fruits. Generally, many people eat vegetables and fruits without cooking (in the form of salad). The continued assumption of such food increases the health risk factor for foodborne diseases. So, from the last decades, many researchers working to understand about the relationship of endophytic microbes with plants either isolated bacteria are pathogenic or nonpathogenic. Moreover, most of the endophytes were identified by using 16S rRNA sequencing method. Hence, this review elaborates on the differences and similarities between nonpathogenic and pathogenic endophytes in terms of host plant response, colonization strategy, and genome content. Furthermore, it is emphasized on the environmental effects and biotic interactions within plant microbiota that influence pathogenesis and the pathogenesis.
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14
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Aabed K, Moubayed N, Alzahrani S. Antimicrobial resistance patterns among different Escherichia coli isolates in the Kingdom of Saudi Arabia. Saudi J Biol Sci 2021; 28:3776-3782. [PMID: 34220231 PMCID: PMC8241624 DOI: 10.1016/j.sjbs.2021.03.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 11/25/2022] Open
Abstract
Antimicrobial resistance patterns among different Escherichia coli isolates in the Kingdom of Saudi Arabia. This study aimed to investigate the patterns of antimicrobial resistance in E. coli isolated from different samples, and to identify potential pathogenic isolates in Riyadh, Kingdom of Saudi Arabia (KSA). In total, 51 bacterial isolates were recovered from 113 samples of human urine, food (raw meat, raw chicken, raw egg surface, and fresh vegetables), water, and air. Twenty-four E. coli isolates were tested for susceptibility to 26 antibiotics. The air sample isolates were most resistant to amoxicillin, ampicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, piperacillin/tazobactam, cefalotin, cefuroxime, cefoxitin, cefixime, nitrofurantoin, and trimethoprim/sulfamethoxazol. The isolates from vegetable samples were resistant to amoxicillin, ampicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, cefalotin, cefuroxime, cefoxitin, and cefixime. By contrast, the isolates from the water samples were resistant only to amoxicillin and ampicillin. The isolates from the human urine samples were most frequently resistant to norfloxacin (80%) followed by amoxicillin and ampicillin (70%), trimethoprim/sulfamethoxazole (55%), ciprofloxacin and ofloxacin (50%), cefalotin (30%), cefuroxime, cefixime and cefotaxime (25%), ceftazidime, ceftriaxone, cefepime and aztreonam (20%), amoxicillin/clavulanic acid, piperacillin/tazobactam and gentamicin (10%), and amoxicillin/sulbactam and cefoxitin (5%). Almost all (23/25, 95.8%) (n = 23) of the isolates were multi-drug resistant (MDR) (i.e., resistant to 3 or more classes of antibiotics), and 16.7% (n = 4) of those were positive for extended spectrum β-lactamase (ESBL). Of the 4 ESBL-producers, 3 were positive for blaCTX-M-15 and blaCTX-M1group, 2 were positive for blaCMY-2, and 1 each was positive for blaCTX-M-2 group, blaSHV, and blaOXA-47. The quinolone resistance gene qnrS was detected in 25% (n = 6) of the E. coli strains isolated from urine (N = 5) and air (N = 1) samples. The considerable number of antimicrobial resistance genes detected among E. coli isolates tested here is alarming and should raise public health concern.
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Affiliation(s)
- Kawther Aabed
- Biology Department, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Nadine Moubayed
- Botany and Microbiology Department, Sciences College, King Saud University, Riyadh, Saudi Arabia
| | - Saleha Alzahrani
- Biology Department, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
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15
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Martínez‐Romero E, Aguirre‐Noyola JL, Bustamante‐Brito R, González‐Román P, Hernández‐Oaxaca D, Higareda‐Alvear V, Montes‐Carreto LM, Martínez‐Romero JC, Rosenblueth M, Servín‐Garcidueñas LE. We and herbivores eat endophytes. Microb Biotechnol 2021; 14:1282-1299. [PMID: 33320440 PMCID: PMC8313258 DOI: 10.1111/1751-7915.13688] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 12/16/2022] Open
Abstract
Health depends on the diet and a vegetal diet promotes health by providing fibres, vitamins and diverse metabolites. Remarkably, plants may also provide microbes. Fungi and bacteria that reside inside plant tissues (endophytes) seem better protected to survive digestion; thus, we investigated the reported evidence on the endophytic origin of some members of the gut microbiota in animals such as panda, koala, rabbits and tortoises and several herbivore insects. Data examined here showed that some members of the herbivore gut microbiota are common plant microbes, which derived to become stable microbiota in some cases. Endophytes may contribute to plant fibre or antimetabolite degradation and synthesis of metabolites with the plethora of enzymatic activities that they display; some may have practical applications, for example, Lactobacillus plantarum found in the intestinal tract, plants and in fermented food is used as a probiotic that may defend animals against bacterial and viral infections as other endophytic-enteric bacteria do. Clostridium that is an endophyte and a gut bacterium has remarkable capabilities to degrade cellulose by having cellulosomes that may be considered the most efficient nanomachines. Cellulose degradation is a challenge in animal digestion and for biofuel production. Other endophytic-enteric bacteria may have cellulases, pectinases, xylanases, tannases, proteases, nitrogenases and other enzymatic capabilities that may be attractive for biotechnological developments, indeed many endophytes are used to promote plant growth. Here, a cycle of endophytic-enteric-soil-endophytic microbes is proposed which has relevance for health and comprises the fate of animal faeces as natural microbial inoculants for plants that constitute bacterial sources for animal guts.
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Affiliation(s)
| | | | | | - Pilar González‐Román
- Programa de Ecología GenómicaCentro de Ciencias GenómicasUNAMCuernavacaMorelosMexico
| | | | | | | | | | - Mónica Rosenblueth
- Programa de Ecología GenómicaCentro de Ciencias GenómicasUNAMCuernavacaMorelosMexico
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16
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Andreadelli A, Petrakis S, Tsoureki A, Tsiolas G, Michailidou S, Baltzopoulou P, van Merkestein R, Hodgson P, Sceats M, Karagiannakis G, Makris AM. Effects of Magnesium Oxide and Magnesium Hydroxide Microparticle Foliar Treatment on Tomato PR Gene Expression and Leaf Microbiome. Microorganisms 2021; 9:microorganisms9061217. [PMID: 34199815 PMCID: PMC8228823 DOI: 10.3390/microorganisms9061217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 11/20/2022] Open
Abstract
Recently, metal oxides and magnesium hydroxide nanoparticles (NPs) with high surface-to-volume ratios were shown to possess antibacterial properties with applications in biomedicine and agriculture. To assess recent observations from field trials on tomatoes showing resistance to pathogen attacks, porous micron-scale particles composed of nano-grains of MgO were hydrated and sprayed on the leaves of healthy tomato (Solanum lycopersicum) plants in a 20-day program. The results showed that the spray induced (a) a modest and selective stress gene response that was consistent with the absence of phytotoxicity and the production of salicylic acid as a signalling response to pathogens; (b) a shift of the phylloplane microbiota from near 100% dominance by Gram (−) bacteria, leaving extremophiles and cyanobacteria to cover the void; and (c) a response of the fungal leaf phylloplane that showed that the leaf epiphytome was unchanged but the fungal load was reduced by about 70%. The direct microbiome changes together with the low level priming of the plant’s immune system may explain the previously observed resistance to pathogen assaults in field tomato plants sprayed with the same hydrated porous micron-scale particles.
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Affiliation(s)
- Aggeliki Andreadelli
- Institute of Applied Biosciences, Centre for Research & Technology, Hellas (CERTH), 570 01 Thessaloniki, Greece; (A.A.); (S.P.); (A.T.); (G.T.); (S.M.)
| | - Spyros Petrakis
- Institute of Applied Biosciences, Centre for Research & Technology, Hellas (CERTH), 570 01 Thessaloniki, Greece; (A.A.); (S.P.); (A.T.); (G.T.); (S.M.)
| | - Antiopi Tsoureki
- Institute of Applied Biosciences, Centre for Research & Technology, Hellas (CERTH), 570 01 Thessaloniki, Greece; (A.A.); (S.P.); (A.T.); (G.T.); (S.M.)
| | - George Tsiolas
- Institute of Applied Biosciences, Centre for Research & Technology, Hellas (CERTH), 570 01 Thessaloniki, Greece; (A.A.); (S.P.); (A.T.); (G.T.); (S.M.)
| | - Sofia Michailidou
- Institute of Applied Biosciences, Centre for Research & Technology, Hellas (CERTH), 570 01 Thessaloniki, Greece; (A.A.); (S.P.); (A.T.); (G.T.); (S.M.)
| | - Penelope Baltzopoulou
- Chemical Process & Energy Resources Institute, Centre for Research & Technology, Hellas (CERTH), 570 01 Thessaloniki, Greece; (P.B.); (G.K.)
| | | | - Philip Hodgson
- Calix Limited, Pymble, NSW 2073, Australia; (R.v.M.); (P.H.); (M.S.)
| | - Mark Sceats
- Calix Limited, Pymble, NSW 2073, Australia; (R.v.M.); (P.H.); (M.S.)
| | - George Karagiannakis
- Chemical Process & Energy Resources Institute, Centre for Research & Technology, Hellas (CERTH), 570 01 Thessaloniki, Greece; (P.B.); (G.K.)
| | - Antonios M. Makris
- Institute of Applied Biosciences, Centre for Research & Technology, Hellas (CERTH), 570 01 Thessaloniki, Greece; (A.A.); (S.P.); (A.T.); (G.T.); (S.M.)
- Correspondence: ; Tel.: +30-2311-257-541
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17
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Medina-Cordoba LK, Chande AT, Rishishwar L, Mayer LW, Valderrama-Aguirre LC, Valderrama-Aguirre A, Gaby JC, Kostka JE, Jordan IK. Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields. Sci Rep 2021; 11:9187. [PMID: 33911103 PMCID: PMC8080613 DOI: 10.1038/s41598-021-88380-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 04/07/2021] [Indexed: 01/26/2023] Open
Abstract
Previous studies have shown the sugarcane microbiome harbors diverse plant growth promoting microorganisms, including nitrogen-fixing bacteria (diazotrophs), which can serve as biofertilizers. The genomes of 22 diazotrophs from Colombian sugarcane fields were sequenced to investigate potential biofertilizers. A genome-enabled computational phenotyping approach was developed to prioritize sugarcane associated diazotrophs according to their potential as biofertilizers. This method selects isolates that have potential for nitrogen fixation and other plant growth promoting (PGP) phenotypes while showing low risk for virulence and antibiotic resistance. Intact nitrogenase (nif) genes and operons were found in 18 of the isolates. Isolates also encode phosphate solubilization and siderophore production operons, and other PGP genes. The majority of sugarcane isolates showed uniformly low predicted virulence and antibiotic resistance compared to clinical isolates. Six strains with the highest overall genotype scores were experimentally evaluated for nitrogen fixation, phosphate solubilization, and the production of siderophores, gibberellic acid, and indole acetic acid. Results from the biochemical assays were consistent and validated computational phenotype predictions. A genotypic and phenotypic threshold was observed that separated strains by their potential for PGP versus predicted pathogenicity. Our results indicate that computational phenotyping is a promising tool for the assessment of bacteria detected in agricultural ecosystems.
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Affiliation(s)
- Luz K Medina-Cordoba
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Aroon T Chande
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | - Lavanya Rishishwar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | - Leonard W Mayer
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | - Lina C Valderrama-Aguirre
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,Laboratory of Microorganismal Production (Bioinoculums), Department of Field Research in Sugarcane, INCAUCA S.A.S., Cali, Valle del Cauca, Colombia
| | - Augusto Valderrama-Aguirre
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia.,Universidad Santiago de Cali, Cali, Colombia
| | - John Christian Gaby
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA. .,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia. .,School of Biological Sciences, Georgia Institute of Technology, 310 Ferst Dr NW, Atlanta, GA, 30332, USA.
| | - I King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA. .,PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia. .,Applied Bioinformatics Laboratory, Atlanta, GA, USA. .,School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr NW, Atlanta, GA, 30332, USA.
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18
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Bartholomew HP, Bradshaw M, Jurick WM, Fonseca JM. The Good, the Bad, and the Ugly: Mycotoxin Production During Postharvest Decay and Their Influence on Tritrophic Host-Pathogen-Microbe Interactions. Front Microbiol 2021; 12:611881. [PMID: 33643240 PMCID: PMC7907610 DOI: 10.3389/fmicb.2021.611881] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/22/2021] [Indexed: 12/18/2022] Open
Abstract
Mycotoxins are a prevalent problem for stored fruits, grains, and vegetables. Alternariol, aflatoxin, and patulin, produced by Alternaria spp., Aspergillus spp., and Penicillium spp., are the major mycotoxins that negatively affect human and animal health and reduce fruit and produce quality. Control strategies for these toxins are varied, but one method that is increasing in interest is through host microbiome manipulation, mirroring a biocontrol approach. While the majority of mycotoxins and other secondary metabolites (SM) produced by fungi impact host–fungal interactions, there is also an interplay between the various organisms within the host microbiome. In addition to SMs, these interactions involve compounds such as signaling molecules, plant defense and growth hormones, and metabolites produced by both the plants and microbial community. Therefore, studies to understand the impact of the various toxins impacting the beneficial and harmful microorganisms that reside within the microbiome is warranted, and could lead to identification of safe analogs for antimicrobial activity to reduce fruit decay. Additionally, exploring the composition of the microbial carposphere of host plants is likely to shed light on developing a microbial consortium to maintain quality during storage and abate mycotoxin contamination.
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Affiliation(s)
- Holly P Bartholomew
- Food Quality Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Michael Bradshaw
- Food Quality Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Wayne M Jurick
- Food Quality Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Jorge M Fonseca
- Food Quality Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
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19
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Taîbi A, Rivallan R, Broussolle V, Pallet D, Lortal S, Meile JC, Constancias F. Terroir Is the Main Driver of the Epiphytic Bacterial and Fungal Communities of Mango Carposphere in Reunion Island. Front Microbiol 2021; 11:619226. [PMID: 33584584 PMCID: PMC7874004 DOI: 10.3389/fmicb.2020.619226] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/18/2020] [Indexed: 12/22/2022] Open
Abstract
The diversity of both bacterial and fungal communities associated with mango surface was explored using a metabarcoding approach targeting fungal ITS2 and bacterial 16S (V3-V4) genomic regions. Fruits were collected in Reunion Island from two different orchards according to a sampling method which allowed the effect of several pre-harvest factors such as geographical location (terroir), cultivars, fruit parts, tree position in the plot, fruit position on the tree (orientation and height), as well as the harvest date to be investigated. A total of 4,266,546 fungal and 2,049,919 bacterial reads were recovered then respectively assigned to 3,153 fungal and 24,087 to bacterial amplicon sequence variants (ASVs). Alpha and beta diversity, as well as differential abundance analyses revealed variations in both bacterial and fungal communities detected on mango surfaces depended upon the studied factor. Results indicated that Burkholderiaceae (58.8%), Enterobacteriaceae (5.2%), Pseudomonadaceae (4.8%), Sphingomonadaceae (4.1%), Beijerinckiaceae (3.5%), and Microbacteriaceae (3.1%) were the dominant bacterial families across all samples. The majority of fungal sequences were assigned to Mycosphaerellaceae (34.5%), Cladosporiaceae (23.21%), Aureobasidiaceae (13.09%), Pleosporaceae (6.92%), Trichosphaeriaceae (5.17%), and Microstromatales_fam_Incertae_sedis (4.67%). For each studied location, mango fruit from each cultivar shared a core microbiome, and fruits of the same cultivar harvested in two different locations shared about 80% fungal and bacterial family taxa. The various factors tested in this study affected bacterial and fungal taxa differently, suggesting that some taxa could act as geographical (terroir) markers and in some cases as cultivar fingerprints. The ranking of the factors investigated in the present study showed that in decreasing order of importance: the plot (terroir), cultivar, fruit parts, harvest date and the position of the fruits are respectively the most impacting factors of the microbial flora, when compared to the orientation and the fruit position (height) on the tree. Overall, these findings provided insights on both bacterial and fungal diversity associated with the mango surface, their patterns from intra-fruit scale to local scale and the potential parameters shaping the mango microbiota.
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Affiliation(s)
- Ahmed Taîbi
- CIRAD, UMR Qualisud, Saint-Pierre, France
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, Université de La Réunion, Montpellier, France
| | - Ronan Rivallan
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Véronique Broussolle
- INRAE, Avignon Université, Sécurité et Qualité des Produits d’Origine Végétale, Avignon, France
| | - Dominique Pallet
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, Université de La Réunion, Montpellier, France
- CIRAD, UMR Qualisud, Montpellier, France
| | - Sylvie Lortal
- INRAE, Département Microbiologie et Chaine alimentaire, Jouy-en-Josas, France
| | - Jean-Christophe Meile
- CIRAD, UMR Qualisud, Saint-Pierre, France
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, Université de La Réunion, Montpellier, France
| | - Florentin Constancias
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, Université de La Réunion, Montpellier, France
- CIRAD, UMR Qualisud, Montpellier, France
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20
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Cho GS, Stein M, Fiedler G, Igbinosa EO, Koll LP, Brinks E, Rathje J, Neve H, Franz CMAP. Polyphasic study of antibiotic-resistant enterobacteria isolated from fresh produce in Germany and description of Enterobacter vonholyi sp. nov. isolated from marjoram and Enterobacter dykesii sp. nov. isolated from mung bean sprout. Syst Appl Microbiol 2020; 44:126174. [PMID: 33370657 DOI: 10.1016/j.syapm.2020.126174] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 11/29/2022]
Abstract
Forty-two antibiotic-resistant enterobacteria strains were isolated from fresh produce obtained from the northern German retail market. A polyphasic characterization based on both phenotypic and genotypic methods was used to identify predominant strains as Citrobacter (C.) gillenii, C. portucalensis, Enterobacter (En.) ludwigii, Escherichia (E.) coli and Klebsiella (K.) pneumoniae. 38.1% of the enterobacteria strains were resistant to tetracycline, while 23.8% and 9.5% of strains were resistant to streptomycin and chloramphenicol, respectively. A high percentage of Klebsiella (100%), Enterobacter (57.1%) and Citrobacter (42.9%) strains were also resistant to ampicillin, with some strains showing multiple resistances. For unequivocal species identification, the genomes of thirty strains were sequenced. Multilocus sequence analysis, average nucleotide identity and digital DNA-DNA hybridization showed that Enterobacter strains E1 and E13 were clearly clustered apart from Enterobacter species type strains below the species delineation cutoff values. Thus, strains E1T (=DSM 111347T, LMG 31875T) represents a novel species proposed as Enterobacter dykesii sp. nov., while strain E13T (=DSM 110788T, LMG 31764T) represent a novel species proposed as Enterobacter vonholyi sp. nov. Strains often possessed different serine β-lactamase genes, tet(A) and tet(D) tetracycline resistance genes and other acquired antibiotic resistance genes. Typical plasmid replicon types were determined. This study thus accurately identified the enterobacteria from fresh produce as species belonging to the genera Citrobacter, Enterobacter, Escherichia and Klebsiella, but also showed that these can carry potentially transferable antibiotic resistance genes and may thus contribute to the spread of these via the food route.
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Affiliation(s)
- Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut Kiel, Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
| | - Maria Stein
- Department of Microbiology and Biotechnology, Max Rubner-Institut Kiel, Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
| | - Gregor Fiedler
- Department of Microbiology and Biotechnology, Max Rubner-Institut Kiel, Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
| | - Etinosa O Igbinosa
- Department of Microbiology and Biotechnology, Max Rubner-Institut Kiel, Hermann-Weigmann-Str. 1, 24103 Kiel, Germany; Department of Microbiology, Faculty of Life Sciences, University of Benin, Benin City, Nigeria
| | - Linnéa Philine Koll
- Department of Microbiology and Biotechnology, Max Rubner-Institut Kiel, Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
| | - Erik Brinks
- Department of Microbiology and Biotechnology, Max Rubner-Institut Kiel, Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
| | - Jana Rathje
- Department of Microbiology and Biotechnology, Max Rubner-Institut Kiel, Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut Kiel, Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut Kiel, Hermann-Weigmann-Str. 1, 24103 Kiel, Germany.
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Kusstatscher P, Cernava T, Abdelfattah A, Gokul J, Korsten L, Berg G. Microbiome approaches provide the key to biologically control postharvest pathogens and storability of fruits and vegetables. FEMS Microbiol Ecol 2020; 96:5857999. [PMID: 32542314 DOI: 10.1093/femsec/fiaa119] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/14/2020] [Indexed: 01/07/2023] Open
Abstract
Microbes play an important role in plants and interact closely with their host starting from sprouting seeds, continuing during growth and after harvest. The discovery of their importance for plant and postharvest health initiated a biotechnological development of various antagonistic bacteria and fungi for disease control. Nevertheless, their application often showed inconsistent effects. Recently, high-throughput sequencing-based techniques including advanced microscopy reveal fruits and vegetables as holobionts. At harvest, all fruits and vegetables harbor a highly abundant and specific microbiota including beneficial, pathogenic and spoilage microorganisms. Especially, a high microbial diversity and resilient microbial networks were shown to be linked to fruit and vegetable health, while diseased products showed severe dysbiosis. Field and postharvest handling of fruits and vegetables was shown to affect the indigenous microbiome and therefore has a substantial impact on the storability of fruits and vegetables. Microbiome tracking can be implemented as a new tool to evaluate and assess all postharvest processes and contribute to fruit and vegetable health. Here, we summarize current research advancements in the emerging field of postharvest microbiomes and elaborate its importance. The generated knowledge provides profound insights into postharvest microbiome dynamics and sets a new basis for targeted, microbiome-driven and sustainable control strategies.
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Affiliation(s)
- Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria.,Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
| | - Jarishma Gokul
- Department of Plant and Soil Sciences, University of Pretoria, New Agricultural Building, Lunnon Road, Hillcrest 0083, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, New Agricultural Building, Lunnon Road, Hillcrest 0083, South Africa
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
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22
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Gamalero E, Bona E, Novello G, Boatti L, Mignone F, Massa N, Cesaro P, Berta G, Lingua G. Discovering the bacteriome of Vitis vinifera cv. Pinot Noir in a conventionally managed vineyard. Sci Rep 2020; 10:6453. [PMID: 32296119 PMCID: PMC7160115 DOI: 10.1038/s41598-020-63154-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/16/2020] [Indexed: 01/22/2023] Open
Abstract
The structure of the bacteriome associated with grapevine roots can affect plant development, health and grape quality. We previously investigated the bacterial biodiversity of the Vitis vinifera cv. Pinot Noir rhizosphere in a vineyard subjected to integrated pest management. The aim of this work is to characterize the bacteriome of V. vinifera cv. Pinot Noir in a conventionally managed vineyard using a metabarcoding approach. Comparisons between the microbial community structure in bulk soil and rhizosphere (variable space) were performed and shifts of bacteriome according to two sampling times (variable time) were characterized. Bacterial biodiversity was higher at the second than at the first sampling and did not differ according to the variable space. Actinobacteria was the dominant class, with Gaiella as the most represented genus in all the samples. Among Proteobacteria, the most represented classes were Alpha, Beta and Gamma-Proteobacteria, with higher abundance at the second than at the first sampling time. Bradyrhizobium was the most frequent genus among Alpha-Proteobacteria, while Burkholderia was the predominant Beta-Proteobacteria. Among Firmicutes, the frequency of Staphylococcus was higher than 60% in bulk soil and rhizosphere. Finally, the sampling time can be considered as one of the drivers responsible for the bacteriome variations assessed.
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Affiliation(s)
- Elisa Gamalero
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy
| | - Elisa Bona
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Piazza San Eusebio 5, 13100, Vercelli, Italy
| | - Giorgia Novello
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy
| | - Lara Boatti
- SmartSeq s.r.l., spin-off of the Università del Piemonte Orientale, Viale T. Michel 11, Alessandria, 15121, Italy
| | - Flavio Mignone
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy.,SmartSeq s.r.l., spin-off of the Università del Piemonte Orientale, Viale T. Michel 11, Alessandria, 15121, Italy
| | - Nadia Massa
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy
| | - Patrizia Cesaro
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy.
| | - Graziella Berta
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy
| | - Guido Lingua
- Università del Piemonte Orientale, Dipartimento di Scienze e Innovazione Tecnologica, Viale T. Michel 11, Alessandria, 15121, Italy
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23
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Quantitative analysis and influences of contact dynamics on bacterial cross-contamination from contaminated fresh produce. J FOOD ENG 2020. [DOI: 10.1016/j.jfoodeng.2019.109771] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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24
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Krishna SBN, Dubey A, Malla MA, Kothari R, Upadhyay CP, Adam JK, Kumar A. Integrating Microbiome Network: Establishing Linkages Between Plants, Microbes and Human Health. Open Microbiol J 2019. [DOI: 10.2174/1874285801913020330] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The trillions of microbes that colonize and live around us govern the health of both plants and animals through a cascade of direct and indirect mechanisms. Understanding of this enormous and largely untapped microbial diversity has been the focus of microbial research from the past few decades or so. Amidst the advancements in sequencing technologies, significant progress has been made to taxonomically and functionally catalogue these microbes and also to establish their exact role in the health and disease state. In comparison to the human microbiome, plants are also surrounded by a vast diversity of microbes that form complex ecological communities that affect plant growth and health through collective metabolic activities and interactions. This plant microbiome has a substantial influence on human health and environment via its passage through the nasal route and digestive tract and is responsible for changing our gut microbiome. This review primarily focused on the advances and challenges in microbiome research at the interface of plant and human, and role of microbiome at different compartments of the body’s ecosystems along with their correlation to health and diseases. This review also highlighted the potential therapies in modulating the gut microbiota and technologies for studying the microbiome.
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25
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Li D, Wong CH, Seet MF, Kuan N. Isolation, Characterization, and Inactivation of Stenotrophomonas maltophilia From Leafy Green Vegetables and Urban Agriculture Systems. Front Microbiol 2019; 10:2718. [PMID: 31849874 PMCID: PMC6895016 DOI: 10.3389/fmicb.2019.02718] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 11/08/2019] [Indexed: 12/04/2022] Open
Abstract
Stenotrophomonas maltophilia is an emerging opportunistic pathogen that, on the one hand, causes severe nosocomial infection in immunocompromised populations with a high mortality rate and, on the other hand, is present ubiquitously in the environment. This study, for the first time to the best of our knowledge, isolated and characterized S. maltophilia from leafy green vegetables produced by hydroponic farms and from a hydroponic farming facility in Singapore. Eleven S. maltophilia isolates were obtained from three types of leafy green vegetables (sweet basil, kale, and parsley) and from the nutrient solution used by a hydroponic farm. The antimicrobial resistance (AMR), biofilm-forming ability, and resistance to UV and quaternary ammonium compound (QAC) treatments were investigated, as was the fate of S. maltophilia in a simulated leafy green vegetable environment during a storage period of 6 days at different temperatures. The results showed that high population levels of S. maltophilia could be reached on leafy green vegetables, especially after being stored at abused temperatures (>8-log CFU/ml in basil juice after 6 days storage at 20°C) and on hydroponic farming facilities, probably due to biofilm formation (8 to 9-log CFU/well in biofilms). At 4°C, S. maltophilia was able to survive, but no growth was observed during storage in either bacteria culture media or basil juice for a period of 6 days. UV treatment, which induced substantial reductions in S. maltophilia in both single-species and dual-species biofilms mixed with Salmonella enterica serovar Typhimurium reference strain (ATCC 14028) or self-isolated Pseudomonas fluorescens (>4-log reductions by 250 mJ/cm2 UV), is recommended for employment by hydroponic farms to treat their nutrient solutions and farming facilities so as to enhance microbial safety.
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Affiliation(s)
- Dan Li
- Department of Food Science & Technology, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Chun Hong Wong
- Department of Food Science & Technology, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Mei Fang Seet
- Department of Food Science & Technology, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Nicole Kuan
- Department of Food Science & Technology, Faculty of Science, National University of Singapore, Singapore, Singapore
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26
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Shen Y, Stedtfeld RD, Guo X, Bhalsod GD, Jeon S, Tiedje JM, Li H, Zhang W. Pharmaceutical exposure changed antibiotic resistance genes and bacterial communities in soil-surface- and overhead-irrigated greenhouse lettuce. ENVIRONMENT INTERNATIONAL 2019; 131:105031. [PMID: 31336252 DOI: 10.1016/j.envint.2019.105031] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 06/29/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
New classes of emerging contaminants such as pharmaceuticals, antibiotic resistant bacteria (ARB), and antibiotic resistance genes (ARGs) have received increasing attention due to rapid increases of their abundance in agroecosystems. As food consumption is a direct exposure pathway of pharmaceuticals, ARB, and ARGs to humans, it is important to understand changes of bacterial communities and ARG profiles in food crops produced with contaminated soils and waters. This study examined the level and type of ARGs and bacterial community composition in soil, and lettuce shoots and roots under soil-surface or overhead irrigation with pharmaceuticals-contaminated water, using high throughput qPCR and 16S rRNA amplicon sequencing techniques, respectively. In total 52 ARG subtypes were detected in the soil, lettuce shoot and root samples, with mobile genetic elements (MGEs), and macrolide-lincosamide-streptogramin B (MLSB) and multidrug resistance (MDR) genes as dominant types. The overall abundance and diversity of ARGs and bacteria associated with lettuce shoots under soil-surface irrigation were lower than those under overhead irrigation, indicating soil-surface irrigation may have lower risks of producing food crops with high abundance of ARGs. ARG profiles and bacterial communities were sensitive to pharmaceutical exposure, but no consistent patterns of changes were observed. MGE intl1 was consistently more abundant with pharmaceutical exposure than in the absence of pharmaceuticals. Pharmaceutical exposure enriched Proteobacteria (specifically Methylophilaceae) and decreased bacterial alpha diversity. Finally, there were significant interplays among bacteria community, antibiotic concentrations, and ARG abundance possibly involving hotspots including Sphingomonadaceae, Pirellulaceae, and Chitinophagaceae, MGEs (intl1 and tnpA_1) and MDR genes (mexF and oprJ).
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Affiliation(s)
- Yike Shen
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States; Environmental Science and Policy Program, Michigan State University, East Lansing, MI 48824, United States; Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, United States
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48823, United States
| | - Xueping Guo
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States; Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, United States; College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Gemini D Bhalsod
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States; Cook County Unit, University of Illinois Extension, Arlington Heights, IL 60004, United States
| | - Sangho Jeon
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States; National Institute of Agricultural Sciences, Rural Development Administration, Wanju 54875, Republic of Korea
| | - James M Tiedje
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States; Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, United States
| | - Hui Li
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States
| | - Wei Zhang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States; Environmental Science and Policy Program, Michigan State University, East Lansing, MI 48824, United States.
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27
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Aijuka M, Buys EM. Persistence of foodborne diarrheagenic Escherichia coli in the agricultural and food production environment: Implications for food safety and public health. Food Microbiol 2019; 82:363-370. [DOI: 10.1016/j.fm.2019.03.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 03/11/2019] [Accepted: 03/16/2019] [Indexed: 02/07/2023]
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28
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Wassermann B, Müller H, Berg G. An Apple a Day: Which Bacteria Do We Eat With Organic and Conventional Apples? Front Microbiol 2019; 10:1629. [PMID: 31396172 PMCID: PMC6667679 DOI: 10.3389/fmicb.2019.01629] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/02/2019] [Indexed: 12/12/2022] Open
Abstract
Apples are among the most consumed fruits world-wide. They represent a source of direct human exposure to bacterial communities, which is less studied. We analyzed the apple microbiome to detect differences between tissues and the impact of organic and conventional management by a combined approach of 16S rRNA gene amplicon analysis and qPCR, and visualization using fluorescence in situ hybridization and confocal laser scanning microscopy (FISH-CLSM). Each apple fruit harbors different tissues (stem, peel, fruit pulp, seeds, and calyx), which were colonized by distinct bacterial communities. Interestingly, fruit pulp and seeds were bacterial hot spots, while the peel was less colonized. In all, approximately 108 16S rRNA bacterial gene copy numbers were determined in each g apple. Abundances were not influenced by the management practice but we found a strong reduction in bacterial diversity and evenness in conventionally managed apples. In addition, despite the similar structure in general dominated by Proteobacteria (80%), Bacteroidetes (9%), Actinobacteria (5%), and Firmicutes (3%), significant shifts of almost 40% of bacterial genera and orders were monitored. Among them, especially bacterial signatures known for health-affecting potential were found to be enhanced in conventionally managed apples. Our results suggest that we consume about 100 million bacterial cells with one apple. Although this amount was the same, the bacterial composition was significantly different in conventionally and organically produced apples.
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Affiliation(s)
- Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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29
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Keshri J, Krouptiski Y, Abu-Fani L, Achmon Y, Bauer TS, Zarka O, Maler I, Pinto R, Sela Saldinger S. Dynamics of bacterial communities in alfalfa and mung bean sprouts during refrigerated conditions. Food Microbiol 2019; 84:103261. [PMID: 31421775 DOI: 10.1016/j.fm.2019.103261] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 06/07/2019] [Accepted: 07/05/2019] [Indexed: 02/08/2023]
Abstract
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.
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Affiliation(s)
- Jitendra Keshri
- Department of Food Science, Institute for Postharvest and Food Sciences, The Volcani Center, Agriculture Research Organization, Rishon-LeZion, Israel; College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, 91766, USA
| | - Yulia Krouptiski
- Department of Food Science, Institute for Postharvest and Food Sciences, The Volcani Center, Agriculture Research Organization, Rishon-LeZion, Israel
| | - Lareen Abu-Fani
- Department of Food Science, Institute for Postharvest and Food Sciences, The Volcani Center, Agriculture Research Organization, Rishon-LeZion, Israel
| | - Ygal Achmon
- Department of Food Science, Institute for Postharvest and Food Sciences, The Volcani Center, Agriculture Research Organization, Rishon-LeZion, Israel; Department of Biotechnology and Food Engineering, Guangdong Technion Israel Institute of Technology, Shantou, China
| | - Tal Stern Bauer
- Department of Food Science, Institute for Postharvest and Food Sciences, The Volcani Center, Agriculture Research Organization, Rishon-LeZion, Israel; Department of Biochemistry and Food Science, Hebrew University of Jerusalem, Israel
| | - Omri Zarka
- Department of Food Science, Institute for Postharvest and Food Sciences, The Volcani Center, Agriculture Research Organization, Rishon-LeZion, Israel
| | - Ilana Maler
- The Laboratory of Food Microbiology, Kimron Veterinary Institute, P.O. Box 12, Bet Dagan, 50250, Israel
| | - Riky Pinto
- Department of Food Science, Institute for Postharvest and Food Sciences, The Volcani Center, Agriculture Research Organization, Rishon-LeZion, Israel
| | - Shlomo Sela Saldinger
- Department of Food Science, Institute for Postharvest and Food Sciences, The Volcani Center, Agriculture Research Organization, Rishon-LeZion, Israel.
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30
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Metagenomic Characterization of Bacterial Communities on Ready-to-Eat Vegetables and Effects of Household Washing on their Diversity and Composition. Pathogens 2019; 8:pathogens8010037. [PMID: 30893890 PMCID: PMC6471099 DOI: 10.3390/pathogens8010037] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/14/2019] [Accepted: 03/15/2019] [Indexed: 02/07/2023] Open
Abstract
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.
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31
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Caniça M, Manageiro V, Abriouel H, Moran-Gilad J, Franz CM. Antibiotic resistance in foodborne bacteria. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2018.08.001] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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32
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Kõiv V, Arbo K, Maiväli Ü, Kisand V, Roosaare M, Remm M, Tenson T. Endophytic bacterial communities in peels and pulp of five root vegetables. PLoS One 2019; 14:e0210542. [PMID: 30633764 PMCID: PMC6329509 DOI: 10.1371/journal.pone.0210542] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 12/27/2018] [Indexed: 12/20/2022] Open
Abstract
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.
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Affiliation(s)
- Viia Kõiv
- Institute of Technology, University of Tartu, Tartu, Estonia
- * E-mail:
| | - Krõõt Arbo
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Ülo Maiväli
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Veljo Kisand
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Märt Roosaare
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maido Remm
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Tartu, Estonia
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Wang J, Tao D, Wang S, Li C, Li Y, Zheng F, Wu Z. Disinfection of lettuce using organic acids: an ecological analysis using 16S rRNA sequencing. RSC Adv 2019; 9:17514-17520. [PMID: 35519892 PMCID: PMC9064555 DOI: 10.1039/c9ra03290h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 05/23/2019] [Indexed: 12/15/2022] Open
Abstract
Comparing disinfection efficacies of same type sanitizer using a combined microbial reduction/16S rRNA analysis strategy.
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Affiliation(s)
- Jiayi Wang
- College of Food Science
- Shenyang Agricultural University
- Shenyang
- China
| | - Dongbing Tao
- College of Food Science
- Shenyang Agricultural University
- Shenyang
- China
| | - Shan Wang
- College of Food Science
- Shenyang Agricultural University
- Shenyang
- China
| | - Chen Li
- College of Food Science
- Shenyang Agricultural University
- Shenyang
- China
| | - Yanru Li
- College of Food Science
- Shenyang Agricultural University
- Shenyang
- China
| | - Fenge Zheng
- Shenyang Product Quality Supervision and Inspection Institute
- Shenyang
- China
| | - Zhaoxia Wu
- College of Food Science
- Shenyang Agricultural University
- Shenyang
- China
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Wassermann B, Müller H, Berg G. An Apple a Day: Which Bacteria Do We Eat With Organic and Conventional Apples? Front Microbiol 2019. [PMID: 31396172 DOI: 10.3389/fmicb.2019.01629/full] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Apples are among the most consumed fruits world-wide. They represent a source of direct human exposure to bacterial communities, which is less studied. We analyzed the apple microbiome to detect differences between tissues and the impact of organic and conventional management by a combined approach of 16S rRNA gene amplicon analysis and qPCR, and visualization using fluorescence in situ hybridization and confocal laser scanning microscopy (FISH-CLSM). Each apple fruit harbors different tissues (stem, peel, fruit pulp, seeds, and calyx), which were colonized by distinct bacterial communities. Interestingly, fruit pulp and seeds were bacterial hot spots, while the peel was less colonized. In all, approximately 108 16S rRNA bacterial gene copy numbers were determined in each g apple. Abundances were not influenced by the management practice but we found a strong reduction in bacterial diversity and evenness in conventionally managed apples. In addition, despite the similar structure in general dominated by Proteobacteria (80%), Bacteroidetes (9%), Actinobacteria (5%), and Firmicutes (3%), significant shifts of almost 40% of bacterial genera and orders were monitored. Among them, especially bacterial signatures known for health-affecting potential were found to be enhanced in conventionally managed apples. Our results suggest that we consume about 100 million bacterial cells with one apple. Although this amount was the same, the bacterial composition was significantly different in conventionally and organically produced apples.
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Affiliation(s)
- Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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New Insight of Apparently Healthy Animals as a Potential Reservoir for Clostridium Perfringens: A Public Health Implication. J Vet Res 2018; 62:457-462. [PMID: 30729202 PMCID: PMC6364162 DOI: 10.2478/jvetres-2018-0073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 12/04/2018] [Indexed: 12/19/2022] Open
Abstract
Introduction Clostridium perfringens is commonly found in the gastrointestinal tract of animals and humans and continues to cause one of the most prevalent foodborne diseases in man. Material and Methods A total of 355 samples were examined for the occurrence of C. perfringens: rectal swabs from cattle, sheep, and goats, fresh stool samples from diarrhoea sufferers having been in contact with these animals, irrigation water and soil samples from the husbandry sites, and pre-harvesting fresh produce from farms irrigated with the sampled water. All samples were collected from Cairo and Giza governorates, Egypt. PCR analysis was carried out with positive isolates using the α-toxin gene. Sequence analysis of the gene of C. perfringens isolates was performed using the neighbour-joining approach. Bootstrap analysis was executed with 1,000 resamplings. Results 174 C. perfringens strains were isolated with a 49.01% prevalence. The highest prevalence of C. perfringens in apparently healthy animals was found in sheep (65.45%) followed by goats (58%), buffaloes (55%), and cattle (47.1%). Its prevalence in humans being in contact with these animals was 47.5%. The bacterium’s isolation from the soil and irrigation water was achieved in 40% and 31.7% of samples, respectively, posing a risk, particularly when the water and soil contact food in the field, shown by the fresh produce isolation of 40%. A significant relationship between the prevalence of C. perfringens in animal and environmental samples was identified (P < 0.05). A significant relationship was identified neither between animal species and C. perfringens prevalence, nor between the environmental source and C. perfringens prevalence (P > 0.05). All isolates were positive for the α-toxin gene by PCR. The sequence analysis and the phylogenetic relationship of the α-toxin genes from different samples revealed that C. perfringens from faeces of apparently healthy cattle, buffaloes, sheep, and goats is a significant threat in places where it can contaminate the soil and water. In addition, the sequence of C. perfringens from humans suffering from diarrhoea was found in the same cluster with the sequence from cows, goats, and sheep. Conclusion The role of apparently healthy animals in transmitting C. perfringens to humans, either through being in direct or indirect contact via water or soil in the cultivation of vegetables and fruits, was demonstrated.
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Flandroy L, Poutahidis T, Berg G, Clarke G, Dao MC, Decaestecker E, Furman E, Haahtela T, Massart S, Plovier H, Sanz Y, Rook G. The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 627:1018-1038. [PMID: 29426121 DOI: 10.1016/j.scitotenv.2018.01.288] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/28/2018] [Accepted: 01/28/2018] [Indexed: 05/03/2023]
Abstract
Plants, animals and humans, are colonized by microorganisms (microbiota) and transiently exposed to countless others. The microbiota affects the development and function of essentially all organ systems, and contributes to adaptation and evolution, while protecting against pathogenic microorganisms and toxins. Genetics and lifestyle factors, including diet, antibiotics and other drugs, and exposure to the natural environment, affect the composition of the microbiota, which influences host health through modulation of interrelated physiological systems. These include immune system development and regulation, metabolic and endocrine pathways, brain function and epigenetic modification of the genome. Importantly, parental microbiotas have transgenerational impacts on the health of progeny. Humans, animals and plants share similar relationships with microbes. Research paradigms from humans and other mammals, amphibians, insects, planktonic crustaceans and plants demonstrate the influence of environmental microbial ecosystems on the microbiota and health of organisms, and indicate links between environmental and internal microbial diversity and good health. Therefore, overlapping compositions, and interconnected roles of microbes in human, animal and plant health should be considered within the broader context of terrestrial and aquatic microbial ecosystems that are challenged by the human lifestyle and by agricultural and industrial activities. Here, we propose research priorities and organizational, educational and administrative measures that will help to identify safe microbe-associated health-promoting modalities and practices. In the spirit of an expanding version of "One health" that includes environmental health and its relation to human cultures and habits (EcoHealth), we urge that the lifestyle-microbiota-human health nexus be taken into account in societal decision making.
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Affiliation(s)
- Lucette Flandroy
- Federal Public Service Health, Food Chain Safety and Environment, Belgium
| | - Theofilos Poutahidis
- Laboratory of Pathology, Faculty of Health Sciences, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Gabriele Berg
- Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioural Science, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Maria-Carlota Dao
- ICAN, Institute of Cardiometabolism and Nutrition, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris, France; INSERM, UMRS U1166 (Eq 6) Nutriomics, Paris 6, France; UPMC, Sorbonne University, Pierre et Marie Curie-Paris 6, France
| | - Ellen Decaestecker
- Aquatic Biology, Department Biology, Science, Engineering & Technology Group, KU Leuven, Campus Kortrijk. E. Sabbelaan 53, B-8500 Kortrijk, Belgium
| | - Eeva Furman
- Finnish Environment Institute (SYKE), Helsinki, Finland
| | - Tari Haahtela
- Skin and Allergy Hospital, Helsinki University Hospital, University of Helsinki, Finland
| | - Sébastien Massart
- Laboratory of Integrated and Urban Phytopathology, TERRA, Gembloux Agro-Bio Tech, University of Liège, Passage des deportes, 2, 5030 Gembloux, Belgium
| | - Hubert Plovier
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Yolanda Sanz
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Graham Rook
- Centre for Clinical Microbiology, Department of Infection, UCL (University College London), London, UK.
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Carrot Juice Fermentations as Man-Made Microbial Ecosystems Dominated by Lactic Acid Bacteria. Appl Environ Microbiol 2018; 84:AEM.00134-18. [PMID: 29654180 PMCID: PMC5981062 DOI: 10.1128/aem.00134-18] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/30/2018] [Indexed: 12/11/2022] Open
Abstract
Spontaneous vegetable fermentations, with their rich flavors and postulated health benefits, are regaining popularity. However, their microbiology is still poorly understood, therefore raising concerns about food safety. In addition, such spontaneous fermentations form interesting cases of man-made microbial ecosystems. Here, samples from 38 carrot juice fermentations were collected through a citizen science initiative, in addition to three laboratory fermentations. Culturing showed that Enterobacteriaceae were outcompeted by lactic acid bacteria (LAB) between 3 and 13 days of fermentation. Metabolite-target analysis showed that lactic acid and mannitol were highly produced, as well as the biogenic amine cadaverine. High-throughput 16S rRNA gene sequencing revealed that mainly species of Leuconostoc and Lactobacillus (as identified by 8 and 20 amplicon sequence variants [ASVs], respectively) mediated the fermentations in subsequent order. The analyses at the DNA level still detected a high number of Enterobacteriaceae, but their relative abundance was low when RNA-based sequencing was performed to detect presumptive metabolically active bacterial cells. In addition, this method greatly reduced host read contamination. Phylogenetic placement indicated a high LAB diversity, with ASVs from nine different phylogenetic groups of the Lactobacillus genus complex. However, fermentation experiments with isolates showed that only strains belonging to the most prevalent phylogenetic groups preserved the fermentation dynamics. The carrot juice fermentation thus forms a robust man-made microbial ecosystem suitable for studies on LAB diversity and niche specificity. IMPORTANCE The usage of fermented food products by professional chefs is steadily growing worldwide. Meanwhile, this interest has also increased at the household level. However, many of these artisanal food products remain understudied. Here, an extensive microbial analysis was performed of spontaneous fermented carrot juices which are used as nonalcoholic alternatives for wine in a Belgian Michelin star restaurant. Samples were collected through an active citizen science approach with 38 participants, in addition to three laboratory fermentations. Identification of the main microbial players revealed that mainly species of Leuconostoc and Lactobacillus mediated the fermentations in subsequent order. In addition, a high diversity of lactic acid bacteria was found; however, fermentation experiments with isolates showed that only strains belonging to the most prevalent lactic acid bacteria preserved the fermentation dynamics. Finally, this study showed that the usage of RNA-based 16S rRNA amplicon sequencing greatly reduces host read contamination.
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Aydogan EL, Moser G, Müller C, Kämpfer P, Glaeser SP. Long-Term Warming Shifts the Composition of Bacterial Communities in the Phyllosphere of Galium album in a Permanent Grassland Field-Experiment. Front Microbiol 2018; 9:144. [PMID: 29487575 PMCID: PMC5816784 DOI: 10.3389/fmicb.2018.00144] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 01/23/2018] [Indexed: 11/13/2022] Open
Abstract
Global warming is currently a much discussed topic with as yet largely unexplored consequences for agro-ecosystems. Little is known about the warming effect on the bacterial microbiota inhabiting the plant surface (phyllosphere), which can have a strong impact on plant growth and health, as well as on plant diseases and colonization by human pathogens. The aim of this study was to investigate the effect of moderate surface warming on the diversity and composition of the bacterial leaf microbiota of the herbaceous plant Galium album. Leaves were collected from four control and four surface warmed (+2°C) plots located at the field site of the Environmental Monitoring and Climate Impact Research Station Linden in Germany over a 6-year period. Warming had no effect on the concentration of total number of cells attached to the leaf surface as counted by Sybr Green I staining after detachment, but changes in the diversity and phylogenetic composition of the bacterial leaf microbiota analyzed by bacterial 16S rRNA gene Illumina amplicon sequencing were observed. The bacterial phyllosphere microbiota were dominated by Proteobacteria, Bacteroidetes, and Actinobacteria. Warming caused a significant higher relative abundance of members of the Gammaproteobacteria, Actinobacteria, and Firmicutes, and a lower relative abundance of members of the Alphaproteobacteria and Bacteroidetes. Plant beneficial bacteria like Sphingomonas spp. and Rhizobium spp. occurred in significantly lower relative abundance in leaf samples of warmed plots. In contrast, several members of the Enterobacteriaceae, especially Enterobacter and Erwinia, and other potential plant or human pathogenic genera such as Acinetobacter and insect-associated Buchnera and Wolbachia spp. occurred in higher relative abundances in the phyllosphere samples from warmed plots. This study showed for the first time the long-term impact of moderate (+2°C) surface warming on the phyllosphere microbiota on plants. A reduction of beneficial bacteria and an enhancement of potential pathogenic bacteria in the phyllosphere of plants may indicate that this aspect of the ecosystem which has been largely neglected up till now, can be a potential risk for pathogen transmission in agro-ecosystems in the near future.
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Affiliation(s)
- Ebru L. Aydogan
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Gerald Moser
- Institute for Plant Ecology, Justus Liebig University Giessen, Giessen, Germany
| | - Christoph Müller
- Institute for Plant Ecology, Justus Liebig University Giessen, Giessen, Germany
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Peter Kämpfer
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Stefanie P. Glaeser
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
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Wassermann B, Rybakova D, Müller C, Berg G. Harnessing the microbiomes of Brassica vegetables for health issues. Sci Rep 2017; 7:17649. [PMID: 29247170 PMCID: PMC5732279 DOI: 10.1038/s41598-017-17949-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/14/2017] [Indexed: 02/01/2023] Open
Abstract
Plant health is strongly connected with plants´ microbiome. In case of raw-eaten plants, the microbiome can also affect human health. To study potential impacts on health issues of both hosts, the microbiome composition of seven different Brassica vegetables, originating from different food processing pathways, was analyzed by a combined approach of amplicon sequencing, metagenomic mining and cultivation. All Brassica vegetables harbored a highly diverse microbiota as identified by 16S rRNA gene amplicon sequencing. The composition of the microbiota was found to be rather driven by the plant genotype than by the processing pathway. We characterized isolates with potential cancer-preventing properties by tracing myrosinase activity as well as isolates with biological control activity towards plant pathogens. We identified a novel strain with myrosinase activity and we found bacterial myrosinase genes to be enriched in rhizosphere and phyllosphere metagenomes of Brassica napus and Eruca sativa in comparison to the surrounding soil. Strains which were able to suppress plant pathogens were isolated from naturally processed vegetables and represent a substantial part (4.1%) of all vegetable microbiomes. Our results shed first light on the microbiome of edible plants and open the door to harnessing the Brassica microbiome for plant disease resistance and human health.
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Affiliation(s)
- Birgit Wassermann
- Graz University of Technology, Institute of Environmental Biotechnology, Petersgasse 12, 8010, Graz, Austria
| | - Daria Rybakova
- Graz University of Technology, Institute of Environmental Biotechnology, Petersgasse 12, 8010, Graz, Austria
| | - Christina Müller
- Graz University of Technology, Institute of Environmental Biotechnology, Petersgasse 12, 8010, Graz, Austria
| | - Gabriele Berg
- Graz University of Technology, Institute of Environmental Biotechnology, Petersgasse 12, 8010, Graz, Austria.
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40
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Food recalls and warnings due to the presence of foodborne pathogens — a focus on fresh fruits, vegetables, dairy and eggs. Curr Opin Food Sci 2017. [DOI: 10.1016/j.cofs.2017.11.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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41
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Impact of the source of organic manure on persistence of E. coli O157:H7 gfp + in rocket ( Diplotaxis tenuifolia ) and Swiss chard ( Beta vulgaris cicla). Food Control 2017. [DOI: 10.1016/j.foodcont.2017.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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42
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Myszka K, Schmidt MT, Majcher M, Juzwa W, Czaczyk K. β-Caryophyllene-rich pepper essential oils suppress spoilage activity of Pseudomonas fluorescens KM06 in fresh-cut lettuce. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2017.05.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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43
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Novello G, Gamalero E, Bona E, Boatti L, Mignone F, Massa N, Cesaro P, Lingua G, Berta G. The Rhizosphere Bacterial Microbiota of Vitis vinifera cv. Pinot Noir in an Integrated Pest Management Vineyard. Front Microbiol 2017; 8:1528. [PMID: 28855895 PMCID: PMC5557794 DOI: 10.3389/fmicb.2017.01528] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 07/28/2017] [Indexed: 12/22/2022] Open
Abstract
Microorganisms associated with Vitis vinifera (grapevine) can affect its growth, health and grape quality. The aim of this study was to unravel the biodiversity of the bacterial rhizosphere microbiota of grapevine in an integrated pest management vineyard located in Piedmont, Italy. Comparison between the microbial community structure in the bulk and rhizosphere soil (variable: space) were performed. Moreover, the possible shifts of the bulk and rhizosphere soil microbiota according to two phenological stages such as flowering and early fruit development (variable: time) were characterized. The grapevine microbiota was identified using metagenomics and next-generation sequencing. Biodiversity was higher in the rhizosphere than in the bulk soil, independent of the phenological stage. Actinobacteria were the dominant class with frequencies ≥ 50% in all the soil samples, followed by Proteobacteria, Gemmatimonadetes, and Bacteroidetes. While Actinobacteria and Proteobacteria are well-known as being dominant in soil, this is the first time the presence of Gemmatimonadetes has been observed in vineyard soils. Gaiella was the dominant genus of Actinobacteria in all the samples. Finally, the microbiota associated with grapevine differed from the bulk soil microbiota and these variations were independent of the phenological stage of the plant.
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Affiliation(s)
- Giorgia Novello
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte OrientaleAlessandria, Italy
| | - Elisa Gamalero
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte OrientaleAlessandria, Italy
| | - Elisa Bona
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte OrientaleAlessandria, Italy
| | - Lara Boatti
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte OrientaleAlessandria, Italy.,SmartSeq s.r.l.Alessandria, Italy
| | - Flavio Mignone
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte OrientaleAlessandria, Italy.,SmartSeq s.r.l.Alessandria, Italy
| | - Nadia Massa
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte OrientaleAlessandria, Italy
| | - Patrizia Cesaro
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte OrientaleAlessandria, Italy
| | - Guido Lingua
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte OrientaleAlessandria, Italy
| | - Graziella Berta
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte OrientaleAlessandria, Italy
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Djouadi LN, Selama O, Abderrahmani A, Bouanane-Darenfed A, Abdellaziz L, Amziane M, Fardeau ML, Nateche F. Multiresistant opportunistic pathogenic bacteria isolated from polluted rivers and first detection of nontuberculous mycobacteria in the Algerian aquatic environment. JOURNAL OF WATER AND HEALTH 2017; 15:566-579. [PMID: 28771154 DOI: 10.2166/wh.2017.309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Opportunistic infections constitute a major challenge for modern medicine mainly because the involved bacteria are usually multiresistant to antibiotics. Most of these bacteria possess remarkable ability to adapt to various ecosystems, including those exposed to anthropogenic activities. This study isolated and identified 21 multiresistant opportunistic bacteria from two polluted rivers, located in Algiers. Cadmium, lead, and copper concentrations were determined for both water samples to evaluate heavy metal pollution. High prevalence of Enterobacteria and non-fermentative Gram-negative rods was found and a nontuberculous Mycobacterium (NTM) strain was isolated. To the best of our knowledge, this is the first detection of NTM in the Algerian environment. The strains were tested for their resistance against 34 antibiotics and 8 heavy metals. Multiple antibiotics and heavy metals resistance was observed in all isolates. The two most resistant strains, identified as Acinetobacter sp. and Citrobacter freundii, were submitted to plasmid curing to determine if resistance genes were plasmid or chromosome encoded. Citrobacter freundii strain P18 showed a high molecular weight plasmid which seems to code for resistance to zinc, lead, and tetracycline, at the same time. These findings strongly suggest that anthropized environments constitute a reservoir for multiresistant opportunistic bacteria and for circulating resistance genes.
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Affiliation(s)
- Lydia Neïla Djouadi
- Laboratory of Cellular and Molecular Biology, Microbiology team, Faculty of Biological Sciences, USTHB, Bab ezzouar -BP n°32, Algiers, Algeria
| | - Okba Selama
- Laboratory of Cellular and Molecular Biology, Microbiology team, Faculty of Biological Sciences, USTHB, Bab ezzouar -BP n°32, Algiers, Algeria
| | - Ahmed Abderrahmani
- Laboratory of Cellular and Molecular Biology, Microbiology team, Faculty of Biological Sciences, USTHB, Bab ezzouar -BP n°32, Algiers, Algeria
| | - Amel Bouanane-Darenfed
- Laboratory of Cellular and Molecular Biology, Microbiology team, Faculty of Biological Sciences, USTHB, Bab ezzouar -BP n°32, Algiers, Algeria
| | - Lamia Abdellaziz
- Laboratory of Cellular and Molecular Biology, Microbiology team, Faculty of Biological Sciences, USTHB, Bab ezzouar -BP n°32, Algiers, Algeria
| | - Meriam Amziane
- Laboratory of Cellular and Molecular Biology, Microbiology team, Faculty of Biological Sciences, USTHB, Bab ezzouar -BP n°32, Algiers, Algeria
| | - Marie-Laure Fardeau
- Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, Marseille 13288 cedex 09, France E-mail:
| | - Farida Nateche
- Laboratory of Cellular and Molecular Biology, Microbiology team, Faculty of Biological Sciences, USTHB, Bab ezzouar -BP n°32, Algiers, Algeria
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Nithya A, Babu S. Prevalence of plant beneficial and human pathogenic bacteria isolated from salad vegetables in India. BMC Microbiol 2017; 17:64. [PMID: 28288566 PMCID: PMC5348887 DOI: 10.1186/s12866-017-0974-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/07/2017] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The study aimed at enumerating, identifying and categorizing the endophytic cultivable bacterial community in selected salad vegetables (carrot, cucumber, tomato and onion). Vegetable samples were collected from markets of two vegetable hot spot growing areas, during two different crop harvest seasons. Crude and diluted vegetable extracts were plated and the population of endophytic bacteria was assessed based on morphologically distinguishable colonies. The bacterial isolates were identified by growth in selective media, biochemical tests and 16S rRNA gene sequencing. RESULTS The endophytic population was found to be comparably higher in cucumber and tomato in both of the sampling locations, whereas lower in carrot and onion. Bacterial isolates belonged to 5 classes covering 46 distinct species belonging to 19 genera. Human opportunistic pathogens were predominant in carrot and onion, whereas plant beneficial bacteria dominated in cucumber and tomato. Out of the 104 isolates, 16.25% are human pathogens and 26.5% are human opportunistic pathogens. CONCLUSIONS Existence of a high population of plant beneficial bacteria was found to have suppressed the population of plant and human pathogens. There is a greater potential to study the native endophytic plant beneficial bacteria for developing them as biocontrol agents against human pathogens that are harboured by plants.
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Affiliation(s)
- Angamuthu Nithya
- School of Bio Sciences and Technology, VIT University, Vellore, 632014, India
| | - Subramanian Babu
- School of Bio Sciences and Technology, VIT University, Vellore, 632014, India.
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Analysis of the bacterial biodiversity of peaches under refrigerated storage after treatment by high hydrostatic pressure. FOOD AND BIOPRODUCTS PROCESSING 2017. [DOI: 10.1016/j.fbp.2016.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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47
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van Dyk BN, de Bruin W, du Plessis EM, Korsten L. Microbiological Food Safety Status of Commercially Produced Tomatoes from Production to Marketing. J Food Prot 2016; 79:392-406. [PMID: 26939649 DOI: 10.4315/0362-028x.jfp-15-300] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Tomatoes have been implicated in various microbial disease outbreaks and are considered a potential vehicle for foodborne pathogens. Traceback studies mostly implicate contamination during production and/or processing. The microbiological quality of commercially produced tomatoes was thus investigated from the farm to market, focusing on the impact of contaminated irrigation and washing water, facility sanitation, and personal hygiene. A total of 905 samples were collected from three largescale commercial farms from 2012 through 2014. The farms differed in water sources used (surface versus well) and production methods (open field versus tunnel). Levels of total coliforms and Escherichia coli and prevalence of E. coli O157:H7 and Salmonella Typhimurium were determined. Dominant coliforms were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. No pathogens or E. coli were detected on any of the tomatoes tested throughout the study despite the high levels of coliforms (4.2 to 6.2 log CFU/g) present on the tomatoes at the market. The dominant species associated with tomatoes belonged to the genera Enterobacter, Klebsiella, and Citrobacter. Water used on the farm for irrigation considered not fit for purpose according to national agricultural irrigation standards, with high E. coli levels resulting from either a highly contaminated source water (river water at 3.19 log most probable number [MPN]/100 ml) or improper storage of source water (stored well water at 1.72 log MPN/100 ml). Salmonella Typhimurium was detected on two occasions on a contact surface in the processing facility of the first farm in 2012. Contact surface coliform counts were 2.9 to 4.8 log CFU/cm(2). Risk areas identified in this study were water used for irrigation and poor sanitation practices in the processing facility. Implementation of effective food safety management systems in the fresh produce industry is of the utmost importance to ensure product safety for consumers.
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Affiliation(s)
- Brigitte N van Dyk
- Institute for Food, Nutrition and Well-being, Department of Plant Sciences, University of Pretoria, Pretoria 0002, South Africa
| | - Willeke de Bruin
- Institute for Food, Nutrition and Well-being, Department of Plant Sciences, University of Pretoria, Pretoria 0002, South Africa
| | - Erika M du Plessis
- Institute for Food, Nutrition and Well-being, Department of Plant Sciences, University of Pretoria, Pretoria 0002, South Africa
| | - Lise Korsten
- Institute for Food, Nutrition and Well-being, Department of Plant Sciences, University of Pretoria, Pretoria 0002, South Africa.
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Hiding in Fresh Fruits and Vegetables: Opportunistic Pathogens May Cross Geographical Barriers. Int J Microbiol 2016; 2016:4292417. [PMID: 26989419 PMCID: PMC4772400 DOI: 10.1155/2016/4292417] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/24/2016] [Indexed: 01/11/2023] Open
Abstract
Different microbial groups of the microbiome of fresh produce can have diverse effects on human health. This study was aimed at identifying some microbial communities of fresh produce by analyzing 105 samples of imported fresh fruits and vegetables originated from different countries in the world including local samples (Oman) for aerobic plate count and the counts of Enterobacteriaceae, Enterococcus, and Staphylococcus aureus. The isolated bacteria were identified by molecular (PCR) and biochemical methods (VITEK 2). Enterobacteriaceae occurred in 60% of fruits and 91% of vegetables. Enterococcus was isolated from 20% of fruits and 42% of vegetables. E. coli and S. aureus were isolated from 22% and 7% of vegetables, respectively. Ninety-seven bacteria comprising 21 species were similarly identified by VITEK 2 and PCR to species level. E. coli, Klebsiella pneumoniae, Enterococcus casseliflavus, and Enterobacter cloacae were the most abundant species; many are known as opportunistic pathogens which may raise concern to improve the microbial quality of fresh produce. Phylogenetic trees showed no relationship between clustering of the isolates based on the 16S rRNA gene and the original countries of fresh produce. Intercountry passage of opportunistic pathogens in fresh produce cannot be ruled out, which requires better management.
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Brandwein M, Al-Quntar A, Goldberg H, Mosheyev G, Goffer M, Marin-Iniesta F, López-Gómez A, Steinberg D. Mitigation of Biofilm Formation on Corrugated Cardboard Fresh Produce Packaging Surfaces Using a Novel Thiazolidinedione Derivative Integrated in Acrylic Emulsion Polymers. Front Microbiol 2016; 7:159. [PMID: 26909074 PMCID: PMC4754437 DOI: 10.3389/fmicb.2016.00159] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 01/29/2016] [Indexed: 11/29/2022] Open
Abstract
Various surfaces associated with the storage and packing of food are known to harbor distinct bacterial pathogens. Conspicuously absent among the plethora of studies implicating food packaging materials and machinery is the study of corrugated cardboard packaging, the worldwide medium for transporting fresh produce. In this study, we observed the microbial communities of three different store-bought fruits and vegetables, along with their analog cardboard packaging using high throughput sequencing technology. We further developed an anti-biofilm polymer meant to coat corrugated cardboard surfaces and mediate bacterial biofilm growth on said surfaces. Integration of a novel thiazolidinedione derivative into the acrylic emulsion polymers was assessed using Energy Dispersive X-ray Spectrometry (EDS) analysis and surface topography was visualized and quantified on corrugated cardboard surfaces. Biofilm growth was measured using q-PCR targeting the gene encoding 16s rRNA. Additionally, architectural structure of the biofilm was observed using SEM. The uniform integration of the thiazolidinedione derivative TZD-6 was confirmed, and it was determined via q-PCR to reduce biofilm growth by ~80% on tested surfaces. A novel and effective method for reducing microbial load and preventing contamination on food packaging is thereby proposed.
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Affiliation(s)
- Michael Brandwein
- Biofilm Research Laboratory, Faculty of Dental Medicine, Institute of Dental Sciences, The Hebrew University of JerusalemJerusalem, Israel
| | - Abed Al-Quntar
- Biofilm Research Laboratory, Faculty of Dental Medicine, Institute of Dental Sciences, The Hebrew University of JerusalemJerusalem, Israel
- Institute for Drug Science, School of Pharmacy, The Hebrew University of JerusalemJerusalem, Israel
| | | | | | | | - Fulgencio Marin-Iniesta
- Food Technology, Nutrition and Bromatology Department, Facultad de Veterinaria, Universidad de MurciaMurcia, Spain
| | - Antonio López-Gómez
- Department of Food Engineering and Agricultural Equipment, Technical University of CartagenaCartagena, Spain
| | - Doron Steinberg
- Biofilm Research Laboratory, Faculty of Dental Medicine, Institute of Dental Sciences, The Hebrew University of JerusalemJerusalem, Israel
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50
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Berg G, Rybakova D, Grube M, Köberl M. The plant microbiome explored: implications for experimental botany. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:995-1002. [PMID: 26547794 PMCID: PMC5395086 DOI: 10.1093/jxb/erv466] [Citation(s) in RCA: 206] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The importance of microbial root inhabitants for plant growth and health was recognized as early as 100 years ago. Recent insights reveal a close symbiotic relationship between plants and their associated microorganisms, and high structural and functional diversity within plant microbiomes. Plants provide microbial communities with specific habitats, which can be broadly categorized as the rhizosphere, phyllosphere, and endosphere. Plant-associated microbes interact with their host in essential functional contexts. They can stimulate germination and growth, help plants fend off disease, promote stress resistance, and influence plant fitness. Therefore, plants have to be considered as metaorganisms within which the associated microbes usually outnumber the cells belonging to the plant host. The structure of the plant microbiome is determined by biotic and abiotic factors but follows ecological rules. Metaorganisms are co-evolved species assemblages. The metabolism and morphology of plants and their microbiota are intensively connected with each other, and the interplay of both maintains the functioning and fitness of the holobiont. Our study of the current literature shows that analysis of plant microbiome data has brought about a paradigm shift in our understanding of the diverse structure and functioning of the plant microbiome with respect to the following: (i) the high interplay of bacteria, archaea, fungi, and protists; (ii) the high specificity even at cultivar level; (iii) the vertical transmission of core microbiomes; (iv) the extraordinary function of endophytes; and (v) several unexpected functions and metabolic interactions. The plant microbiome should be recognized as an additional factor in experimental botany and breeding strategies.
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Affiliation(s)
- Gabriele Berg
- Graz University of Technology, Institute of Environmental Biotechnology, 8010 Graz, Austria Austrian Centre of Industrial Biotechnology (ACIB GmbH), 8010 Graz, Austria
| | - Daria Rybakova
- Graz University of Technology, Institute of Environmental Biotechnology, 8010 Graz, Austria
| | - Martin Grube
- University of Graz, Institute of Plant Sciences, 8010 Graz, Austria
| | - Martina Köberl
- Graz University of Technology, Institute of Environmental Biotechnology, 8010 Graz, Austria Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA 99352, USA
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