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Dor S, Nudel K, Eagan JL, Cohen R, Hull CM, Keller NP, Prusky D, Afriat-Jurnou L. Bacterial-fungal crosstalk is defined by a fungal lactone mycotoxin and its degradation by a bacterial lactonase. Appl Environ Microbiol 2024; 90:e0029924. [PMID: 38786360 DOI: 10.1128/aem.00299-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
Bacteria, fungi, and mammals contain lactonases that can degrade the Gram-negative bacterial quorum sensing (QS) molecules N-acyl homoserine lactones (AHLs). AHLs are critical for bacteria to coordinate gene expression and pathogenicity with population density. However, AHL-degrading lactonases present variable substrate ranges, including degradation of the Pencillium expansum lactone mycotoxin patulin. We selected Erwinia spp. as our model bacteria to further investigate this interaction. We find both native apple microbiome Erwinia spp. and the fruit tree pathogen Erwinia amylovora to be inhibited by patulin. At patulin concentrations that inhibited E. amylovora growth, expression of E. amylovora lactonase encoded by EaaiiA was increased. EaAiiA demonstrated the ability to degrade patulin in vitro, as well, as in vivo where it reduced apple disease and patulin production by P. expansum. Fungal-bacterial co-cultures revealed that the E. amylovora Δeaaiia strain failed to protect apples from P. expansum infections, which contained significant amounts of patulin. Our results suggest that bacterial lactonase production can modulate the pathogenicity of P. expansum in response to the secretion of toxic patulin. IMPORTANCE Chemical signaling in the microbial world facilitates the regulation of gene expression as a function of cell population density. This is especially true for the Gram-negative bacterial signal N-acyl homoserine lactone (AHL). Lactonases that deactivate AHLs have attracted a lot of attention because of their antibacterial potential. However, the involvement of these enzymes in inhibiting fungal pathogens and the potential role of these enzymes in bacterial-fungal interactions are unknown. Here, we find that a bacterial enzyme involved in the degradation of AHLs is also induced by and degrades the fungal lactone mycotoxin, patulin. This work supports the potential use of bacterial enzymes and/or the producing bacteria in controlling the post-harvest fruit disease caused by the patulin-producing fungus Penicillium expansum.
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Affiliation(s)
- Shlomit Dor
- Department of Molecular and Computational Biosciences and Biotechnology, Migal-Galilee Research Institute, Kiryat Shmona, Israel
| | - Keren Nudel
- Department of Molecular and Computational Biosciences and Biotechnology, Migal-Galilee Research Institute, Kiryat Shmona, Israel
- Faculty of Sciences and Technology, Tel-Hai College, Upper Galilee, Israel
| | - Justin L Eagan
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Rami Cohen
- Department of Molecular and Computational Biosciences and Biotechnology, Migal-Galilee Research Institute, Kiryat Shmona, Israel
| | - Christina M Hull
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Dov Prusky
- Department of Postharvest Science, Agricultural Research Organization, Rishon LeZion, Israel
| | - Livnat Afriat-Jurnou
- Department of Molecular and Computational Biosciences and Biotechnology, Migal-Galilee Research Institute, Kiryat Shmona, Israel
- Faculty of Sciences and Technology, Tel-Hai College, Upper Galilee, Israel
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Boutin S, Lussier E, Laforest-Lapointe I. Investigating the spatiotemporal dynamics of apple tree phyllosphere bacterial and fungal communities across cultivars in orchards. Can J Microbiol 2024; 70:238-251. [PMID: 38452350 DOI: 10.1139/cjm-2023-0215] [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] [Indexed: 03/09/2024]
Abstract
The phyllosphere, a reservoir of diverse microbial life associated with plant health, harbors microbial communities that are subject to various complex ecological processes acting at multiple scales. In this study, we investigated the determinants of the spatiotemporal variation in bacterial and fungal communities within the apple tree phyllosphere, employing 16S and ITS amplicon sequencing. Our research assessed the impact of key factors-plant compartment, site, time, and cultivar-on the composition and diversity of leaf and flower microbial communities. Our analyses, based on samples collected from three cultivars in three orchards in 2022, revealed that site and time are the strongest drivers of apple tree phyllosphere microbial communities. Conversely, plant compartment and cultivar exhibited minor roles in explaining community composition and diversity. Predominantly, bacterial communities comprised Hymenobacter (25%) and Sphingomonas (10%), while the most relatively abundant fungal genera included Aureobasidium (27%) and Sporobolomyces (10%). Additionally, our results show a gradual decrease in alpha-diversity throughout the growth season. These findings emphasize the necessity to consider local microbial ecology dynamics in orchards, especially as many groups worldwide aim for the development of biocontrol strategies (e.g., by manipulating plant-microbe interactions). More research is needed to improve our understanding of the determinants of time and site-specific disparities within apple tree phyllosphere microbial communities across multiple years, locations, and cultivars.
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Affiliation(s)
- Sophie Boutin
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Ema Lussier
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Isabelle Laforest-Lapointe
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
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3
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Ribič A, Trček J. Customized 16S-23S rDNA ITS Amplicon Metagenomics for Acetic Acid Bacteria Species Identification in Vinegars and Kombuchas. Microorganisms 2024; 12:1023. [PMID: 38792851 PMCID: PMC11123803 DOI: 10.3390/microorganisms12051023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/04/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Acetic acid bacteria (AAB) are involved in food and beverage production bioprocesses, like those in vinegar and kombucha. They oxidize sugars and alcohols into various metabolites, resulting in the final products' pleasant taste and aroma. The 16S rDNA amplicon metagenomics using Illumina technology is usually used to follow the microbiological development of these processes. However, the 16S rRNA gene sequences among different species of AAB are very similar, thus not enabling a reliable identification down to the species level but only to the genus. In this study, we have constructed primers for amplifying half of the 16S-23S rRNA gene internal transcribed spacer (ITS) for library construction and further sequencing using Illumina technology. This approach was successfully used to estimate the relative abundance of AAB species in defined consortia. Further application of this method for the analysis of different vinegar and kombucha samples proves it suitable for assessing the relative abundance of AAB species when these bacteria represent a predominant part of a microbial community.
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Affiliation(s)
- Alja Ribič
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, SI-2000 Maribor, Slovenia;
| | - Janja Trček
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, SI-2000 Maribor, Slovenia;
- Faculty of Chemistry and Chemical Engineering, University of Maribor, SI-2000 Maribor, Slovenia
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Hartmann A, Binder T, Rothballer M. Quorum sensing-related activities of beneficial and pathogenic bacteria have important implications for plant and human health. FEMS Microbiol Ecol 2024; 100:fiae076. [PMID: 38744663 PMCID: PMC11149725 DOI: 10.1093/femsec/fiae076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/28/2024] [Accepted: 05/13/2024] [Indexed: 05/16/2024] Open
Abstract
Eukaryotic organisms coevolved with microbes from the environment forming holobiotic meta-genomic units. Members of host-associated microbiomes have commensalic, beneficial/symbiotic, or pathogenic phenotypes. More than 100 years ago, Lorenz Hiltner, pioneer of soil microbiology, introduced the term 'Rhizosphere' to characterize the observation that a high density of saprophytic, beneficial, and pathogenic microbes are attracted by root exudates. The balance between these types of microbes decide about the health of the host. Nowadays we know, that for the interaction of microbes with all eukaryotic hosts similar principles and processes of cooperative and competitive functions are in action. Small diffusible molecules like (phyto)hormones, volatiles and quorum sensing signals are examples for mediators of interspecies and cross-kingdom interactions. Quorum sensing of bacteria is mediated by different autoinducible metabolites in a density-dependent manner. In this perspective publication, the role of QS-related activities for the health of hosts will be discussed focussing mostly on N-acyl-homoserine lactones (AHL). It is also considered that in some cases very close phylogenetic relations exist between plant beneficial and opportunistic human pathogenic bacteria. Based on a genome and system-targeted new understanding, sociomicrobiological solutions are possible for the biocontrol of diseases and the health improvement of eukaryotic hosts.
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Affiliation(s)
- Anton Hartmann
- Faculty of Biology, Microbe-Host Interactions, Ludwig-Maximilian-University Munich, Grosshaderner Str. 2, D-82152 Planegg/Martinsried, Germany
- Department of Environmental Sciences, Helmholtz Zentrum Munich, German Research Center for Health and Environment, Research Unit Microbe-Plant Interactions, Ingolstädter Landstr. 1, D-85762 Neuherberg, Germany
| | - Tatiana Binder
- Department of Environmental Sciences, Helmholtz Zentrum Munich, German Research Center for Health and Environment, Research Unit Microbe-Plant Interactions, Ingolstädter Landstr. 1, D-85762 Neuherberg, Germany
| | - Michael Rothballer
- Department of Environmental Sciences, Helmholtz Zentrum Munich, German Research Center for Health and Environment, Research Unit Microbe-Plant Interactions, Ingolstädter Landstr. 1, D-85762 Neuherberg, Germany
- Helmholtz Zentrum Munich, German Research Center for Health and Environment, Institute of Network Biology, Ingolstädter Landstr. 1 D-85762 Neuherberg, Germany
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Goforth M, Cooper MA, Oliver AS, Pinzon J, Skots M, Obergh V, Suslow TV, Flores GE, Huynh S, Parker CT, Mackelprang R, Cooper KK. Bacterial community shifts of commercial apples, oranges, and peaches at different harvest points across multiple growing seasons. PLoS One 2024; 19:e0297453. [PMID: 38625898 PMCID: PMC11020611 DOI: 10.1371/journal.pone.0297453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/04/2024] [Indexed: 04/18/2024] Open
Abstract
Assessing the microbes present on tree fruit carpospheres as the fruit enters postharvest processing could have useful applications, as these microbes could have a major influence on spoilage, food safety, verification of packing process controls, or other aspects of processing. The goal of this study was to establish a baseline profile of bacterial communities associated with apple (pome fruit), peach (stone fruit), and Navel orange (citrus fruit) at harvest. We found that commercial peaches had the greatest bacterial richness followed by oranges then apples. Time of harvest significantly changed bacterial diversity in oranges and peaches, but not apples. Shifts in diversity varied by fruit type, where 70% of the variability in beta diversity on the apple carposphere was driven by the gain and loss of species (i.e., nestedness). The peach and orange carposphere bacterial community shifts were driven by nearly an even split between turnover (species replacement) and nestedness. We identified a small core microbiome for apples across and between growing seasons that included only Methylobacteriaceae and Sphingomonadaceae among the samples, while peaches had a larger core microbiome composed of five bacterial families: Bacillaceae, Geodermtophilaceae, Nocardioidaceae, Micrococcaeceae, and Trueperaceae. There was a relatively diverse core microbiome for oranges that shared all the families present on apples and peaches, except for Trueperaceae, but also included an additional nine bacterial families not shared including Oxalobacteraceae, Cytophagaceae, and Comamonadaceae. Overall, our findings illustrate the important temporal dynamics of bacterial communities found on major commercial tree fruit, but also the core bacterial families that constantly remain with both implications being important entering postharvest packing and processing.
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Affiliation(s)
- Madison Goforth
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, United States of America
| | - Margarethe A. Cooper
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, United States of America
| | - Andrew S. Oliver
- USDA-ARS Western Human Nutrition Research Center, Davis, California, United States of America
| | - Janneth Pinzon
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Mariya Skots
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Victoria Obergh
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, United States of America
| | - Trevor V. Suslow
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Gilberto E. Flores
- Department of Biology, California State University, Northridge, Northridge, California, United States of America
| | - Steven Huynh
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, USDA, Albany, California, United States of America
| | - Craig T. Parker
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, USDA, Albany, California, United States of America
| | - Rachel Mackelprang
- Department of Biology, California State University, Northridge, Northridge, California, United States of America
| | - Kerry K. Cooper
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
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Tenea GN, Reyes P, Molina D. Fungal Mycobiome of Mature Strawberry Fruits ( Fragaria x ananassa Variety 'Monterey') Suggests a Potential Market Site Contamination with Harmful Yeasts. Foods 2024; 13:1175. [PMID: 38672848 PMCID: PMC11049331 DOI: 10.3390/foods13081175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
An amplicon metagenomic approach based on the ITS2 region of fungal rDNA was used to investigate the diversity of fungi associated with mature strawberries collected from a volcanic orchard and open-air market stands. Based on the Kruskal-Wallis test, no statistically significant differences were observed in both non-phylogenetic and phylogenetic alpha diversity indices. According to beta diversity analyses, significant differences in fungal communities were found between groups (orchard vs. market). Taxonomic assignment of amplicon sequence variables (ASVs) revealed 7 phyla and 31 classes. The prevalent fungal phyla were Basidiomycota (29.59-84.58%), Ascomycota (15.33-70.40%), and Fungi-phy-Insertae-sedis (0.45-2.89%). The most predominant classes among the groups were Saccharomycetes in the market group, and Microbotryomycetes and Tremellomycetes in the orchard group. Based on the analysis of microbiome composition (ANCOM), we found that the most differentially fungal genera were Hanseniaspora, Kurtzmaniella, and Phyllozyma. Endophytic yeasts Curvibasidium cygneicollum were prevalent in both groups, while Candida railenensis was detected in fruits originating only from the market. In addition, Rhodotorula graminis (relative abundance varying from 1.7% to 21.18%) and Papiliotrema flavescens (relative abundance varying from 1.58% to 16.55%) were detected in all samples regardless of origin, while Debaryomyces prosopidis was detected in samples from the market only, their relative abundance varying with the sample (from 0.80% to 19.23%). Their role in fruit quality and safety has not been yet documented. Moreover, several clinically related yeasts, such as Meyerozyma guilliermondii and Candida parapsilosis, were detected in samples only from the market. Understanding the variety and makeup of the mycobiome in ripe fruits during the transition from the orchard to the market is crucial for fruit safety after harvest.
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Affiliation(s)
- Gabriela N. Tenea
- Biofood and Nutraceutics Research and Development Group, Faculty of Engineering in Agricultural and Environmental Sciences, Universidad Técnica del Norte, 100150 Ibarra, Ecuador
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Wentzien NM, Fernández-González AJ, Valverde-Corredor A, Lasa AV, Villadas PJ, Wicaksono WA, Cernava T, Berg G, Fernández-López M, Mercado-Blanco J. Pitting the olive seed microbiome. ENVIRONMENTAL MICROBIOME 2024; 19:17. [PMID: 38491515 PMCID: PMC10943921 DOI: 10.1186/s40793-024-00560-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/10/2024] [Indexed: 03/18/2024]
Abstract
BACKGROUND The complex and co-evolved interplay between plants and their microbiota is crucial for the health and fitness of the plant holobiont. However, the microbiota of the seeds is still relatively unexplored and no studies have been conducted with olive trees so far. In this study, we aimed to characterize the bacterial, fungal and archaeal communities present in seeds of ten olive genotypes growing in the same orchard through amplicon sequencing to test whether the olive genotype is a major driver in shaping the seed microbial community, and to identify the origin of the latter. Therefore, we have developed a methodology for obtaining samples from the olive seed's endosphere under sterile conditions. RESULTS A diverse microbiota was uncovered in olive seeds, the plant genotype being an important factor influencing the structure and composition of the microbial communities. The most abundant bacterial phylum was Actinobacteria, accounting for an average relative abundance of 41%. At genus level, Streptomyces stood out because of its potential influence on community structure. Within the fungal community, Basidiomycota and Ascomycota were the most abundant phyla, including the genera Malassezia, Cladosporium, and Mycosphaerella. The shared microbiome was composed of four bacterial (Stenotrophomonas, Streptomyces, Promicromonospora and Acidipropionibacterium) and three fungal (Malassezia, Cladosporium and Mycosphaerella) genera. Furthermore, a comparison between findings obtained here and earlier results from the root endosphere of the same trees indicated that genera such as Streptomyces and Malassezia were present in both olive compartments. CONCLUSIONS This study provides the first insights into the composition of the olive seed microbiota. The highly abundant fungal genus Malassezia and the bacterial genus Streptomyces reflect a unique signature of the olive seed microbiota. The genotype clearly shaped the composition of the seed's microbial community, although a shared microbiome was found. We identified genera that may translocate from the roots to the seeds, as they were present in both organs of the same trees. These findings set the stage for future research into potential vertical transmission of olive endophytes and the role of specific microbial taxa in seed germination, development, and seedling survival.
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Affiliation(s)
- Nuria M Wentzien
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Antonio J Fernández-González
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | | | - Ana V Lasa
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Pablo J Villadas
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, 8010, Graz, Austria
| | - Tomislav Cernava
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, 8010, Graz, Austria
| | - Manuel Fernández-López
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Jesús Mercado-Blanco
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
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Tenea GN, Reyes P. Bacterial community changes in strawberry fruits ( Fragaria × ananassa variety "Monterey") from farm field to retail market stands, an indicator of postharvest contamination. Front Microbiol 2024; 15:1348316. [PMID: 38435684 PMCID: PMC10904649 DOI: 10.3389/fmicb.2024.1348316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/29/2024] [Indexed: 03/05/2024] Open
Abstract
Background Strawberry (Fragaria × ananassa) fruits are vulnerable to bacterial contamination; some species are pathogenic and can affect human health. Comprehending the bacterial composition and diversity at different ripe stages is a key determinant of the fruit health, productivity, and quality. Methodology An amplicon metagenomic approach on the 16S rRNA region was used to identify the bacterial diversity in exocarp of fruits collected from a farm field at two ripe stages: breaking (white, phase two) and ripe (red, phase four) and purchased from different retail market stands at ripe (red, phase four, ready-to-eat) stage. Besides, the fruit quality was assessed. Results Strawberries carries a high microorganisms diversity, with Pseudomonaceae, Yearsiniaceae, and Hafniaceae being the most abundant families across the samples. Among the groups, Pseudomonaceae and Clostridiaceae were the most abundant families at breaking (phase two) and ripe (phase four), whereas Yearsiniaceae, Hafniaceae, Aeromonadaceae, and Streptococcaceae were the most abundant families in the market group. Although samples from group four-field and market were at the same ripe stage, the bacterial species composition was divergent. Serratia spp. were prevalent (above 60%) in samples collected from the market group, and Pseudomonas (above 70%) species were mostly found in the samples collected from the field settings regardless of the phase. Besides, Escherichia coli and Salmonella enterica were detected in the ready-to-eat samples from both the field and the market, while Enterococcus gallinarum was detected in the samples that originated from the market. Interestingly, Shewanella putrefaciens and Shewanella profunda, two human opportunistic pathogens, were detected in the fruits from the market only. According to alpha and beta diversity analyses, strawberry fruits displayed significant differences (P < 0.05) in bacterial communities within the ripe group, with the samples from the market showing the most bacterial diversity. Although we do not directly correlate the quality attributes with bacterial diversity, the results indicated a clear separation between groups according with their ripe stage and origin. Conclusion This study provides a comprehensive framework of the bacterial diversity throughout the transition from unripe to ripe strawberries which may aid in the development of preventative measures to manage the postharvest contamination.
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Affiliation(s)
- Gabriela N. Tenea
- Biofood and Nutraceutics Research and Development Group, Faculty of Engineering in Agricultural and Environmental Sciences, Universidad Técnica del Norte, Ibarra, Ecuador
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McLaughlin MS, Yurgel SN, Abbasi PA, Ali S. The effects of chemical fungicides and salicylic acid on the apple microbiome and fungal disease incidence under changing environmental conditions. Front Microbiol 2024; 15:1342407. [PMID: 38374916 PMCID: PMC10875086 DOI: 10.3389/fmicb.2024.1342407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/18/2024] [Indexed: 02/21/2024] Open
Abstract
Epiphytic and endophytic micro-organisms associated with plants form complex communities on or in their host plant. These communities influence physiological traits, development, and host susceptibility to abiotic and biotic stresses, and these communities are theorized to have evolved alongside their hosts, forming a unit of selection known as the holobiont. The microbiome is highly variable and can be influenced by abiotic factors, including applied exogenous agents. In this study, we compared the impact of chemical fungicide and salicylic acid treatments on the fungal communities of "Honeycrisp" apples at harvest over two consecutive growing years. We demonstrated variations in fungal community structure and composition by tissue type, growing season, and treatment regimes and that fungicide treatments were associated with reduced network complexity. Finally, we show that the inclusion of salicylic acid with 50% less chemical fungicides in an integrated spray program allowed a reduction in fungicide use while maintaining effective control of disease at harvest and following storage.
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Affiliation(s)
- Michael S. McLaughlin
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, Kentville, NS, Canada
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Svetlana N. Yurgel
- United States Department of Agriculture (USDA), Agricultural Research Service, Grain Legume Genetics and Physiology Research Unit, Prosser, WA, United States
| | - Pervaiz A. Abbasi
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, Kentville, NS, Canada
| | - Shawkat Ali
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, Kentville, NS, Canada
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Wicaksono WA, Cernava T, Wassermann B, Abdelfattah A, Soto-Giron MJ, Toledo GV, Virtanen SM, Knip M, Hyöty H, Berg G. The edible plant microbiome: evidence for the occurrence of fruit and vegetable bacteria in the human gut. Gut Microbes 2023; 15:2258565. [PMID: 37741805 PMCID: PMC10519362 DOI: 10.1080/19490976.2023.2258565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/08/2023] [Indexed: 09/25/2023] Open
Abstract
Diversity of the gut microbiota is crucial for human health. However, whether fruit and vegetable associated bacteria contribute to overall gut bacterial diversity is still unknown. We reconstructed metagenome-assembled genomes from 156 fruit and vegetable metagenomes to investigate the prevalence of associated bacteria in 2,426 publicly available gut metagenomes. The microbiomes of fresh fruits and vegetables and the human gut are represented by members in common such as Enterobacterales, Burkholderiales, and Lactobacillales. Exposure to bacteria via fruit and vegetable consumption potentially has a beneficial impact on the functional diversity of gut microbiota particularly due to the presence of putative health-promoting genes for the production of vitamin and short-chain fatty acids. In the human gut, they were consistently present, although at a low abundance, approx. 2.2%. Host age, vegetable consumption frequency, and the diversity of plants consumed were drivers favoring a higher proportion. Overall, these results provide one of the primary links between the human microbiome and the environmental microbiome. This study revealed evidence that fruit and vegetable-derived microbes could be found in the human gut and contribute to gut microbiome diversity.
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Affiliation(s)
- Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | | | | | - Suvi M. Virtanen
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Center for Child Health Research, Tampere University and Tampere University Hospital, Tampere, Finland
- Faculty of Social Sciences, Tampere University, Tampere, Finland
- Research, Development and Innovation Center, Tampere University Hospital, Tampere, Finland
| | - Mikael Knip
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Pediatric Research Center, Children’s Hospital, University of Helsinki, Helsinki, Finland
| | - Heikki Hyöty
- Faculty of Medicine and Health Technology, Tampere University, and Fimlab Laboratories, Tampere, Finland
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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11
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Sessitsch A, Wakelin S, Schloter M, Maguin E, Cernava T, Champomier-Verges MC, Charles TC, Cotter PD, Ferrocino I, Kriaa A, Lebre P, Cowan D, Lange L, Kiran S, Markiewicz L, Meisner A, Olivares M, Sarand I, Schelkle B, Selvin J, Smidt H, van Overbeek L, Berg G, Cocolin L, Sanz Y, Fernandes WL, Liu SJ, Ryan M, Singh B, Kostic T. Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet. Microbiol Mol Biol Rev 2023; 87:e0021222. [PMID: 37367231 PMCID: PMC10521359 DOI: 10.1128/mmbr.00212-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023] Open
Abstract
Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, and water filtration. Microbiomes are also intimately associated with complex multicellular organisms such as humans, other animals, plants, and insects and perform crucial roles for the health of their hosts. Although we are starting to understand that microbiomes in different systems are interconnected, there is still a poor understanding of microbiome transfer and connectivity. In this review we show how microbiomes are connected within and transferred between different habitats and discuss the functional consequences of these connections. Microbiome transfer occurs between and within abiotic (e.g., air, soil, and water) and biotic environments, and can either be mediated through different vectors (e.g., insects or food) or direct interactions. Such transfer processes may also include the transmission of pathogens or antibiotic resistance genes. However, here, we highlight the fact that microbiome transmission can have positive effects on planetary and human health, where transmitted microorganisms potentially providing novel functions may be important for the adaptation of ecosystems.
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Affiliation(s)
| | | | | | - Emmanuelle Maguin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Tomislav Cernava
- University of Southampton, Faculty of Environmental and Life Sciences, Southampton, United Kingdom
| | | | | | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, APC Microbiome Ireland and VistaMilk, Cork, Ireland
| | | | - Aicha Kriaa
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pedro Lebre
- University of Pretoria, Pretoria, South Africa
| | - Don Cowan
- University of Pretoria, Pretoria, South Africa
| | - Lene Lange
- LL-BioEconomy, Valby, Copenhagen, Denmark
| | | | - Lidia Markiewicz
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Department of Immunology and Food Microbiology, Olsztyn, Poland
| | - Annelein Meisner
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | - Marta Olivares
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Inga Sarand
- Tallinn University of Technology, Department of Chemistry and Biotechnology, Tallinn, Estonia
| | | | | | - Hauke Smidt
- Wageningen University and Research, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Leo van Overbeek
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | | | | | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | | | - S. J. Liu
- Chinese Academy of Sciences, Institute of Microbiology, Beijing, China
| | - Matthew Ryan
- Genetic Resources Collection, CABI, Egham, United Kingdom
| | - Brajesh Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Tanja Kostic
- AIT Austrian Institute of Technology GmbH, Tulln, Austria
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12
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Bartuv R, Berihu M, Medina S, Salim S, Feygenberg O, Faigenboim-Doron A, Zhimo VY, Abdelfattah A, Piombo E, Wisniewski M, Freilich S, Droby S. Functional analysis of the apple fruit microbiome based on shotgun metagenomic sequencing of conventional and organic orchard samples. Environ Microbiol 2023; 25:1728-1746. [PMID: 36807446 DOI: 10.1111/1462-2920.16353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 02/16/2023] [Indexed: 02/23/2023]
Abstract
Fruits harbour abundant and diverse microbial communities that protect them from post-harvest pathogens. Identification of functional traits associated with a given microbiota can provide a better understanding of their potential influence. Here, we focused on the epiphytic microbiome of apple fruit. We suggest that shotgun metagenomic data can indicate specific functions carried out by different groups and provide information on their potential impact. Samples were collected from the surface of 'Golden Delicious' apples from four orchards that differ in their geographic location and management practice. Approximately 1 million metagenes were predicted based on a high-quality assembly. Functional profiling of the microbiome of fruits from orchards differing in their management practice revealed a functional shift in the microbiota. The organic orchard microbiome was enriched in pathways involved in plant defence activities; the conventional orchard microbiome was enriched in pathways related to the synthesis of antibiotics. The functional significance of the variations was explored using microbial network modelling algorithms to reveal the metabolic role of specific phylogenetic groups. The analysis identified several associations supported by other published studies. For example, the analysis revealed the nutritional dependencies of the Capnodiales group, including the Alternaria pathogen, on aromatic compounds.
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Affiliation(s)
- Rotem Bartuv
- Agricultural Research Organization (A.R.O.), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Institute, Rishon LeZion, Israel
| | - Maria Berihu
- Agricultural Research Organization (A.R.O.), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | - Shlomit Medina
- Agricultural Research Organization (A.R.O.), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | - Shoshana Salim
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Institute, Rishon LeZion, Israel
| | - Oleg Feygenberg
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Institute, Rishon LeZion, Israel
| | - Adi Faigenboim-Doron
- Agricultural Research Organization (A.R.O.), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | - V Yeka Zhimo
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Institute, Rishon LeZion, Israel
| | - Ahmed Abdelfattah
- Department of Microbiome Biotechnology, Leibniz Institute for Agricultural Engineering and Bioeconomy, Potsdam, Germany
| | - Edoardo Piombo
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Grugliasco, Italy
| | - Michael Wisniewski
- Department of Biological Sciences, Virginia Polytechnic Institute, and State University, Blacksburg, Virginia, USA
| | - Shiri Freilich
- Agricultural Research Organization (A.R.O.), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | - Samir Droby
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Institute, Rishon LeZion, Israel
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13
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Lee SI, Cho G, Kim SH, Kim DR, Kwak YS. Mycobiota community and fungal species response to development stage and fire blight disease in apples. AIMS Microbiol 2023; 9:554-569. [PMID: 37649796 PMCID: PMC10462452 DOI: 10.3934/microbiol.2023029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/29/2023] [Accepted: 07/12/2023] [Indexed: 09/01/2023] Open
Abstract
Fire blight disease, caused by the bacterial pathogen Erwinia amylovora, has been a significant concern for over 50 countries worldwide. The efficacy of chemical pesticides currently available for disease control is limited. To address this issue, research is being conducted to explore environmentally friendly control methods, particularly biological control using beneficial microorganisms. However, there is limited research on the apple microbiota community and minimal research has been conducted on fungal communities that may exhibit reliable performance in apple trees. Therefore, our objective was to analyze the fungal communities present in apples at different developmental stages and in different tissues, aiming to identify potential biological control agents for fire blight disease. Our findings indicate that the fungal communities present in apple buds, flowers and leaves play an important role in inhibiting the invasion of E. amylovora. Specifically, we propose GS11 and Lipomyces starkeyi as potential keystone taxa that respond to fire blight disease. These findings provide insights into the continuity and discontinuity of fungal community structure in different developmental stages of apples and offer predictions for potential biological control agents for fire blight disease.
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Affiliation(s)
- Su In Lee
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Gyeongjun Cho
- Division of Agricultural Microbiology, National Institute of Agriculture Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Su-Hyeon Kim
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Da-Ran Kim
- Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Youn-Sig Kwak
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Republic of Korea
- Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
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14
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Olmo R, Wetzels SU, Berg G, Cocolin L, Hartmann M, Hugas M, Kostic T, Rattei T, Ruthsatz M, Rybakova D, Sessitsch A, Shortt C, Timmis K, Selberherr E, Wagner M. Food systems microbiome-related educational needs. Microb Biotechnol 2023; 16:1412-1422. [PMID: 37338855 DOI: 10.1111/1751-7915.14263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/20/2023] [Accepted: 03/30/2023] [Indexed: 06/21/2023] Open
Abstract
Within the European-funded Coordination and Support Action MicrobiomeSupport (https://www.microbiomesupport.eu/), the Workshop 'Education in Food Systems Microbiome Related Sciences: Needs for Universities, Industry and Public Health Systems' brought together over 70 researchers, public health and industry partners from all over the world to work on elaborating microbiome-related educational needs in food systems. This publication provides a summary of discussions held during and after the workshop and the resulting recommendations.
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Affiliation(s)
- Rocío Olmo
- FFoQSI GmbH - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Stefanie Urimare Wetzels
- FFoQSI GmbH - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Luca Cocolin
- Department of Agricultural, Forest and Food Sciences, University of Turin, Turin, Italy
| | - Moritz Hartmann
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Marta Hugas
- European Food Safety Authority (EFSA), EU, Parma, Italy
| | - Tanja Kostic
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | - Daria Rybakova
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Angela Sessitsch
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | | | - Kenneth Timmis
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Evelyne Selberherr
- FFoQSI GmbH - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Martin Wagner
- FFoQSI GmbH - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
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15
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Murali AP, Trząskowska M, Trafialek J. Microorganisms in Organic Food-Issues to Be Addressed. Microorganisms 2023; 11:1557. [PMID: 37375059 DOI: 10.3390/microorganisms11061557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/28/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The review aimed to analyse the latest data on microorganisms present in organic food, both beneficial and unwanted. In conclusion, organic food's microbial quality is generally similar to that of conventionally produced food. However, some studies suggest that organic food may contain fewer pathogens, such as antibiotic-resistant strains, due to the absence of antibiotic use in organic farming practices. However, there is little discussion and data regarding the importance of some methods used in organic farming and the risk of food pathogens presence. Concerning data gaps, it is necessary to plan and perform detailed studies of the microbiological safety of organic food, including foodborne viruses and parasites and factors related to this method of cultivation and specific processing requirements. Such knowledge is essential for more effective management of the safety of this food. The use of beneficial bacteria in organic food production has not yet been widely addressed in the scientific literature. This is particularly desirable due to the properties of the separately researched probiotics and the organic food matrix. The microbiological quality of organic food and its potential impact on human health is worth further research to confirm its safety and to assess the beneficial properties resulting from the addition of probiotics.
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Affiliation(s)
- Aparna P Murali
- Department of Food Gastronomy and Food Hygiene, Institute of Human Nutrition Sciences, Warsaw University of Life Sciences (WULS), Nowoursynowska 159C, 02-776 Warsaw, Poland
| | - Monika Trząskowska
- Department of Food Gastronomy and Food Hygiene, Institute of Human Nutrition Sciences, Warsaw University of Life Sciences (WULS), Nowoursynowska 159C, 02-776 Warsaw, Poland
| | - Joanna Trafialek
- Department of Food Gastronomy and Food Hygiene, Institute of Human Nutrition Sciences, Warsaw University of Life Sciences (WULS), Nowoursynowska 159C, 02-776 Warsaw, Poland
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16
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Gao Q, Zhang Y, Gao C, Li H, Cheng Y, Qian X, Zhang L, Liu J, Ogunyemi SO, Guan J. The Microbial Diversity in Relation to Postharvest Quality and Decay: Organic vs. Conventional Pear Fruit. Foods 2023; 12:foods12101980. [PMID: 37238797 DOI: 10.3390/foods12101980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/24/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
(1) Background: Organic food produced in environmentally friendly farming systems has become increasingly popular. (2) Methods: We used a DNA metabarcoding approach to investigate the differences in the microbial community between organic and conventional 'Huangguan' pear fruit; and (3) Results: Compared to a conventional orchard, the fruit firmness in the organic orchard had significantly lowered after 30 days of shelf-life storage at 25 °C, and the soluble solids content (SSC), titratable acid (TA), and decay index were higher. There were differences in the microbial diversity between organic and conventional orchards pears. After 30 days of storage, Fusarium and Starmerella became the main epiphytic fungi in organic fruits, while Meyerozyma was dominant in conventional fruits. Gluconobacter, Acetobacter, and Komagataeibacter were dominant epiphytic bacteria on pears from both organic and conventional orchards after a 30-day storage period. Bacteroides, Muribaculaceae, and Nesterenkonia were the main endophytic bacteria throughout storage. There was a negative correlation between fruit firmness and decay index. Moreover, the abundance of Acetobacter and Starmerella were positively correlated with fruit firmness, while Muribaculaceae was negatively correlated, implying that these three microorganisms may be associated with the postharvest decay of organic fruit; (4) Conclusions: The difference in postharvest quality and decay in organic and conventional fruits could potentially be attributed to the variation in the microbial community during storage.
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Affiliation(s)
- Qi Gao
- Institute of Biotechnology and Food Science, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China
- Key Laboratory of Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Yang Zhang
- Institute of Biotechnology and Food Science, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China
- Key Laboratory of Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Congcong Gao
- Institute of Biotechnology and Food Science, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China
- Key Laboratory of Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Huimin Li
- Institute of Biotechnology and Food Science, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China
- Key Laboratory of Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
- School of Landscape and Ecological Engineering, Hebei Engineering University, Handan 056021, China
| | - Yudou Cheng
- Institute of Biotechnology and Food Science, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China
- Key Laboratory of Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Xun Qian
- Institute of Biotechnology and Food Science, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China
- Key Laboratory of Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Lishu Zhang
- Cangzhou Academy of Agricultural and Forestry Sciences, Cangzhou 061001, China
| | - Jinyu Liu
- Cangzhou Academy of Agricultural and Forestry Sciences, Cangzhou 061001, China
| | - Solabomi Olaitan Ogunyemi
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310013, China
| | - Junfeng Guan
- Institute of Biotechnology and Food Science, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China
- Key Laboratory of Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
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17
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Garnås E. Fermented Vegetables as a Potential Treatment for Irritable Bowel Syndrome. Curr Dev Nutr 2023; 7:100039. [PMID: 37181929 PMCID: PMC10111609 DOI: 10.1016/j.cdnut.2023.100039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 02/22/2023] Open
Abstract
Foods and supplements containing microorganisms with expected beneficial effects are increasingly investigated and utilized in the treatment of human illness, including irritable bowel syndrome (IBS). Research points to a prominent role of gut dysbiosis in the multiple aberrations in gastrointestinal function, immune balance, and mental health seen in IBS. The proposition of the current Perspective is that fermented vegetable foods, in combination with a healthy and stable diet, may be particularly useful for addressing these disturbances. This is based on the recognition that plants and their associated microorganisms have contributed to shaping human microbiota and adaptation over evolutionary time. In particular, lactic acid bacteria with immunomodulatory, antipathogenic, and digestive properties are prevalent in products such as sauerkraut and kimchi. Additionally, by adjusting the salt content and fermentation time, products with a microbial and therapeutic potential beyond that of regular ferments could potentially be produced. Although more clinical data are required to make firm assertions, the low-risk profile, combined with biological considerations and reasoning and considerable circumstantial and anecdotal evidence, indicate that fermented vegetables are worthy of consideration by health professionals and patients dealing with IBS-related issues. To maximize microbial diversity and limit the risk of adverse effects, small doses of multiple products, containing different combinations of traditionally fermented vegetables and/or fruits, is suggested for experimental research and care.
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18
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Gontier N, Sukhoverkhov A. Reticulate evolution underlies synergistic trait formation in human communities. Evol Anthropol 2023; 32:26-38. [PMID: 36205197 DOI: 10.1002/evan.21962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 04/19/2022] [Accepted: 09/18/2022] [Indexed: 11/11/2022]
Abstract
This paper investigates how reticulate evolution contributes to a better understanding of human sociocultural evolution in general, and community formation in particular. Reticulate evolution is evolution as it occurs by means of symbiosis, symbiogenesis, lateral gene transfer, infective heredity, and hybridization. From these mechanisms and processes, we mainly zoom in on symbiosis and we investigate how it underlies the rise of (1) human, plant, animal, and machine interactions typical of agriculture, animal husbandry, farming, and industrialization; (2) diet-microbiome relationships; and (3) host-virome and other pathogen interactions that underlie human health and disease. We demonstrate that reticulate evolution necessitates an understanding of behavioral and cultural evolution at a community level, where reticulate causal processes underlie the rise of synergistic organizational traits.
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Affiliation(s)
- Nathalie Gontier
- Applied Evolutionary Epistemology Lab, Centro de Filosofia das Ciências, Departamento de História e Filosofia das Ciências, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Anton Sukhoverkhov
- Department of Philosophy, Kuban State Agrarian University, Krasnodar, Russia
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19
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Wolfgang A, Temme N, Tilcher R, Berg G. Understanding the sugar beet holobiont for sustainable agriculture. Front Microbiol 2023; 14:1151052. [PMID: 37138624 PMCID: PMC10149816 DOI: 10.3389/fmicb.2023.1151052] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/31/2023] [Indexed: 05/05/2023] Open
Abstract
The importance of crop-associated microbiomes for the health and field performance of plants has been demonstrated in the last decades. Sugar beet is the most important source of sucrose in temperate climates, and-as a root crop-yield heavily depends on genetics as well as on the soil and rhizosphere microbiomes. Bacteria, fungi, and archaea are found in all organs and life stages of the plant, and research on sugar beet microbiomes contributed to our understanding of the plant microbiome in general, especially of microbiome-based control strategies against phytopathogens. Attempts to make sugar beet cultivation more sustainable are increasing, raising the interest in biocontrol of plant pathogens and pests, biofertilization and -stimulation as well as microbiome-assisted breeding. This review first summarizes already achieved results on sugar beet-associated microbiomes and their unique traits, correlating to their physical, chemical, and biological peculiarities. Temporal and spatial microbiome dynamics during sugar beet ontogenesis are discussed, emphasizing the rhizosphere formation and highlighting knowledge gaps. Secondly, potential or already tested biocontrol agents and application strategies are discussed, providing an overview of how microbiome-based sugar beet farming could be performed in the future. Thus, this review is intended as a reference and baseline for further sugar beet-microbiome research, aiming to promote investigations in rhizosphere modulation-based biocontrol options.
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Affiliation(s)
- Adrian Wolfgang
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Nora Temme
- KWS SAAT SE & Co. KGaA, Einbeck, Germany
| | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Microbiome Biotechnology Department, Leibniz-Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- *Correspondence: Gabriele Berg
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20
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Wicaksono WA, Buko A, Kusstatscher P, Cernava T, Sinkkonen A, Laitinen OH, Virtanen SM, Hyöty H, Berg G. Impact of Cultivation and Origin on the Fruit Microbiome of Apples and Blueberries and Implications for the Exposome. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02157-8. [PMID: 36542126 DOI: 10.1007/s00248-022-02157-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Vegetables and fruits are a crucial part of the planetary health diet, directly affecting human health and the gut microbiome. The objective of our study was to understand the variability of the fruit (apple and blueberry) microbiome in the frame of the exposome concept. The study covered two fruit-bearing woody species, apple and blueberry, two countries of origin (Austria and Finland), and two fruit production methods (naturally grown and horticultural). Microbial abundance, diversity, and community structures were significantly different for apples and blueberries and strongly influenced by the growing system (naturally grown or horticultural) and country of origin (Austria or Finland). Our results indicated that bacterial communities are more responsive towards these factors than fungal communities. We found that fruits grown in the wild and within home gardens generally carry a higher microbial diversity, while commercial horticulture homogenized the microbiome independent of the country of origin. This can be explained by horticultural management, including pesticide use and post-harvest treatments. Specific taxonomic indicators were identified for each group, i.e., for horticultural apples: Pseudomonas, Ralstonia, and Stenotrophomonas. Interestingly, Ralstonia was also found to be enriched in horticultural blueberries in comparison to such that were home and wildly grown. Our study showed that the origin of fruits can strongly influence the diversity and composition of their microbiome, which means that we are exposed to different microorganisms by eating fruits from different origins. Thus, the fruit microbiome needs to be considered an important but relatively unexplored external exposomic factor.
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Affiliation(s)
- Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Aisa Buko
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Aki Sinkkonen
- Natural Resources Institute Finland Luke, Turku, Finland
| | - Olli H Laitinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Suvi M Virtanen
- Health and Well-Being Promotion Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
- Faculty of Social Sciences, Unit of Health Sciences, Tampere University, Tampere, Finland
- Research, Development and Innovation Center, Tampere University Hospital, Tampere, Finland
- Center for Child Health Research, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Heikki Hyöty
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany.
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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21
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Schnyder A, Eberl L, Agnoli K. Investigating the Biocontrol Potential of the Natural Microbiota of the Apple Blossom. Microorganisms 2022; 10:microorganisms10122480. [PMID: 36557734 PMCID: PMC9784478 DOI: 10.3390/microorganisms10122480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Erwinia amylovora, the causative agent of fire blight, leads to important economic losses of apple and pear crops worldwide. This study aimed to investigate the potential of the resident microbiota of the apple blossom in combatting plant disease-causing organisms, with a focus on controlling fire blight. We obtained 538 isolates from sites around Canton Zurich, which we tested for activity against Pectobacterium carotovorum and E. amylovora. We also evaluated the isolates' activity against oomycete and fungal pathogens. Nine isolates showed activity against P. carotovorum, and eight of these against E. amylovora. Furthermore, 117 showed antifungal, and 161 anti-oomycete, activity. We assigned genera and in some cases species to 238 of the isolates by sequencing their 16S RNA-encoding gene. Five strains showed activity against all pathogens and were tested in a detached apple model for anti-E. amylovora activity. Of these five strains, two were able to antagonize E. amylovora, namely Bacillus velezensis #124 and Pantoea agglomerans #378. We sequenced the P. agglomerans #378 genome and analyzed it for secondary metabolite clusters using antiSMASH, revealing the presence of a putative bacteriocin cluster. We also showed that B. velezensis #124 exhibits strong activity against three different fungi and two oomycetes in vitro, suggesting a broader capacity for biocontrol. Our results showcase the protective potential of the natural apple blossom microbiota. We isolated two candidate biocontrol strains from apple blossoms, suggesting that they might persist at the most common entry point for the causative agent of fire blight. Furthermore, they are probably already part of the human diet, suggesting they might be safe for consumption, and thus are promising candidates for biocontrol applications.
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Affiliation(s)
- Anya Schnyder
- Institut für Veterinärbakteriologie, Universität Bern, 3001 Bern, Switzerland
| | - Leo Eberl
- Department of Microbiology, Institute of Plant and Microbial Biology, University of Zürich, 8008 Zurich, Switzerland
| | - Kirsty Agnoli
- Department of Microbiology, Institute of Plant and Microbial Biology, University of Zürich, 8008 Zurich, Switzerland
- Correspondence:
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22
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Callens K, Fontaine F, Sanz Y, Bogdanski A, D‘Hondt K, Lange L, Smidt H, van Overbeek L, Kostic T, Maguin E, Meisner A, Sarand I, Sessitsch A. Microbiome-based solutions to address new and existing threats to food security, nutrition, health and agrifood systems' sustainability. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.1047765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In addition to challenges like climate change and biodiversity loss, the sustainability and resilience of agrifood systems worldwide are currently challenged by new threats, such as the COVID-19 pandemic and the Ukraine war. Furthermore, the resilience and sustainability of our agrifood systems need to be enhanced in ways that simultaneously increase agricultural production, decrease post-harvest food losses and food waste, protect the climate, environment and health, and preserve biodiversity. The precarious situation of agrifood systems is also illustrated by the fact that overall, around 3 billion people worldwide still do not have regular access to a healthy diet. This results in various forms of malnutrition, as well as increasing number of people suffering from overweight and obesity, and diet-related, non-communicable diseases (NCDs) around the world. Findings from microbiome research have shown that the human gut microbiome plays a key role in nutrition and diet-related diseases and thus human health. Furthermore, the microbiome of soils, plants, and animals play an equally important role in environmental health and agricultural production. Upcoming, microbiome-based solutions hold great potential for more resilient, sustainable, and productive agrifood systems and open avenues toward preventive health management. Microbiome-based solutions will also be key to make better use of natural resources and increase the resilience of agrifood systems to future emerging and already-known crises. To realize the promises of microbiome science and innovation, there is a need to invest in enhancing the role of microbiomes in agrifood systems in a holistic One Health approach and to accelerate knowledge translation and implementation.
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23
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Palumbo M, Attolico G, Capozzi V, Cozzolino R, Corvino A, de Chiara MLV, Pace B, Pelosi S, Ricci I, Romaniello R, Cefola M. Emerging Postharvest Technologies to Enhance the Shelf-Life of Fruit and Vegetables: An Overview. Foods 2022; 11:foods11233925. [PMID: 36496732 PMCID: PMC9737221 DOI: 10.3390/foods11233925] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/09/2022] Open
Abstract
Quality losses in fresh produce throughout the postharvest phase are often due to the inappropriate use of preservation technologies. In the last few decades, besides the traditional approaches, advanced postharvest physical and chemical treatments (active packaging, dipping, vacuum impregnation, conventional heating, pulsed electric field, high hydrostatic pressure, and cold plasma) and biocontrol techniques have been implemented to preserve the nutritional value and safety of fresh produce. The application of these methodologies after harvesting is useful when addressing quality loss due to the long duration when transporting products to distant markets. Among the emerging technologies and contactless and non-destructive techniques for quality monitoring (image analysis, electronic noses, and near-infrared spectroscopy) present numerous advantages over the traditional, destructive methods. The present review paper has grouped original studies within the topic of advanced postharvest technologies, to preserve quality and reduce losses and waste in fresh produce. Moreover, the effectiveness and advantages of some contactless and non-destructive methodologies for monitoring the quality of fruit and vegetables will also be discussed and compared to the traditional methods.
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Affiliation(s)
- Michela Palumbo
- Department of Science of Agriculture, Food and Environment, University of Foggia, Via Napoli, 25, 71122 Foggia, Italy
- Institute of Sciences of Food Production, National Research Council of Italy (CNR), c/o CS-DAT, Via Michele Protano, 71121 Foggia, Italy
| | - Giovanni Attolico
- Institute on Intelligent Industrial Systems and Technologies for Advanced Manufacturing, National Research Council of Italy (CNR), Via G. Amendola, 122/O, 70126 Bari, Italy
| | - Vittorio Capozzi
- Institute of Sciences of Food Production, National Research Council of Italy (CNR), c/o CS-DAT, Via Michele Protano, 71121 Foggia, Italy
| | - Rosaria Cozzolino
- Institute of Food Science, National Research Council (CNR), Via Roma 64, 83100 Avellino, Italy
- Correspondence: (R.C.); (B.P.); Tel.: +39-0825-299111 (R.C.); +39-0881-630210 (B.P.)
| | - Antonia Corvino
- Institute of Sciences of Food Production, National Research Council of Italy (CNR), c/o CS-DAT, Via Michele Protano, 71121 Foggia, Italy
| | - Maria Lucia Valeria de Chiara
- Department of Science of Agriculture, Food and Environment, University of Foggia, Via Napoli, 25, 71122 Foggia, Italy
- Institute of Sciences of Food Production, National Research Council of Italy (CNR), c/o CS-DAT, Via Michele Protano, 71121 Foggia, Italy
| | - Bernardo Pace
- Institute of Sciences of Food Production, National Research Council of Italy (CNR), c/o CS-DAT, Via Michele Protano, 71121 Foggia, Italy
- Correspondence: (R.C.); (B.P.); Tel.: +39-0825-299111 (R.C.); +39-0881-630210 (B.P.)
| | - Sergio Pelosi
- Institute of Sciences of Food Production, National Research Council of Italy (CNR), c/o CS-DAT, Via Michele Protano, 71121 Foggia, Italy
| | - Ilde Ricci
- Institute of Sciences of Food Production, National Research Council of Italy (CNR), c/o CS-DAT, Via Michele Protano, 71121 Foggia, Italy
| | - Roberto Romaniello
- Department of Science of Agriculture, Food and Environment, University of Foggia, Via Napoli, 25, 71122 Foggia, Italy
| | - Maria Cefola
- Institute of Sciences of Food Production, National Research Council of Italy (CNR), c/o CS-DAT, Via Michele Protano, 71121 Foggia, Italy
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24
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Microbiome-based biotechnology for reducing food loss post harvest. Curr Opin Biotechnol 2022; 78:102808. [PMID: 36183451 DOI: 10.1016/j.copbio.2022.102808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/21/2022] [Accepted: 08/29/2022] [Indexed: 12/14/2022]
Abstract
Microbiomes have an immense potential to enhance plant resilience to various biotic and abiotic stresses. However, intrinsic microbial communities respond to changes in their host's physiology and environment during plant's life cycle. The potential of the inherent plant microbiome has been neglected for a long time, especially for the postharvest period. Currently, close to 50% of all produced fruits and vegetables are lost either during production or storage. Biological control of spoilage and storage diseases is still lacking sufficiency. Today, novel multiomics technologies allow us to study the microbiome and its responses on a community level, which will help to advance current classic approaches and develop more effective and robust microbiome-based solutions for fruit and vegetable storability, quality, and safety.
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25
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Trinchera A, Migliore M, Warren Raffa D, Ommeslag S, Debode J, Shanmugam S, Dane S, Babry J, Kivijarvi P, Kristensen HL, Lepse L, Salo T, Campanelli G, Willekens K. Can multi-cropping affect soil microbial stoichiometry and functional diversity, decreasing potential soil-borne pathogens? A study on European organic vegetable cropping systems. FRONTIERS IN PLANT SCIENCE 2022; 13:952910. [PMID: 36237499 PMCID: PMC9552534 DOI: 10.3389/fpls.2022.952910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Crop diversification in spatial and temporal patterns can optimize the synchronization of nutrients plant demand and availability in soils, as plant diversity and soil microbial communities are the main drivers of biogeochemical C and nutrient cycling. The introduction of multi-cropping in organic vegetable production can represent a key strategy to ensure efficient complementation mediated by soil microbiota, including beneficial mycorrhizal fungi. This study shows the effect of the introduction of multi-cropping in five European organic vegetable systems (South-West: Italy; North-West: Denmark and Belgium; North-East: Finland and Latvia) on: (i) soil physicochemical parameters; (ii) soil microbial biomass stoichiometry; (iii) crop root mycorrhization; (iv) bacterial and fungal diversity and composition in crop rhizosphere; (v) relative abundance of selected fungal pathogens species. In each site, three cropping systems were considered: (1) crop 1-monocropping; (2) crop 2-monocropping; (3) crop 1-crop 2-intercropping or strip cropping. Results showed that, just before harvest, multi-cropping can increase soil microbial biomass amount and shape microbial community toward a predominance of some bacteria or fungi phyla, in the function of soil nutrient availability. We mainly observed a selection effect of crop type on rhizosphere microbiota. Particularly, Bacteroidetes and Mortierellomycota relative abundances in rhizosphere soil resulted in suitable ecological indicators of the positive effect of plant diversity in field, the first ones attesting an improved C and P cycles in soil and the second ones a reduced soil pathogens' pressure. Plant diversity also increased the root mycorrhizal colonization between the intercropped crops that, when properly selected, can also reduce the relative abundance of potential soil-borne pathogens, with a positive effect on crop productivity in long term.
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Affiliation(s)
- Alessandra Trinchera
- Council for Agricultural Research and Economics-Research Centre for Agriculture and Environment, Rome, Italy
| | - Melania Migliore
- Council for Agricultural Research and Economics-Research Centre for Agriculture and Environment, Rome, Italy
| | - Dylan Warren Raffa
- Council for Agricultural Research and Economics-Research Centre for Agriculture and Environment, Rome, Italy
| | - Sarah Ommeslag
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Jane Debode
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | | | - Sandra Dane
- Latvian Institute of Horticulture, LatHort, Dobeles Novads, Latvia
| | | | - Pirjo Kivijarvi
- LUKE (FI) Natural Resources Institute Finland, Helsinki, Finland
| | | | - Liga Lepse
- Latvian Institute of Horticulture, LatHort, Dobeles Novads, Latvia
| | - Tapio Salo
- LUKE (FI) Natural Resources Institute Finland, Helsinki, Finland
| | - Gabriele Campanelli
- Council for Agricultural Research and Economics-Research Centre for Vegetable and Ornamental Crops, Monsampolo del Tronto, Italy
| | - Koen Willekens
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
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26
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Ward S, Bedale W, Glass KA. Listeria monocytogenes Outbreaks Related to Commercially Produced Caramel Apples: Developments in Sanitation, Product Formulation, and Packaging: A Review. J Food Prot 2022; 85:1287-1299. [PMID: 35666586 DOI: 10.4315/jfp-22-069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/27/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT Prior to a deadly 2014 listeriosis outbreak, caramel apples were not thought to be vehicles for the foodborne pathogen Listeria monocytogenes. The purpose of this review article is to summarize what has been learned from research prompted by this outbreak. This overview includes descriptions of the two L. monocytogenes infection outbreaks related to prepackaged caramel apples and a brief discussion of apple sanitation, the production processes used to make caramel apples, and research on ways to prevent future outbreaks associated with caramel apples. A qualitative analysis of the literature and interviews with current caramel apple manufacturers were conducted. Sanitation, packaging, and storage procedures used by manufacturers in the past may not effectively inactivate L. monocytogenes from contaminated product. Novel apple sanitation methods and product formulations to control L. monocytogenes on caramel apples have been developed and, in some cases, implemented in commercial production. HIGHLIGHTS
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Affiliation(s)
- Stevie Ward
- Food Research Institute, University of Wisconsin-Madison, 1550 Linden Drive, Madison, Wisconsin 53706, USA
| | - Wendy Bedale
- Food Research Institute, University of Wisconsin-Madison, 1550 Linden Drive, Madison, Wisconsin 53706, USA
| | - Kathleen A Glass
- Food Research Institute, University of Wisconsin-Madison, 1550 Linden Drive, Madison, Wisconsin 53706, USA
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27
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Fikri S, Lessard MH, Perreault V, Doyen A, Labrie S. Candida krusei is the major contaminant of ultrafiltration and reverse osmosis membranes used for cranberry juice production. Food Microbiol 2022; 109:104146. [DOI: 10.1016/j.fm.2022.104146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 09/06/2022] [Accepted: 09/14/2022] [Indexed: 10/14/2022]
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28
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Gerna D, Clara D, Allwardt D, Mitter B, Roach T. Tailored Media Are Key to Unlocking the Diversity of Endophytic Bacteria in Distinct Compartments of Germinating Seeds. Microbiol Spectr 2022; 10:e0017222. [PMID: 35867396 PMCID: PMC9431621 DOI: 10.1128/spectrum.00172-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 07/01/2022] [Indexed: 11/24/2022] Open
Abstract
Seeds offer an internal microbial niche, termed the endosphere, colonized by communities of endophytic bacteria. To elucidate the functions of seed endophytes during germination and early plant growth, studies with culturable isolates are essential. Conventional growth media favor few fast-growing taxa, while micro organisms with restricted nutrient requirements are usually outcompeted prior to isolation. Consequently, current knowledge of the interaction between seeds and their endophytes remains limited to only few bacterial taxa, despite a "black box" of unculturable isolates colonizing the endosphere. Here, we designed various solid media to mimic the endosphere of germinating soybean (Glycine max L.) seeds and assessed their effect on the diversity of culturable endophytic bacteria. The embryonic axis (i.e., the future plant) possessed higher richness and harbored more unique genera (i.e., Brevundimonas, Methylobacterium, Microbacterium, Pseudoclavibacter, and Rathayibacter) than cotyledons (i.e., seed storage organs). Overall, media containing germinating and ground seeds enabled culturing and isolation of the broadest diversity of endophytic bacteria, viewed through the molecular identification of 246 isolates. The use of multiple tailored media helped uncover trophic adaptation of the core taxa. Furthermore, comparison of seeds from four lots of distinct cultivars and origin revealed few overlapping taxa, indicating that the parental environment, including soil and fertilization regime, influenced seed endophytic diversity. Extended diversity of native seed endophytic bacteria revealed the functional relevance of unique Arthrobacter, Bacillus, and Curtobacterium strains to seed germination under salt stress, exemplifying the importance of enhanced culturing approaches to elucidate the role of microbiota in seed germination. IMPORTANCE Plant growth-promoting endophytic isolates that appear to advance seed germination are often obtained from plant niches other than the seed endosphere. Isolating pure cultures of native endophytes from seeds during germination is crucial to investigate their function during early plant growth. Here, the diversity of endophytic bacteria isolated from seeds during soybean germination was enhanced by combining media tailored to the nutritional composition of the seed endosphere, including pregerminated seeds themselves. Our results show that isolation from distinct soybean seed compartments affected such diversity, with the embryonic axis harboring more unique taxa while displaying higher endophytic richness. Furthermore, using pools of seeds from separate lots, each corresponding to a certain cultivar and field site, supported isolation of further unique strains that often unveiled substantial effects on germination performance. Such findings are relevant to assist studies on the interactions between seeds and their native endophytic bacteria.
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Affiliation(s)
- Davide Gerna
- Department of Botany and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - David Clara
- Department of Botany and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Dorothee Allwardt
- Bioresources Unit, Austrian Institute of Technology GmbH, Tulln, Austria
| | - Birgit Mitter
- Bioresources Unit, Austrian Institute of Technology GmbH, Tulln, Austria
| | - Thomas Roach
- Department of Botany and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
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29
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Zhimo VY, Kumar A, Biasi A, Abdelfattah A, Sharma VK, Salim S, Feygenberg O, Bartuv R, Freilich S, Whitehead SR, Wisniewski M, Droby S. Assembly and dynamics of the apple carposphere microbiome during fruit development and storage. Front Microbiol 2022; 13:928888. [PMID: 36016781 PMCID: PMC9395710 DOI: 10.3389/fmicb.2022.928888] [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: 04/26/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Microbial communities associated with fruit can contribute to quality and pathogen resistance, but little is known about their assembly and dynamics during fruit development and storage. Three apple cultivars growing under the same environmental conditions were utilized to examine the apple carposphere microbiome composition and structure at different developmental stages and storage. There was a significant effect (Adonis, p ≤ 0.001) of fruit genotype and its developmental stages and storage times on the fruit surface microbial assemblage and a strong temporal microbial community succession was detected (Mantel test: R ≤ 0.5, p = 0.001) in both bacterial and fungal communities. A set of 15 bacterial and 35 fungal core successional taxa and members exhibiting differential abundances at different fruit stages were identified. For the first time, we show the existence of underlying universal dynamics in the assembly of fruit-associated microbiomes. We also provide evidence of strong microbial cross-domain associations and uncover potential microbe-microbe correlations in the apple carposphere. Together our findings shed light on how the fruit carposphere assemble and change over time, and provide new insights into fruit microbial ecology.
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Affiliation(s)
- V. Yeka Zhimo
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Ajay Kumar
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Antonio Biasi
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Ahmed Abdelfattah
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee, Potsdam, Germany
| | - Vijay Kumar Sharma
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Shoshana Salim
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Oleg Feygenberg
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Rotem Bartuv
- Department of Natural Resources, Institute of Plant Sciences, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishay, Israel
- Faculty of Agriculture, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shiri Freilich
- Department of Natural Resources, Institute of Plant Sciences, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishay, Israel
| | - Susan R. Whitehead
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Michael Wisniewski
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Samir Droby
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
- *Correspondence: Samir Droby,
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30
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Soil and Soilless Tomato Cultivation Promote Different Microbial Communities That Provide New Models for Future Crop Interventions. Int J Mol Sci 2022; 23:ijms23158820. [PMID: 35955951 PMCID: PMC9369415 DOI: 10.3390/ijms23158820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/01/2022] [Accepted: 08/04/2022] [Indexed: 12/13/2022] Open
Abstract
The cultivation of soilless tomato in greenhouses has increased considerably, but little is known about the assembly of the root microbiome compared to plants grown in soil. To obtain such information, we constructed an assay in which we traced the bacterial and fungal communities by amplicon-based metagenomics during the cultivation chain from nursery to greenhouse. In the greenhouse, the plants were transplanted either into agricultural soil or into coconut fiber bags (soilless). At the phylum level, bacterial and fungal communities were primarily constituted in all microhabitats by Proteobacteria and Ascomycota, respectively. The results showed that the tomato rhizosphere microbiome was shaped by the substrate or soil in which the plants were grown. The microbiome was different particularly in terms of the bacterial communities. In agriculture, enrichment has been observed in putative biological control bacteria of the genera Pseudomonas and Bacillus and in potential phytopathogenic fungi. Overall, the study describes the different shaping of microbial communities in the two cultivation methods.
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31
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Feeding Our Microbiota: Stimulation of the Immune/Semiochemical System and the Potential Amelioration of Non-Communicable Diseases. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081197. [PMID: 36013376 PMCID: PMC9410320 DOI: 10.3390/life12081197] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 12/12/2022]
Abstract
Non-communicable diseases are those conditions to which causative infectious agents cannot readily be assigned. It is increasingly likely that at least some of these conditions are due to the breakdown of the previously mutualistic intestinal microbiota under the influence of a polluted, biocide-rich, environment. Following the mid-20th century African studies of Denis Burkitt, the environmental cause of conditions such as obesity has been ascribed to the absence of sufficient fibre in the modern diet, however in itself that is insufficient to explain the parallel rise of problems with both the immune system and of mental health. Conversely, Burkitt himself noted that the Maasai, a cattle herding people, remained healthy even with their relatively low intake of dietary fibre. Interestingly, however, Burkitt also emphasised that levels of non-communicable disease within a population rose as faecal weight decreased significantly, to about one third of the levels found in healthy populations. Accordingly, a more cogent explanation for all the available facts is that the fully functioning, adequately diverse microbiome, communicating through what has been termed the microbiota–gut–brain axis, helps to control the passage of food through the digestive tract to provide itself with the nutrition it needs. The method of communication is via the production of semiochemicals, interkingdom signalling molecules, potentially including dopamine. In turn, the microbiome aids the immune system of both adult and, most importantly, the neonate. In this article we consider the role of probiotics and prebiotics, including fermented foods and dietary fibre, in the stimulation of the immune system and of semiochemical production in the gut lumen. Finally, we reprise our suggestion of an ingestible sensor, calibrated to the detection of such semiochemicals, to assess both the effectiveness of individual microbiomes and methods of amelioration of the associated non-communicable diseases.
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32
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Wicaksono WA, Buko A, Kusstatscher P, Sinkkonen A, Laitinen OH, Virtanen SM, Hyöty H, Cernava T, Berg G. Modulation of the food microbiome by apple fruit processing. Food Microbiol 2022; 108:104103. [DOI: 10.1016/j.fm.2022.104103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 11/04/2022]
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33
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Vermote L, Verce M, Mozzi F, De Vuyst L, Weckx S. Microbiomes Associated With the Surfaces of Northern Argentinian Fruits Show a Wide Species Diversity. Front Microbiol 2022; 13:872281. [PMID: 35898900 PMCID: PMC9309516 DOI: 10.3389/fmicb.2022.872281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
The fiber, vitamin, and antioxidant contents of fruits contribute to a balanced human diet. In countries such as Argentina, several tropical fruits are witnessing a high yield in the harvest season, with a resulting surplus. Fruit fermentation using autochthonous starter cultures can provide a solution for food waste. However, limited knowledge exists about the microbiota present on the surfaces of fruits and the preceding flowers. In the present exploratory study, the microbiomes associated with the surfaces of tropical fruits from Northern Argentina, such as white guava, passion fruit and papaya were investigated using a shotgun metagenomic sequencing approach. Hereto, one sample composed of 14 white guava fruits, two samples of passion fruits with each two to three fruits representing the almost ripe and ripe stage of maturity, four samples of papaya with each two to three fruits representing the unripe, almost ripe, and ripe stage of maturity were processed, as well as a sample of closed and a sample of open Japanese medlar flowers. A considerable heterogeneity was found in the composition of the fruits’ surface microbiota at the genus and species level. While bacteria dominated the microbiota of the fruits and flowers, a small number of the metagenomic sequence reads corresponded with yeasts and filamentous fungi. A minimal abundance of bacterial species critical in lactic acid and acetic acid fermentations was found. A considerable fraction of the metagenomic sequence reads from the fruits’ surface microbiomes remained unidentified, which suggested that intrinsic species are to be sequenced or discovered.
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Affiliation(s)
- Louise Vermote
- Faculty of Sciences and Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
| | - Marko Verce
- Faculty of Sciences and Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
| | - Fernanda Mozzi
- Technology and Development Laboratory, Centro de Referencia para Lactobacilos (CERELA)-CONICET, San Miguel de Tucumán, Argentina
| | - Luc De Vuyst
- Faculty of Sciences and Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
| | - Stefan Weckx
- Faculty of Sciences and Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
- *Correspondence: Stefan Weckx,
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Bill M, Gokul JK, Viljoen F, Korsten L. Fungal microbiome shifts on avocado fruit associated with a combination of postharvest chemical and physical interventions. J Appl Microbiol 2022; 133:1905-1918. [PMID: 35776004 DOI: 10.1111/jam.15693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/27/2022] [Accepted: 06/26/2022] [Indexed: 11/27/2022]
Abstract
AIM OF THE STUDY To characterise the baseline microbial population of the avocado carposphere and understand shifts in community structure from the harvest to ready-to-eat stages. METHODS AND RESULTS The changes in surface or stem-end fungal microbiomes at the postharvest stage of avocado fruit were studied using next-generation sequencing of the internal transcribed spacer (ITS) region. Avocado fructoplane and stem-end pulp fungal richness differed significantly between postharvest stages with a decline following prochloraz dip treatments. Known postharvest decay-causing genera, Colletotrichum, Fusarium, Alternaria, Epicoccum, Penicillium and Neofusicoccum were detected, with Papiliotrema, Meyerozyma and Aureobasidium confirmed as the most dominant potentially beneficial genera. Postharvest interventions such as prochloraz had a negative non-target effect on the presence of Papiliotrema flavescens on the avocado fructoplane. CONCLUSION Our findings reveal a core community of beneficial and pathogenic taxa in the avocado fructoplane, and further highlights the reduction of pathogenic fungi as a consequence of fungicide use. SIGNIFICANCE AND IMPACT OF THE STUDY The current study provides important baseline data for further exploration of fungal population shifts in avocado fruit driven by chemical (fungicide) as well as physical (cold storage) interventions.
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Affiliation(s)
- Malick Bill
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield 0028, South Africa
| | | | - Francois Viljoen
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield 0028, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield 0028, South Africa
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Abdelfattah A, Tack AJM, Wasserman B, Liu J, Berg G, Norelli J, Droby S, Wisniewski M. Evidence for host-microbiome co-evolution in apple. THE NEW PHYTOLOGIST 2022; 234:2088-2100. [PMID: 34823272 PMCID: PMC9299473 DOI: 10.1111/nph.17820] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 10/18/2021] [Indexed: 05/07/2023]
Abstract
Plants evolved in association with a diverse community of microorganisms. The effect of plant phylogeny and domestication on host-microbiome co-evolutionary dynamics are poorly understood. Here we examined the effect of domestication and plant lineage on the composition of the endophytic microbiome of 11 Malus species, representing three major groups: domesticated apple (M. domestica), wild apple progenitors, and wild Malus species. The endophytic community of M. domestica and its wild progenitors showed higher microbial diversity and abundance than wild Malus species. Heirloom and modern cultivars harbored a distinct community composition, though the difference was not significant. A community-wide Bayesian model revealed that the endophytic microbiome of domesticated apple is an admixture of its wild progenitors, with clear evidence for microbiome introgression, especially for the bacterial community. We observed a significant correlation between the evolutionary distance of Malus species and their microbiome. This study supports co-evolution between Malus species and their microbiome during domestication. This finding has major implications for future breeding programs and our understanding of the evolution of plants and their microbiomes.
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Affiliation(s)
- Ahmed Abdelfattah
- Institute of Environmental BiotechnologyGraz University of TechnologyPetersgasse 12Graz8010Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB)Max‐Eyth Allee 10014469PotsdamGermany
| | - Ayco J. M. Tack
- Department of Ecology, Environment and Plant SciencesStockholm UniversitySvante Arrhenius väg 20AStockholmSE‐106 91Sweden
| | - Birgit Wasserman
- Institute of Environmental BiotechnologyGraz University of TechnologyPetersgasse 12Graz8010Austria
| | - Jia Liu
- Chongqing Key Laboratory of Economic Plant BiotechnologyCollege of Landscape Architecture and Life SciencesChongqing University of Arts and SciencesYongchuanChongquing402160China
| | - Gabriele Berg
- Institute of Environmental BiotechnologyGraz University of TechnologyPetersgasse 12Graz8010Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB)Max‐Eyth Allee 10014469PotsdamGermany
- Institute for Biochemistry and BiologyUniversity of Postdam14476Potsdam OT GolmGermany
| | - John Norelli
- Appalachian Fruit Research StationUnited States Department of Agriculture – Agricultural Research ServiceKearneysvilleWV25430USA
| | - Samir Droby
- Department of Postharvest ScienceAgricultural Research OrganizationThe Volcani InstitutePO Box 15159Rishon LeZion7505101Israel
| | - Michael Wisniewski
- Department of Biological SciencesVirginia Polytechnic Institute and State University220 Ag Quad LnBlacksburgVA24061USA
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Leng J, Yu L, Dai Y, Leng Y, Wang C, Chen Z, Wisniewski M, Wu X, Liu J, Sui Y. Recent advances in research on biocontrol of postharvest fungal decay in apples. Crit Rev Food Sci Nutr 2022; 63:10607-10620. [PMID: 35608023 DOI: 10.1080/10408398.2022.2080638] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Apple is the largest fruit crop produced in temperate regions and is a popular fruit worldwide. It is, however, susceptible to a variety of postharvest fungal pathogens, including Penicillium expansum, Botrytis cinerea, Botryosphaeria dothidea, Monilia spp., and Alternaria spp. Decays resulting from fungal infections severely reduce apple quality and marketable yield. Biological control utilizing bacterial and fungal antagonists is an eco-friendly and effective method of managing postharvest decay in horticultural crops. In the current review, research on the pathogenesis of major decay fungi and isolation of antagonists used to manage postharvest decay in apple is presented. The mode of action of postharvest biocontrol agents (BCAs), including recent molecular and genomic studies, is also discussed. Recent research on the apple microbiome and its relationship to disease management is highlighted, and the use of additives and physical treatments to enhance biocontrol efficacy of BCAs is reviewed. Biological control is a critical component of an integrated management system for the sustainable approaches to apple production. Additional research will be required to explore the feasibility of developing beneficial microbial consortia and novel antimicrobial compounds derived from BCAs for postharvest disease management, as well as genetic approaches, such as the use of CRISPR/Cas9 technology.
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Affiliation(s)
- Jinsong Leng
- Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Longfeng Yu
- School of Biotechnology and Bioengineering, West Yunnan University, Lincang, Yunan, China
| | - Yuan Dai
- Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Yan Leng
- School of Biotechnology and Bioengineering, West Yunnan University, Lincang, Yunan, China
| | - Chaowen Wang
- School of Biotechnology and Bioengineering, West Yunnan University, Lincang, Yunan, China
| | - Zhuo Chen
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou, China
| | - Michael Wisniewski
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Xuehong Wu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jia Liu
- Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Yuan Sui
- Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
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Olimi E, Kusstatscher P, Wicaksono WA, Abdelfattah A, Cernava T, Berg G. Insights into the microbiome assembly during different growth stages and storage of strawberry plants. ENVIRONMENTAL MICROBIOME 2022; 17:21. [PMID: 35484554 PMCID: PMC9052558 DOI: 10.1186/s40793-022-00415-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 04/17/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND Microbiome assembly was identified as an important factor for plant growth and health, but this process is largely unknown, especially for the fruit microbiome. Therefore, we analyzed strawberry plants of two cultivars by focusing on microbiome tracking during the different growth stages and storage using amplicon sequencing, qPCR, and microscopic approaches. RESULTS Strawberry plants carried a highly diverse microbiome, therein the bacterial families Sphingomonadaceae (25%), Pseudomonadaceae (17%), and Burkholderiaceae (11%); and the fungal family Mycosphaerella (45%) were most abundant. All compartments were colonized by high number of bacteria and fungi (107-1010 marker gene copies per g fresh weight), and were characterized by high microbial diversity (6049 and 1501 ASVs); both were higher for the belowground samples than in the phyllosphere. Compartment type was the main driver of microbial diversity, structure, and abundance (bacterial: 45%; fungal: 61%) when compared to the cultivar (1.6%; 2.2%). Microbiome assembly was strongly divided for belowground habitats and the phyllosphere; only a low proportion of the microbiome was transferred from soil via the rhizosphere to the phyllosphere. During fruit development, we observed the highest rates of microbial transfer from leaves and flowers to ripe fruits, where most of the bacteria occured inside the pulp. In postharvest fruits, microbial diversity decreased while the overall abundance increased. Developing postharvest decay caused by Botrytis cinerea decreased the diversity as well, and induced a reduction of potentially beneficial taxa. CONCLUSION Our findings provide insights into microbiome assembly in strawberry plants and highlight the importance of microbe transfer during fruit development and storage with potential implications for food health and safety.
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Affiliation(s)
- Expedito Olimi
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Application of prebiotics in apple products and potential health benefits. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2022; 59:1249-1262. [PMID: 35250051 PMCID: PMC8882558 DOI: 10.1007/s13197-021-05062-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 02/25/2021] [Accepted: 03/02/2021] [Indexed: 12/12/2022]
Abstract
Among the fruits, the apple stands out among the most used for elaboration of processed foods. However, the importance of prebiotics in apple products has never been widely analyzed. Prebiotic is a food component resistant to gastric acidity, digestion by mammalian enzymes and gastrointestinal absorption. But following fermentation in the colon, prebiotics result in specific changes in the composition and / or metabolism of the gastrointestinal microbiota, conferring benefits to the health of the host. Therefore, fortifying apple-based products with additional prebiotics is an important strategy for improving consumer health benefits. In this review, after compiling and analyzing scientific and technological studies focusing on prebiotics in apple products, the following benefits of these prebiotics became evident: (1) reduction of water loss in the food matrix; (2) preservation of bioactive and volatile compounds; (3) texture improvement (thickening) in the food industry; (4) increased shelf-live and (5) increased survival of probiotic bacteria, promoting positive effects on microbiota. In addition, this review shows the benefits of different prebiotics for stability and sensory acceptance of apple processed foods.
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Chen Y, Zhang Z, Tian S, Li B. Application of -omic technologies in postharvest pathology: Recent advances and perspectives. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Köberl M, Kusstatscher P, Wicaksono WA, Mpiira S, Kalyango F, Staver C, Berg G. Increased Yield and High Resilience of Microbiota Representatives With Organic Soil Amendments in Smallholder Farms of Uganda. FRONTIERS IN PLANT SCIENCE 2022; 12:815377. [PMID: 35185962 PMCID: PMC8847376 DOI: 10.3389/fpls.2021.815377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Organic matter inputs positively affect soil fertility and quality but management effects on the soil and plant microbiome are less understood. Therefore, we studied the response of microbial colonization of the East African highland banana cultivar "Mpologoma" (AAA genome) under different mulch and manure treatments on three representative smallholder farms in Uganda. In general, the gammaproteobacterial community appeared stable with no significant response to organic matter inputs after 24 months of treatment. Significant differences (p < 0.05) in the plant-associated carpo-, phyllo-, and rhizosphere microbial community composition and diversity were found among individual sampled farms, independent of added soil inputs. Across farms, banana fruit harbored a richer and more balanced gammaproteobacterial community than the rhizo- and endospheres. Gammaproteobacterial beta diversity was shaped by the microenvironment (44%) as well as the sampling site (4%). Global effects of treatments in the rhizosphere analyzed using linear discriminant analysis effect size showed significantly enriched genera, such as Enterobacter, under manure and mulch treatments. As shown in previous works, bunch size and total yield were highly increased with manure and mulch, however, our results highlight general short-term microbial stability of Ugandan banana cropping systems with increases in the gammaproteobacterial community.
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Affiliation(s)
- Martina Köberl
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Samuel Mpiira
- National Agricultural Research Laboratories, National Agricultural Research Organisation, Kampala, Uganda
| | - Francis Kalyango
- National Agricultural Research Laboratories, National Agricultural Research Organisation, Kampala, Uganda
| | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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Shen Y, Zhang J, Nie J, Zhang H, Bacha SAS. Apple microbial communities and differences between two main Chinese producing regions. FOOD QUALITY AND SAFETY 2022. [DOI: 10.1093/fqsafe/fyab033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Microbes on fresh apples are closely associated with fruit disease, preservation and quality control. Investigation into the microbial communities on apples from different producing regions could reveal the microbial specificity and help disease prevention and quality control. In this paper, the apple surface microbes of forty-four samples from two main Chinese apple-producing regions, Bohai Bay (BHB) and the Loess Plateau (LP), were investigated by sequencing fungal internal transcribed spacer (ITS) and bacterial 16S rRNA hypervariable sequences. BHB and LP apples contained significantly different bacterial and fungal communities. BHB apples had a higher fungal diversity than LP apples. A total of 102 different fungal and bacterial taxonomies were obtained between apples from the two regions, in which 24 genera were predominant. BHB apples had higher phytopathogenic fungal genera, such as Tilletiopsis, Acremonium, Candida and Phoma, indicating the higher phytopathogenic risks of apples from the humid climate of the BHB region. LP apples contained more bacterial genera identified as gut microbes, indicating the potential risks of contaminating apples with foodborne pathogens in the arid environment of the LP. This study highlighted the environment-oriented microbial specificity on apples from two main apple-producing regions, and provided a basis for further investigation.
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Affiliation(s)
| | | | | | | | - Syed Asim Shah Bacha
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, China
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Knorr D, Augustin MA. Food systems at a watershed: Unlocking the benefits of technology and ecosystem symbioses. Crit Rev Food Sci Nutr 2022; 63:5680-5697. [PMID: 34989303 DOI: 10.1080/10408398.2021.2023092] [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] [Indexed: 11/03/2022]
Abstract
The current food systems require change to improve sustainability resilience. Humans need food and food requires natural resources which have been consistently reduced, destroyed, or eliminated during human development, and excessive during the last 50-70 years. Though essential, there has been less of a focus on the inter-relations and inter-dependences of our food supply with and on the world's eco-system and organisms. Integrating evidence for the importance of plants, the microbiota in plants, animals and humans and their reciprocal effects of their interactions on food systems is essential for creating more inclusive strategies for future food systems. This review examines the role of plants, microorganisms, plant-microbial, animal-microbial, and human-microbial interactions, their co-evolution on the food supply and human and eco-systems well-being. It also recognizes the contribution of indigenous knowledge for lasting protection of the land, managing resources and biodiversity and the usefulness of food processing for producing safe, tasty, and nutritious food sustainably. We demonstrate that new targets and priorities for harnessing science and technology for improving food and nutritional security and avoiding environmental degradation and biodiversity loss are urgently needed. For improved long-term sustainability, the benefits of technology and ecosystem interactions must be unlocked.
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Affiliation(s)
- Dietrich Knorr
- Food Biotechnology and Food Process Engineering, Technische Universität Berlin, Berlin, Germany
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Escobar Rodríguez C, Novak J, Buchholz F, Uetz P, Bragagna L, Gumze M, Antonielli L, Mitter B. The Bacterial Microbiome of the Tomato Fruit Is Highly Dependent on the Cultivation Approach and Correlates With Flavor Chemistry. FRONTIERS IN PLANT SCIENCE 2021; 12:775722. [PMID: 35003161 PMCID: PMC8740158 DOI: 10.3389/fpls.2021.775722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
The modes of interactions between plants and plant-associated microbiota are manifold, and secondary metabolites often play a central role in plant-microbe interactions. Abiotic and biotic (including both plant pathogens and endophytes) stress can affect the composition and concentration of secondary plant metabolites, and thus have an influence on chemical compounds that make up for the taste and aroma of fruit. While the role of microbiota in growth and health of plants is widely acknowledged, relatively little is known about the possible effect of microorganisms on the quality of fruit of plants they are colonizing. In this work, tomato (Solanum lycopersicum L.) plants of five different cultivars were grown in soil and in hydroponics to investigate the impact of the cultivation method on the flavor of fruit, and to assess whether variations in their chemical composition are attributable to shifts in bacterial microbiota. Ripe fruit were harvested and used for bacterial community analysis and for the analysis of tomato volatiles, sugars and acids, all contributing to flavor. Fruit grown in soil showed significantly higher sugar content, whereas tomatoes from plants under hydroponic conditions had significantly higher levels of organic acids. In contrast, aroma profiles of fruit were shaped by the tomato cultivars, rather than the cultivation method. In terms of bacterial communities, the cultivation method significantly defined the community composition in all cultivars, with the bacterial communities in hydroponic tomatoes being more variable that those in tomatoes grown in soil. Bacterial indicator species in soil-grown tomatoes correlated with higher concentrations of volatiles described to be perceived as "green" or "pungent." A soil-grown specific reproducibly occurring ASV (amplicon sequence variants) classified as Bacillus detected solely in "Solarino" tomatoes, which were the sweetest among all cultivars, correlated with the amount of aroma-relevant volatiles as well as of fructose and glucose in the fruit. In contrast, indicator bacterial species in hydroponic-derived tomatoes correlated with aroma compounds with "sweet" and "floral" notes and showed negative correlations with glucose concentrations in fruit. Overall, our results point toward a microbiota-related accumulation of flavor and aroma compounds in tomato fruit, which is strongly dependent on the cultivation substrate and approach.
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Affiliation(s)
- Carolina Escobar Rodríguez
- FFoQSI GmbH – Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
| | - Johannes Novak
- Institute of Applied Botany and Pharmacognosy (IAB), Veterinary University of Vienna, Vienna, Austria
| | - Franziska Buchholz
- FFoQSI GmbH – Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
| | - Pia Uetz
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Laura Bragagna
- FFoQSI GmbH – Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
| | - Marija Gumze
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Livio Antonielli
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Birgit Mitter
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Tulln, Austria
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The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host. Sci Rep 2021; 11:24017. [PMID: 34911987 PMCID: PMC8674285 DOI: 10.1038/s41598-021-03334-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 11/24/2021] [Indexed: 12/15/2022] Open
Abstract
Plant microbiomes have been extensively studied for their agricultural relevance on growth promotion and pathogenesis, but little is known about their role as part of the diet when fresh fruits and vegetables are consumed raw. Most studies describing these communities are based on 16S rRNA gene amplicon surveys, limiting our understanding of the taxonomic resolution at the species level and functional capabilities. In this study, we characterized microbes colonizing tomatoes, spinach, brined olives, and dried figs using shotgun metagenomics. We recovered metagenome-assembled genomes of novel lactic acid bacteria from green olives and identified high intra- and inter-specific diversity of Pseudomonas in tomatoes. All samples were colonized by Pseudomonas, consistent with other reports with distinct community structure. Functional characterization showed the presence of enzymes involved in vitamin and short chain fatty acid metabolism and degradation of diverse carbohydrate substrates including plant fibers. The dominant bacterial members were isolated, sequenced, and mapped to its metagenome confirming their identity and indicating the microbiota is culturable. Our results reveal high genetic diversity, previously uncultured genera, and specific functions reflecting a likely plant host association. This study highlights the potential that plant microbes can play when consumed as part of our diet and proposes these as transient contributors to the gut microbiome.
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Breman E, Ballesteros D, Castillo-Lorenzo E, Cockel C, Dickie J, Faruk A, O’Donnell K, Offord CA, Pironon S, Sharrock S, Ulian T. Plant Diversity Conservation Challenges and Prospects-The Perspective of Botanic Gardens and the Millennium Seed Bank. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112371. [PMID: 34834734 PMCID: PMC8623176 DOI: 10.3390/plants10112371] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 05/22/2023]
Abstract
There is a pressing need to conserve plant diversity to prevent extinctions and to enable sustainable use of plant material by current and future generations. Here, we review the contribution that living collections and seed banks based in botanic gardens around the world make to wild plant conservation and to tackling global challenges. We focus in particular on the work of Botanic Gardens Conservation International and the Millennium Seed Bank of the Royal Botanic Gardens, Kew, with its associated global Partnership. The advantages and limitations of conservation of plant diversity as both living material and seed collections are reviewed, and the need for additional research and conservation measures, such as cryopreservation, to enable the long-term conservation of 'exceptional species' is discussed. We highlight the importance of networks and sharing access to data and plant material. The skill sets found within botanic gardens and seed banks complement each other and enable the development of integrated conservation (linking in situ and ex situ efforts). Using a number of case studies we demonstrate how botanic gardens and seed banks support integrated conservation and research for agriculture and food security, restoration and reforestation, as well as supporting local livelihoods.
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Affiliation(s)
- Elinor Breman
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath, West Sussex RH17 6TN, UK; (D.B.); (E.C.-L.); (C.C.); (J.D.); (A.F.); (T.U.)
- Correspondence:
| | - Daniel Ballesteros
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath, West Sussex RH17 6TN, UK; (D.B.); (E.C.-L.); (C.C.); (J.D.); (A.F.); (T.U.)
| | - Elena Castillo-Lorenzo
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath, West Sussex RH17 6TN, UK; (D.B.); (E.C.-L.); (C.C.); (J.D.); (A.F.); (T.U.)
| | - Christopher Cockel
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath, West Sussex RH17 6TN, UK; (D.B.); (E.C.-L.); (C.C.); (J.D.); (A.F.); (T.U.)
| | - John Dickie
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath, West Sussex RH17 6TN, UK; (D.B.); (E.C.-L.); (C.C.); (J.D.); (A.F.); (T.U.)
| | - Aisyah Faruk
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath, West Sussex RH17 6TN, UK; (D.B.); (E.C.-L.); (C.C.); (J.D.); (A.F.); (T.U.)
| | - Katherine O’Donnell
- Botanic Gardens Conservation International, Descanso House, 199 Kew Road, London TW9 3BW, UK (S.S.)
| | - Catherine A. Offord
- The Australian Plant Bank, Australian Institute of Botanical Science, Australian Botanic Garden, Mount Annan, Sydney, NSW 2567, Australia;
| | - Samuel Pironon
- Royal Botanic Gardens, Kew, Kew Green, Richmond, Surrey TW9 3AE, UK;
| | - Suzanne Sharrock
- Botanic Gardens Conservation International, Descanso House, 199 Kew Road, London TW9 3BW, UK (S.S.)
| | - Tiziana Ulian
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath, West Sussex RH17 6TN, UK; (D.B.); (E.C.-L.); (C.C.); (J.D.); (A.F.); (T.U.)
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Changes in the Fungal Community Assembly of Apple Fruit Following Postharvest Application of the Yeast Biocontrol Agent Metschnikowia fructicola. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7100360] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recently, increasing focus has been placed on exploring fruit microbiomes and their association with their hosts. Investigation of the fruit surface microbiome of apple has revealed variations in the composition and structure depending on management practices, phenological stages, and spatial distribution on the fruit itself. However, the fate of the fruit surface microbiome assembly and dynamics in apple following interventions such as the application of biocontrol agents remains unknown. The objective of the study was to explore the effect of a postharvest application of a yeast biocontrol agent, Metschnikowia fructicola, on the composition of the epiphytic fungal microbiota on apples during cold storage. Our results demonstrated that the applied biocontrol agent, M. fructicola, persisted in high abundance (>28% relative abundance) on the fruit surface throughout the storage period. The biocontrol application significantly decreased the richness and caused a significant shift in the overall composition and structure of the fungal microbiome relative to untreated or water-treated controls. The yeast application reduced the abundance of several apple fungal pathogens, namely, Alternaria, Aspergillus, Comoclatris, Stemphylium, Nigrospora, Penicillium, and Podosphaera, throughout the cold storage period.
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de Carvalho LAL, Teheran-Sierra LG, Funnicelli MIG, da Silva RC, Campanari MFZ, de Souza RSC, Arruda P, Soares MA, Pinheiro DG. Farming systems influence the compositional, structural, and functional characteristics of the sugarcane-associated microbiome. Microbiol Res 2021; 252:126866. [PMID: 34536678 DOI: 10.1016/j.micres.2021.126866] [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: 03/12/2021] [Revised: 08/24/2021] [Accepted: 09/06/2021] [Indexed: 12/26/2022]
Abstract
Sugarcane (Saccharum spp.) has been produced worldwide as a relevant source of food and sustainable energy. However, the constant need to increase crop yield has led to excessive use of synthetic agrochemical inputs such as inorganic fertilizers, herbicides, and pesticides in plant cultures. It is known that these conventional practices can lead to deleterious effects on health and the environment. Organic farming emerges as a sustainable alternative to conventional systems; however, farm management influences in plant-associated microbiomes remain unclear. Here, the aim is to identify the effects of farming systems on the sugarcane microbiota. To address this issue, we sampled the microbiota from soils and plants under organic and conventional farming from two crop fields in Brazil. Then, we evaluated their compositional, structural, and functional traits through amplification and sequencing of phylogenetic markers of bacteria (16S rRNA gene, V3-V4 region) and fungi (Internal Transcribed Spacer - ITS2). The data processing and analyses by the DADA2 pipeline revealed 12,839 bacterial and 3,222 fungal sequence variants. Moreover, differences between analogous niches were detected considering the contrasting farming systems, with samples from the conventional system showing a slightly greater richness and diversity of microorganisms. The composition is also different between the farming systems, with 389 and 401 differentially abundant taxa for bacteria and fungi, respectively, including taxa capable of promoting plant growth. The microbial co-occurrence networks showed structural changes in microbial communities, where organic networks were more cohesive since they had closer taxa and less modularity by niches. Finally, the functional prediction revealed enriched metabolic pathways, including the increased presence of antimicrobial resistance in the conventional farming system. Taken together, our findings reveal functional, structural, and compositional adaptations of the microbial communities associated with sugarcane plants in the field, according to farming management. With this, we point out the need to unravel the mechanisms driving these adaptations.
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Affiliation(s)
- Lucas Amoroso Lopes de Carvalho
- Laboratory of Bioinformatics, Department of Agricultural and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, 14884-900, SP, Brazil; Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, 14884-900, SP, Brazil.
| | - Luis Guillermo Teheran-Sierra
- Laboratory of Bioinformatics, Department of Agricultural and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, 14884-900, SP, Brazil; Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, 14884-900, SP, Brazil
| | - Michelli Inácio Gonçalves Funnicelli
- Laboratory of Bioinformatics, Department of Agricultural and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, 14884-900, SP, Brazil; Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, 14884-900, SP, Brazil
| | - Rafael Correia da Silva
- Laboratory of Bioinformatics, Department of Agricultural and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, 14884-900, SP, Brazil; Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, 14884-900, SP, Brazil
| | - Maria Fernanda Zaneli Campanari
- Laboratory of Bioinformatics, Department of Agricultural and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, 14884-900, SP, Brazil; Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, 14884-900, SP, Brazil
| | - Rafael Soares Correa de Souza
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, 13083-875, SP, Brazil; Genomics for Climate Change Research Center (GCCRC), University of Campinas (UNICAMP), Campinas, 13083-875, SP, Brazil
| | - Paulo Arruda
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, 13083-875, SP, Brazil; Genomics for Climate Change Research Center (GCCRC), University of Campinas (UNICAMP), Campinas, 13083-875, SP, Brazil; Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas (UNICAMP), Campinas, 13083-970, SP, Brazil
| | - Marcos Antônio Soares
- Department of Botany and Ecology, Federal University of Mato Grosso (UFMT), Av. Fernando Corrêa 2367, Cuiabá, MT, Brazil
| | - Daniel Guariz Pinheiro
- Laboratory of Bioinformatics, Department of Agricultural and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, 14884-900, SP, Brazil.
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Meisner A, Wepner B, Kostic T, van Overbeek LS, Bunthof CJ, de Souza RSC, Olivares M, Sanz Y, Lange L, Fischer D, Sessitsch A, Smidt H. Calling for a systems approach in microbiome research and innovation. Curr Opin Biotechnol 2021; 73:171-178. [PMID: 34479027 DOI: 10.1016/j.copbio.2021.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/27/2021] [Accepted: 08/05/2021] [Indexed: 12/23/2022]
Abstract
Microbiomes are all around us in natural and cultivated ecosystems, for example, soils, plants, animals and our own body. Microbiomes are essential players of biotechnological applications, and their functions drive human, animal, plant and environmental health. The rapidly developing microbiome research landscape was studied by a global mapping excercise and bibliometric analysis. Although microbiome research is performed in many different science fields, using similar concepts within and across fields, microbiomes are mostly investigated one ecosystem at-a-time. In order to fully understand microbiome impacts and leverage microbial functions, research needs to adopt a systems approach connecting microbiomes and research initiatives in divergent fields to create understanding on how microbiomes can be modulated for desirable functions as a basis of sustainable, circular bioeconomy.
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Affiliation(s)
- Annelein Meisner
- Wageningen University & Research,Wageningen Research, Droevendaalsesteeg 4, Wageningen, 6708 PB, The Netherlands
| | - Beatrix Wepner
- AIT Austrian Institute of Technology, Center for Innovation Systems & Policy, Giefinggasse 4, Vienna, 1210, Austria
| | - Tanja Kostic
- AIT Austrian Institute of Technology, Center for Health & Bioresources, Bioresources Unit, Konrad Lorenz Strasse 24, Tulln, 3430, Austria
| | - Leo S van Overbeek
- Wageningen University & Research,Wageningen Research, Droevendaalsesteeg 4, Wageningen, 6708 PB, The Netherlands
| | - Christine J Bunthof
- Wageningen University & Research,Wageningen Research, Droevendaalsesteeg 4, Wageningen, 6708 PB, The Netherlands
| | - Rafael Soares Correa de Souza
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-875, Brazil
| | - Marta Olivares
- Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Paterna-Valencia, 46980, Spain
| | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Paterna-Valencia, 46980, Spain
| | - Lene Lange
- BioEconomy, Research & Advisory, Karensgade 5, Valby, 2500, Denmark
| | - Doreen Fischer
- Helmholtz Zentrum München, National Research Center for Environmental Health, Research Unit for Comparative Microbiome Analysis, Ingolstaedter Landstr. 1, Neuherberg, Munich, D-85764, Germany
| | - Angela Sessitsch
- AIT Austrian Institute of Technology, Center for Health & Bioresources, Bioresources Unit, Konrad Lorenz Strasse 24, Tulln, 3430, Austria
| | - Hauke Smidt
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, Wageningen, 6708 WE, The Netherlands.
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Mills S, Ross RP. Colliding and interacting microbiomes and microbial communities - consequences for human health. Environ Microbiol 2021; 23:7341-7354. [PMID: 34390616 DOI: 10.1111/1462-2920.15722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 11/26/2022]
Abstract
Living 'things' coexist with microorganisms, known as the microbiota/microbiome that provides essential physiological functions to its host. Despite this reliance, the microbiome is malleable and can be altered by several factors including birth-mode, age, antibiotics, nutrition, and disease. In this minireview, we consider how other microbiomes and microbial communities impact the host microbiome and the host through the concept of microbiome collisions (initial exposures) and interactions. Interactions include changes in host microbiome composition and functionality and/or host responses. Understanding the impact of other microbiomes and microbial communities on the microbiome and host are important considering the decline in human microbiota diversity in the developed world - paralleled by the surge of non-communicable, inflammatory-based diseases. Thus, surrounding ourselves with rich and diverse beneficial microbiomes and microbial communities to collide and interact with should help to diminish the loss in microbial diversity and protect from certain diseases. In the same vein, our microbiomes not only influence our health but potentially the health of those close to us. We also consider strategies for enhanced host microbiome collisions and interactions through the surrounding environment that ensure increased microbiome diversity and functionality contributing to enhanced symbiotic return to the host in terms of health benefit.
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Affiliation(s)
- Susan Mills
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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Kim SH, Cho G, Lee SI, Kim DR, Kwak YS. Comparison of Bacterial Community of Healthy and Erwinia amylovora Infected Apples. THE PLANT PATHOLOGY JOURNAL 2021; 37:396-403. [PMID: 34365751 PMCID: PMC8357565 DOI: 10.5423/ppj.nt.04.2021.0062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 05/17/2021] [Indexed: 06/01/2023]
Abstract
Fire blight disease, caused by Erwinia amylovora, could damage rosaceous plants such as apples, pears, and raspberries. In this study, we designed to understand how E. amylovora affected other bacterial communities on apple rhizosphere; twig and fruit endosphere; and leaf, and fruit episphere. Limited studies on the understanding of the microbial community of apples and changes the community structure by occurrence of the fire blight disease were conducted. As result of these experiments, the infected trees had low species richness and operational taxonomic unit diversity when compared to healthy trees. Rhizospheric bacterial communities were stable regardless of infection. But the communities in endosphere and episphere were significanlty affected by E. amylovora infection. We also found that several metabolic pathways differ significantly between infected and healthy trees. In particular, we observed differences in sugar metabolites. The finding provides that sucrose metabolites are important for colonization of E. amylovora in host tissue. Our results provide fundamental information on the microbial community structures between E. amylovora infected and uninfected trees, which will contribute to developing novel control strategies for the fire blight disease.
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Affiliation(s)
- Su-Hyeon Kim
- Division of Applied Life Science (BK21Plus) and Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Gyoengjun Cho
- Division of Applied Life Science (BK21Plus) and Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Su In Lee
- Department of Plant Medicine, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Da-Ran Kim
- Division of Applied Life Science (BK21Plus) and Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Youn-Sig Kwak
- Division of Applied Life Science (BK21Plus) and Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
- Department of Plant Medicine, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Korea
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