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Cowled MS, Phippen CBW, Kromphardt KJK, Clemmensen SE, Frandsen RJN, Frisvad JC, Larsen TO. Unveiling the fungal diversity and associated secondary metabolism on black apples. Appl Environ Microbiol 2024; 90:e0034224. [PMID: 38899884 PMCID: PMC11267942 DOI: 10.1128/aem.00342-24] [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: 03/02/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Black apples are the result of late-stage microbial decomposition after falling to the ground. This phenomenon is highly comparable from year to year, with the filamentous fungus Monilinia fructigena most commonly being the first invader, followed by Penicillium expansum. Motivated by the fact that only little chemistry has been reported from apple microbiomes, we set out to investigate the chemical diversity and potential ecological roles of secondary metabolites (SMs) in a total of 38 black apples. Metabolomics analyses were conducted on either whole apples or small excisions of fungal biomass derived from black apples. Annotation of fungal SMs in black apple extracts was aided by the cultivation of 15 recently isolated fungal strains on 9 different substrates in a One Strain Many Compounds (OSMAC) approach, leading to the identification of 3,319 unique chemical features. Only 6.4% were attributable to known compounds based on analysis of high-performance liquid chromatography-high-resolution mass spectrometry (HPLC-HRMS/MS) data using spectral library matching tools. Of the 1,606 features detected in the black apple extracts, 32% could be assigned as fungal-derived, due to their presence in the OSMAC-based training data set. Notably, the detection of several antifungal compounds indicates the importance of such compounds for the invasion of and control of other microbial competitors on apples. In conclusion, the diversity and abundance of microbial SMs on black apples were found to be much higher than that typically observed for other environmental microbiomes. Detection of SMs known to be produced by the six fungal species tested also highlights a succession of fungal growth following the initial invader M. fructigena.IMPORTANCEMicrobial secondary metabolites constitute a significant reservoir of biologically potent and clinically valuable chemical scaffolds. However, their usefulness is hampered by rapidly developing resistance, resulting in reduced profitability of such research endeavors. Hence, the ecological role of such microbial secondary metabolites must be considered to understand how best to utilize such compounds as chemotherapeutics. Here, we explore an under-investigated environmental microbiome in the case of black apples; a veritable "low-hanging fruit," with relatively high abundances and diversity of microbially produced secondary metabolites. Using both a targeted and untargeted metabolomics approach, the interplay between metabolites, other microbes, and the apple host itself was investigated. This study highlights the surprisingly low incidence of known secondary metabolites in such a system, highlighting the need to study the functionality of secondary metabolites in microbial interactions and complex microbiomes.
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Affiliation(s)
- Michael S. Cowled
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Christopher B. W. Phippen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kresten J. K. Kromphardt
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sidsel E. Clemmensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Rasmus J. N. Frandsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jens C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Thomas O. Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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2
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Zhu Z, Yu C, Dong Z, Mo R, Zhang C, Liu X, Zuo Y, Li Y, Deng W, Hu X. Phylogeny and Fungal Community Structures of Helotiales Associated with Sclerotial Disease of Mulberry Fruits in China. PLANT DISEASE 2024; 108:502-512. [PMID: 37647089 DOI: 10.1094/pdis-02-23-0223-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Mulberry fruit sclerotiniose is a prevalent disease caused by the fungal species Ciboria shiraiana, C. carunculoides, and Scleromitrula shiraiana of the order Helotiales, and severely affects the production of mulberry. However, these species have only been identified using morphological and rDNA-ITS sequence analyses, and their genetic variation is unclear. To address this, morphological and two-locus (ITS and RPB2) phylogenetic analyses were conducted using culture-dependent and independent methods for 49 samples from 31 orchards across four provinces in China. Illumina MiSeq sequencing was used to assess the fungal communities obtained from fruits varying in disease severity and color from an orchard in Wuhan. Conidial suspensions of C. shiraiana and C. carunculoides isolated from diseased fruits, diseased fruits affected with hypertrophy and pellet sorosis sclerotiniose, and mycelia of Sclerotinia sclerotiorum were determined to be pathogenic to the mulberry cultivar YSD10. However, fruits inoculated with S. sclerotiorum mycelia exhibited nontypical disease symptoms, and mycelia and conidia obtained from C. carunculoides and S. shiraiana strains were not pathogenic. Maximum parsimony and Bayesian analyses using the sequences of the assessed loci indicated species variability with no evidence of geographic specialization. Metagenomic analysis revealed that the diversity of fungal communities was reduced with disease progression. Furthermore, within a single fruit, the presence of two Ciboria spp. was detected. These results provide novel insights into Ciboria spp., revealing the secondary infections caused by conidia in diseased fruits, genetic variations of the pathogens, and the occurrence of coinfection. This improved understanding of fungal pathogens will aid in developing effective disease control strategies.
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Affiliation(s)
- Zhixian Zhu
- Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Cui Yu
- Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Zhaoxia Dong
- Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Rongli Mo
- Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Cheng Zhang
- Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Xinxin Liu
- Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Yuanyuan Zuo
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yong Li
- Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Wen Deng
- Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Xingming Hu
- Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
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Abdulsalam RA, Ijabadeniyi OA, Cason ED, Sabiu S. Characterization of Microbial Diversity of Two Tomato Cultivars through Targeted Next-Generation Sequencing 16S rRNA and ITS Techniques. Microorganisms 2023; 11:2337. [PMID: 37764180 PMCID: PMC10534366 DOI: 10.3390/microorganisms11092337] [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: 08/09/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Even though the nutritional and economic values of Solanum lycopersicum (tomato) are substantially impacted by microbial spoilage, the available data on its microbial community, particularly during spoilage, are limited and have primarily been characterized using conventional culture-dependent methods. This study employed a targeted high-throughput next-generation sequencing method to longitudinally characterize the microbial diversity of two South African tomato cultivars (jam and round) at varied storage intervals (1, 6, and 12 days). Throughout the storage period, the bacterial communities of the two cultivars were more diverse than the fungal communities. The microbial diversity of both bacteria and fungi was greater and comparable between the cultivars on day 1, but becomes distinct as the storage period increases, with round tomatoes being more diverse than jam tomato, though, on day 12, jam tomato develops greater diversity than round tomato. Overall, the most abundant phyla (though Proteobacteria was most dominant) were Proteobacteria, Firmicutes, and Bacteriodota in the bacterial communities, while Ascomycota and Basidiomycota formed most fungal communities with Ascomycota being dominant. At the genus level, Pantoea and Klebsiella (bacteria), Hanseniaspora, Stemphylium, and Alternaria (fungi) were prevalent. Taken together, this study casts light on a broad microbial diversity profile thus, confirms the cultivars' diversity and abundance differences.
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Affiliation(s)
- Rukayat Abiola Abdulsalam
- Department of Biotechnology and Food Science, Durban University of Technology, Durban 4000, South Africa
| | | | - Errol D. Cason
- Department of Animal Science, University of the Free State, Bloemfontein 9300, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Durban University of Technology, Durban 4000, South Africa
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Hou Y, Zhang X, Gao Z, Chen T, Zhang L. Relationships between fungal diversity and fruit quality of Yuluxiang pear during low temperature storage. Front Microbiol 2023; 14:1132271. [PMID: 37032901 PMCID: PMC10080050 DOI: 10.3389/fmicb.2023.1132271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/02/2023] [Indexed: 04/11/2023] Open
Abstract
Postharvest decay is an urgent problem that affects the storage of pears. Low temperature storage is one of the most important methods to reduce the prevalence of fruit diseases during storage. In this study, the microbial diversity of postharvest Yuluxiang pear (Pyrus × michauxii "Yu Lu Xiang") fruits stored at low temperature for different lengths of times was analyzed. Illumina MiSeq high-throughput sequencing was used to analyze the composition and diversity of fungal communities. The results showed that the fungi within fruit were classified into 6 phyla, 18 classes, 40 orders, 72 families, and 92 genera based on the 97% sequence similarity level. They belonged to 6 phyla, 18 classes, 40 orders, 72 families, and 92 genera. The highest richness of fungi was obtained after 30 d of treatment. The β-diversity index showed that the fungal community composition of these fruit was significantly different at the beginning of storage compared with the different timepoints of samples at low temperature during storage. The comparison of fungal composition at the phylum level indicated that Ascomycota was dominant in the different timepoints of samples at low temperature, while Alternaria was the primary fungus at the genus level. A correlation analysis was used to further explore the correlation between fungi and fruit firmness, titratable acid, and solid soluble contents at low temperatures during storage. Aureobasidium and Didymella positively correlated with the soluble solids and hardness. Phoma positively correlated with the titratable acid, and Aspergillus positively correlated with titratable acid and hardness. This study can guide the industrial production of Yulu pear and also provide a theoretical basis to prevent and control diseases during the storage period of Yulu pear.
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Abstract
Candida auris is a multidrug-resistant nosocomial fungal pathogen. While the marine environment was recently identified as a natural niche for C. auris, the environment(s) that might have contributed to the development and spread of antifungal resistance in C. auris remains a mystery. Because stored fruits are often treated with fungicides to prevent postharvest spoilage, we hypothesized that stored fruits could serve as a possible selective force for and a transmission reservoir of antifungal-resistant isolates of pathogenic yeasts, including C. auris. To test this hypothesis, we screened fruits to study the diversity of pathogenic yeasts and their antifungal susceptibility profiles. Among the 62 screened apples, the surfaces of 8 were positive for C. auris, and all were stored apples. Whole-genome sequencing (WGS) showed that C. auris strains from apples were genetically diverse and exhibited broad phylogenetic distribution among the subclades within clade I. Interestingly, strains from apples had closely related strains from other sources in India, including from patients, hospitals, and marine environments, and from clinical strains from other parts of the world. A broad range of fungicides, including dimethyl inhibitors (DMIs), were detected in stored apples, and all C. auris isolates exhibited reduced sensitivity to DMIs. Interestingly, C. auris was not isolated from freshly picked apples. Together, the results suggest a potentially complex ecology for C. auris with agriculture fungicide application on stored fruits as a significant selective force for drug resistance in clinics.
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Condessa BMB, da Silva KV, da Silva JFM, de Morais PB, Leal Zimmer FMA, de Almeida AF, Niculau EDS, Nogueira KL, Santos CCADA. Performance of wild
Saccharomyces
and Non‐
Saccharomyces
yeasts as starter cultures in dough fermentation and bread making. Int J Food Sci Technol 2022. [DOI: 10.1111/ijfs.15633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | - Paula Benevides de Morais
- Bionorte – Legal Amazon Biodiversity and Biotechnology Network Federal University of Tocantins Palmas Brazil
| | | | - Alex Fernando de Almeida
- Graduate Program in Food Science and Technology Federal University of Tocantins (UFT) Palmas Brazil
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Hamilton A, Ruiz-Llacsahuanga B, Mendoza M, Mattheis J, Hanrahan I, Critzer FJ. Persistence of Listeria innocua on Fresh Apples during Long-Term Controlled Atmosphere Cold Storage with Postharvest Fungal Decay. J Food Prot 2022; 85:133-141. [PMID: 34499733 DOI: 10.4315/jfp-21-232] [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: 06/03/2021] [Accepted: 09/03/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Recent apple-related recall and outbreak events have exposed a need for better food safety controls along the supply chain. Following harvest, apples can be stored under a controlled atmosphere for up to 1 year after harvest before packing and distribution, making the crop susceptible to many opportunities for contamination that increase the quantity of postharvest losses. Botrytis cinerea and Penicillium expansum cause significant rot-associated losses to the apple industry. These fungi can colonize and destroy apple tissue as storage duration increases, which may also impact the growth of saprophytic foodborne pathogens like Listeria monocytogenes. Thus, the objective of this study was to observe population changes of Listeria innocua as a surrogate for L. monocytogenes on apples inoculated with B. cinerea or P. expansum under long-term controlled atmosphere cold storage conditions to identify the effect of postharvest mold growth on growth patterns of a microorganism relevant to food safety. 'Gala' and 'WA 38' apples (n = 1,080) were harvested, treated with pyrimethanil, and inoculated with L. innocua only or with L. innocua and one of the mold species on wounded and unwounded portions of the apple equator. Apples were treated with 1-methylcyclopropene and stored at a controlled atmosphere (2 kPa O2, 1 kPa CO2, 1°C) for 1 week and 1, 3, 6, 9, and 11 months before enumeration. After 3 months, L. innocua consistently fell below the limit of detection (2.35 Log CFU/g), and samples were enriched following a modified Bacteriological Analytical Manual method with PCR confirmation. Listeria persistence was dependent on the storage duration and type of fungal contamination (P ≤ 0.05). Surface wounding may impact these trends, depending on the apple variety. Prevalence of L. innocua was greater in Gala apples. Future studies should more closely examine the interactions on the fruit surface that occur during the seemingly critical time frame of 3 to 6 months in storage. HIGHLIGHTS
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Affiliation(s)
- Alexis Hamilton
- School of Food Science, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, Washington 99350
| | - Blanca Ruiz-Llacsahuanga
- School of Food Science, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, Washington 99350
| | - Manoella Mendoza
- Washington Tree Fruit Research Commission, 1719 Springwater Avenue, Wenatchee, Washington 98801
| | - James Mattheis
- U.S. Department of Agriculture, Agricultural Research Service, Physiology and Pathology of Tree Fruits Research Unit, 1104 North Western Avenue, Wenatchee, Washington 98801, USA
| | - Ines Hanrahan
- Washington Tree Fruit Research Commission, 1719 Springwater Avenue, Wenatchee, Washington 98801
| | - Faith J Critzer
- School of Food Science, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, Washington 99350
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8
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Mango Endophyte and Epiphyte Microbiome Composition during Fruit Development and Post-Harvest Stages. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7110495] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The influence of the development stage and post-harvest handling on the microbial composition of mango fruit plays a central role in fruit health. Hence, the composition of fungal and bacterial microbiota on the anthoplane, fructoplane, stems and stem-end pulp of mango during fruit development and post-harvest handling were determined using next-generation sequencing of the internal transcribed spacer and 16S rRNA regions. At full bloom, the inflorescence had the richest fungal and bacterial communities. The young developing fruit exhibited lower fungal richness and diversities in comparison to the intermediate and fully developed fruit stages on the fructoplane. At the post-harvest stage, lower fungal and bacterial diversities were observed following prochloraz treatment both on the fructoplane and stem-end pulp. Ascomycota (52.8%) and Basidiomycota (43.2%) were the most dominant fungal phyla, while Penicillium, Botryosphaeria, Alternaria and Mucor were detected as the known post-harvest decay-causing fungal genera. The Cyanobacteria (35.6%), Firmicutes (26.1%) and Proteobacteria (23.1%) were the most dominant bacterial phyla. Changes in the presence of Bacillus subtilis following post-harvest interventions such as prochloraz suggested a non-target effect of the fungicide. The present study, therefore, provides the primary baseline data on mango fungal and bacterial diversity and composition, which can be foundational in the development of effective disease (stem-end rot) management strategies.
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Khwantongyim P, Wansee S, Lu X, Zhang W, Sun G. Variations in the Community Structure of Fungal Microbiota Associated with Apple Fruit Shaped by Fruit Bagging-Based Practice. J Fungi (Basel) 2021; 7:jof7090764. [PMID: 34575802 PMCID: PMC8470174 DOI: 10.3390/jof7090764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/05/2021] [Accepted: 09/13/2021] [Indexed: 11/26/2022] Open
Abstract
The various fungal communities that adhere to apple fruit are influenced by agricultural practices. However, the effects of fruit bagging-based management practice on the fungal microbiota are still unknown, and little is known about the fungal communities of bagged apple fruit. We conducted a study using apple fruit grown in a conventionally managed orchard where pesticide use is an indispensable practice. Fungal communities were collected from the calyx-end and peel tissues of bagged and unbagged fruit and characterized using barcode-type next-generation sequencing. Fruit bagging had a stronger effect on fungal richness, abundance, and diversity of the fungal microbiota in comparison to non-bagging. In addition, bagging also impacted the compositional variation of the fungal communities inhabiting each fruit part. We observed that fruit bagging had a tendency to maintain ecological equilibrium since Ascomycota and Basidiomycota were more distributed in bagged fruit than in unbagged fruit. These fungal communities consist of beneficial fungi rather than potentially harmful fungi. Approximately 50 dominant taxa were detected in bagged fruit, for example, beneficial genera such as Articulospora, Bullera, Cryptococcus, Dioszegia, Erythrobasidium, and Sporobolomyces, as well as pathogenic genera such as Aureobasidium and Taphrina. These results suggested that fruit bagging could significantly increase fungal richness and promote healthy fungal communities, especially the harmless fungal communities, which might be helpful for protecting fruit from the effects of pathogens. This study provides a foundation for understanding the impacts of bagging-based practice on the associated fungal microbiota.
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10
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Surface fungal community diversity change and potential pathogens of Ginkgo biloba seed during cold storage. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.100981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Wu L, Li Z, Zhao F, Zhao B, Phillip FO, Feng J, Liu H, Yu K. Increased Organic Fertilizer and Reduced Chemical Fertilizer Increased Fungal Diversity and the Abundance of Beneficial Fungi on the Grape Berry Surface in Arid Areas. Front Microbiol 2021; 12:628503. [PMID: 34025598 PMCID: PMC8139630 DOI: 10.3389/fmicb.2021.628503] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/12/2021] [Indexed: 01/23/2023] Open
Abstract
Fertilizer practices can significantly impact the fruit quality and microbial diversity of the orchards. The fungi on the surface of fruits are essential for fruit storability and safety. However, it is not clear whether fertilization affects the fungal diversity and community structure on the surface of grape berries. Here, grape quality and the fungal diversity on the surface of grapes harvested from three fertilizer treatments were analyzed shortly after grape picking (T0) and following 8 days of storage (T1). The study involved three treatments: (1) common chemical fertilizer for 2 years (CH); (2) increased organic fertilizer and reduced chemical fertilizer for 1 year (A.O); and (3) increased organic fertilizer and reduced chemical fertilizer for 2 years (B.O). The application of increased organic fertilizer and reduced chemical fertilizer increased the soluble solids content (SSC) of the grape berries and decreased the pH of the grape juice. A total of 827,947 high-quality fungal sequences were recovered and assigned to 527 operational taxonomic units. Members of the Ascomycota phylum were dominant in all samples and accounted for 94.41% of the total number of detected sequences, followed by the Basidiomycota (5.05%), and unidentified fungi (0.54%). Alpha and beta diversity analyses revealed significantly different fungal populations in the three fertilizer treatments over the two time periods. The fungal diversity and richness on the grape berry surface in the B.O and A.O treatments were higher than those in the CH treatment. Among the detected fungi, the B.O treatments were mainly Pichia, Aureobasidium, and Candida genera, while the CH treatments were Botrytis, Aspergillus, and Penicillium. Moreover, significant differences were revealed between the two assessment times (T0 and T1). The samples from the T0 timepoint had higher fungal richness and diversity than the samples from T1 timepoint. Increasing organic fertilizer usage in grape management could improve grape quality and went on to increase the fungal diversity, as well as the relative abundance (RA) of beneficial fungi on grape berry surfaces. The correlation analysis suggested that the pH of the grape juice was significantly negatively correlated with fungal diversity parameters.
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Affiliation(s)
- Linnan Wu
- Department of Horticulture, College of Agriculture, The Key Laboratory of Characteristics of Fruit and Vegetable Cultivation and Utilization of Germoplasm Resources of the Xinjiang Production and Construction Crops, Shihezi University, Shihezi, China
| | - Zhiqiang Li
- Shihezi Academy of Agricultural Sciences, Shihezi, China
| | - Fengyun Zhao
- Department of Horticulture, College of Agriculture, The Key Laboratory of Characteristics of Fruit and Vegetable Cultivation and Utilization of Germoplasm Resources of the Xinjiang Production and Construction Crops, Shihezi University, Shihezi, China
| | - Benzhou Zhao
- Department of Horticulture, College of Agriculture, The Key Laboratory of Characteristics of Fruit and Vegetable Cultivation and Utilization of Germoplasm Resources of the Xinjiang Production and Construction Crops, Shihezi University, Shihezi, China
| | - Fesobi Olumide Phillip
- Department of Horticulture, College of Agriculture, The Key Laboratory of Characteristics of Fruit and Vegetable Cultivation and Utilization of Germoplasm Resources of the Xinjiang Production and Construction Crops, Shihezi University, Shihezi, China
| | - Jianrong Feng
- Department of Horticulture, College of Agriculture, The Key Laboratory of Characteristics of Fruit and Vegetable Cultivation and Utilization of Germoplasm Resources of the Xinjiang Production and Construction Crops, Shihezi University, Shihezi, China
| | - Huaifeng Liu
- Department of Horticulture, College of Agriculture, The Key Laboratory of Characteristics of Fruit and Vegetable Cultivation and Utilization of Germoplasm Resources of the Xinjiang Production and Construction Crops, Shihezi University, Shihezi, China
| | - Kun Yu
- Department of Horticulture, College of Agriculture, The Key Laboratory of Characteristics of Fruit and Vegetable Cultivation and Utilization of Germoplasm Resources of the Xinjiang Production and Construction Crops, Shihezi University, Shihezi, China
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12
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Al Riachy R, Strub C, Durand N, Guibert B, Guichard H, Constancias F, Chochois V, Lopez-Lauri F, Fontana A, Schorr-Galindo S. Microbiome Status of Cider-Apples, from Orchard to Processing, with a Special Focus on Penicillium expansum Occurrence and Patulin Contamination. J Fungi (Basel) 2021; 7:jof7040244. [PMID: 33805022 PMCID: PMC8063962 DOI: 10.3390/jof7040244] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/15/2021] [Accepted: 03/19/2021] [Indexed: 11/22/2022] Open
Abstract
Patulin is a secondary metabolite produced primarily by the fungus Penicillium expansum, responsible for the blue mold disease on apples. It is found in apple products including apple cider when apple juice is added after fermentation. In the present study, two hundred and twenty-five cider-apples of the variety “Bedan”, cultivated in Brittany in France, were sampled from the orchard during harvesting until the storage step, right before processing. The patulin analysis on these samples reported a low contamination at the orchard and a significantly higher-level of contamination in the cider-apples starting from the transporting bin. The percentage of positive samples increased from 6% to 47% after 12 h in the harvesting bin before transporting and reached 95% after 24 h of transporting, decreasing then to 69% at the end of the storage. Penicillium expansum was quantified on the surface of apples using real-time PCR and was observed to be mostly consistent between the harvest and post-harvest steps. It was detected on average, on the surface of 85% of all sampled apples with a mean value around 2.35 × 106Penicillium expansum DNA/g of apple. Moreover, the changes in the fungal and bacterial epiphytic microbiota in the different steps were studied using a metabarcoding approach. The alpha and beta diversity analysis revealed the presence of unique and more diverse bacterial and fungal communities on the surface of apples picked from the orchard compared to the rest of the sampling steps. Potential indigenous biological control agents were identified on the surface of sampled apples. Future perspective includes developing actions of prevention and control of the contamination by Penicillium expansum during the harvest and along the various critical post-harvest stages before transformation in a sustainable development concern.
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Affiliation(s)
- Reem Al Riachy
- Qualisud, Univ Montpellier, CIRAD, Univ d’Avignon, Institut Agro, IRD, Univ de La Réunion, F-34398 Montpellier, France; (N.D.); (B.G.); (F.C.); (V.C.); (F.L.-L.); (A.F.); (S.S.-G.)
- Correspondence: (R.A.R.); (C.S.)
| | - Caroline Strub
- Qualisud, Univ Montpellier, CIRAD, Univ d’Avignon, Institut Agro, IRD, Univ de La Réunion, F-34398 Montpellier, France; (N.D.); (B.G.); (F.C.); (V.C.); (F.L.-L.); (A.F.); (S.S.-G.)
- Correspondence: (R.A.R.); (C.S.)
| | - Noël Durand
- Qualisud, Univ Montpellier, CIRAD, Univ d’Avignon, Institut Agro, IRD, Univ de La Réunion, F-34398 Montpellier, France; (N.D.); (B.G.); (F.C.); (V.C.); (F.L.-L.); (A.F.); (S.S.-G.)
- CIRAD, UMR Qualisud, F-34398 Montpellier, France
| | - Benjamin Guibert
- Qualisud, Univ Montpellier, CIRAD, Univ d’Avignon, Institut Agro, IRD, Univ de La Réunion, F-34398 Montpellier, France; (N.D.); (B.G.); (F.C.); (V.C.); (F.L.-L.); (A.F.); (S.S.-G.)
- CIRAD, UMR Qualisud, F-34398 Montpellier, France
| | - Hugues Guichard
- French Institute for Cider Production (IFPC), Domaine de la Motte, F-35653 Le Rheu, France;
| | - Florentin Constancias
- Qualisud, Univ Montpellier, CIRAD, Univ d’Avignon, Institut Agro, IRD, Univ de La Réunion, F-34398 Montpellier, France; (N.D.); (B.G.); (F.C.); (V.C.); (F.L.-L.); (A.F.); (S.S.-G.)
- CIRAD, UMR Qualisud, F-34398 Montpellier, France
| | - Vincent Chochois
- Qualisud, Univ Montpellier, CIRAD, Univ d’Avignon, Institut Agro, IRD, Univ de La Réunion, F-34398 Montpellier, France; (N.D.); (B.G.); (F.C.); (V.C.); (F.L.-L.); (A.F.); (S.S.-G.)
- CIRAD, UMR Qualisud, F-34398 Montpellier, France
| | - Félicie Lopez-Lauri
- Qualisud, Univ Montpellier, CIRAD, Univ d’Avignon, Institut Agro, IRD, Univ de La Réunion, F-34398 Montpellier, France; (N.D.); (B.G.); (F.C.); (V.C.); (F.L.-L.); (A.F.); (S.S.-G.)
| | - Angélique Fontana
- Qualisud, Univ Montpellier, CIRAD, Univ d’Avignon, Institut Agro, IRD, Univ de La Réunion, F-34398 Montpellier, France; (N.D.); (B.G.); (F.C.); (V.C.); (F.L.-L.); (A.F.); (S.S.-G.)
| | - Sabine Schorr-Galindo
- Qualisud, Univ Montpellier, CIRAD, Univ d’Avignon, Institut Agro, IRD, Univ de La Réunion, F-34398 Montpellier, France; (N.D.); (B.G.); (F.C.); (V.C.); (F.L.-L.); (A.F.); (S.S.-G.)
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Taîbi A, Rivallan R, Broussolle V, Pallet D, Lortal S, Meile JC, Constancias F. Terroir Is the Main Driver of the Epiphytic Bacterial and Fungal Communities of Mango Carposphere in Reunion Island. Front Microbiol 2021; 11:619226. [PMID: 33584584 PMCID: PMC7874004 DOI: 10.3389/fmicb.2020.619226] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/18/2020] [Indexed: 12/22/2022] Open
Abstract
The diversity of both bacterial and fungal communities associated with mango surface was explored using a metabarcoding approach targeting fungal ITS2 and bacterial 16S (V3-V4) genomic regions. Fruits were collected in Reunion Island from two different orchards according to a sampling method which allowed the effect of several pre-harvest factors such as geographical location (terroir), cultivars, fruit parts, tree position in the plot, fruit position on the tree (orientation and height), as well as the harvest date to be investigated. A total of 4,266,546 fungal and 2,049,919 bacterial reads were recovered then respectively assigned to 3,153 fungal and 24,087 to bacterial amplicon sequence variants (ASVs). Alpha and beta diversity, as well as differential abundance analyses revealed variations in both bacterial and fungal communities detected on mango surfaces depended upon the studied factor. Results indicated that Burkholderiaceae (58.8%), Enterobacteriaceae (5.2%), Pseudomonadaceae (4.8%), Sphingomonadaceae (4.1%), Beijerinckiaceae (3.5%), and Microbacteriaceae (3.1%) were the dominant bacterial families across all samples. The majority of fungal sequences were assigned to Mycosphaerellaceae (34.5%), Cladosporiaceae (23.21%), Aureobasidiaceae (13.09%), Pleosporaceae (6.92%), Trichosphaeriaceae (5.17%), and Microstromatales_fam_Incertae_sedis (4.67%). For each studied location, mango fruit from each cultivar shared a core microbiome, and fruits of the same cultivar harvested in two different locations shared about 80% fungal and bacterial family taxa. The various factors tested in this study affected bacterial and fungal taxa differently, suggesting that some taxa could act as geographical (terroir) markers and in some cases as cultivar fingerprints. The ranking of the factors investigated in the present study showed that in decreasing order of importance: the plot (terroir), cultivar, fruit parts, harvest date and the position of the fruits are respectively the most impacting factors of the microbial flora, when compared to the orientation and the fruit position (height) on the tree. Overall, these findings provided insights on both bacterial and fungal diversity associated with the mango surface, their patterns from intra-fruit scale to local scale and the potential parameters shaping the mango microbiota.
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Affiliation(s)
- Ahmed Taîbi
- CIRAD, UMR Qualisud, Saint-Pierre, France
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, Université de La Réunion, Montpellier, France
| | - Ronan Rivallan
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Véronique Broussolle
- INRAE, Avignon Université, Sécurité et Qualité des Produits d’Origine Végétale, Avignon, France
| | - Dominique Pallet
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, Université de La Réunion, Montpellier, France
- CIRAD, UMR Qualisud, Montpellier, France
| | - Sylvie Lortal
- INRAE, Département Microbiologie et Chaine alimentaire, Jouy-en-Josas, France
| | - Jean-Christophe Meile
- CIRAD, UMR Qualisud, Saint-Pierre, France
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, Université de La Réunion, Montpellier, France
| | - Florentin Constancias
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, Université de La Réunion, Montpellier, France
- CIRAD, UMR Qualisud, Montpellier, France
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14
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15
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Jose PA, Krishnamoorthy R, Gandhi PI, Senthilkumar M, Janahiraman V, Kumutha K, Choudhury AR, Samaddar S, Anandham R, Sa T. Endomicrobial Community Profiles of Two Different Mealybugs: Paracoccus marginatus and Ferrisia virgata. J Microbiol Biotechnol 2020; 30:1013-1017. [PMID: 32238776 PMCID: PMC9728186 DOI: 10.4014/jmb.2001.01016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/31/2020] [Indexed: 12/15/2022]
Abstract
Mealybugs (Hemiptera: Coccomorpha: Pseudococcidae) harbour diverse microbial symbionts that play essential roles in host physiology, ecology, and evolution. In this study we aimed to reveal microbial communities associated with two different mealybugs, papaya mealybug (Paracoccus marginatus) and two-tailed mealybug (Ferrisia virgata) collected from the same host plant. Comparative analysis of microbial communities associated with these mealybugs revealed differences that appear to stem from phylogenetic associations and different nutritional requirements. This first report on both bacterial and fungal communities associated with these mealybugs provides a preliminary insight on factors affecting the endomicrobial communities. .
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Affiliation(s)
- Polpass Arul Jose
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Madurai, Tamil Nadu Agricultural University, Tamil Nadu, India
| | - Ramasamy Krishnamoorthy
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Madurai, Tamil Nadu Agricultural University, Tamil Nadu, India
| | - Pandiyan Indira Gandhi
- Regional Research Station, Vridhachalam, Tamil Nadu Agricultural University, Tamil Nadu, India
| | - Murugaiyan Senthilkumar
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Veeranan Janahiraman
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Madurai, Tamil Nadu Agricultural University, Tamil Nadu, India
| | - Karunandham Kumutha
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Madurai, Tamil Nadu Agricultural University, Tamil Nadu, India
| | - Aritra Roy Choudhury
- Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Sandipan Samaddar
- Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Rangasamy Anandham
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Madurai, Tamil Nadu Agricultural University, Tamil Nadu, India,Corresponding authors T.S. Phone: +82-43-261-2561 Fax: +82-43-271-5921 E-mail:
| | - Tongmin Sa
- Department of Environmental and Biological Chemistry, Chungbuk National University, Cheongju 28644, Republic of Korea,Corresponding authors T.S. Phone: +82-43-261-2561 Fax: +82-43-271-5921 E-mail:
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16
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Shen Y, Nie J, Kuang L, Zhang J, Li H. DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables. Microb Biotechnol 2020; 14:323-362. [PMID: 32207561 PMCID: PMC7936329 DOI: 10.1111/1751-7915.13560] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/20/2022] Open
Abstract
The development of DNA sequencing technology has provided an effective method for studying foodborne and phytopathogenic microorganisms on fruits and vegetables (F & V). DNA sequencing has successfully proceeded through three generations, including the tens of operating platforms. These advances have significantly promoted microbial whole‐genome sequencing (WGS) and DNA polymorphism research. Based on genomic and regional polymorphisms, genetic markers have been widely obtained. These molecular markers are used as targets for PCR or chip analyses to detect microbes at the genetic level. Furthermore, metagenomic analyses conducted by sequencing the hypervariable regions of ribosomal DNA (rDNA) have revealed comprehensive microbial communities in various studies on F & V. This review highlights the basic principles of three generations of DNA sequencing, and summarizes the WGS studies of and available DNA markers for major bacterial foodborne pathogens and phytopathogenic fungi found on F & V. In addition, rDNA sequencing‐based bacterial and fungal metagenomics are summarized under three topics. These findings deepen the understanding of DNA sequencing and its application in studies of foodborne and phytopathogenic microbes and shed light on strategies for the monitoring of F & V microbes and quality control.
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Affiliation(s)
- Youming Shen
- 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, 125100, China
| | - Jiyun Nie
- 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, 125100, China.,College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lixue Kuang
- 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, 125100, China
| | - Jianyi Zhang
- 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, 125100, China
| | - Haifei Li
- 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, 125100, China
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17
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Arrigoni E, Albanese D, Longa CMO, Angeli D, Donati C, Ioriatti C, Pertot I, Perazzolli M. Tissue age, orchard location and disease management influence the composition of fungal and bacterial communities present on the bark of apple trees. Environ Microbiol 2020; 22:2080-2093. [PMID: 32114708 DOI: 10.1111/1462-2920.14963] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 01/09/2023]
Abstract
Plants host microbial communities that can be affected by environmental conditions and agronomic practices. Despite the role of bark as a reservoir of plant pathogens and beneficial microorganisms, no information is available on the effects of disease management on the taxonomic composition of the bark-associated communities of apple trees. We assessed the impact of disease management strategies on fungal and bacterial communities on the bark of a scab-resistant apple cultivar in two orchard locations and for two consecutive seasons. The amplicon sequencing revealed that bark age and orchard location strongly affected fungal and bacterial diversity. Microbiota dissimilarity between orchards evolved during the growing season and showed specific temporal series for fungal and bacterial populations in old and young bark. Disease management did not induce global changes in the microbial populations across locations and seasons, but specifically affected the abundance of some taxa according to bark age, orchard location and sampling time. Therefore, the disease management applied to scab-resistant cultivars, which is based on a limited use of fungicides, partially changed the taxonomic composition of bark-associated fungal and bacterial communities, suggesting the need for a more accurate risk assessment regarding possible pathogen outbreaks.
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Affiliation(s)
- Elena Arrigoni
- Research and Innovation Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy.,Department of Agricultural and Environmental Sciences, University of Udine, 33100, Udine, Italy
| | - Davide Albanese
- Research and Innovation Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy
| | | | - Dario Angeli
- Technology Transfer Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy
| | - Claudio Donati
- Research and Innovation Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy
| | - Claudio Ioriatti
- Technology Transfer Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy
| | - Ilaria Pertot
- Research and Innovation Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy.,Center Agriculture Food Environment (C3A), University of Trento, 38010, San Michele all'Adige, Italy
| | - Michele Perazzolli
- Research and Innovation Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy.,Center Agriculture Food Environment (C3A), University of Trento, 38010, San Michele all'Adige, Italy
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18
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Sare AR, Stouvenakers G, Eck M, Lampens A, Goormachtig S, Jijakli MH, Massart S. Standardization of Plant Microbiome Studies: Which Proportion of the Microbiota is Really Harvested? Microorganisms 2020; 8:microorganisms8030342. [PMID: 32121205 PMCID: PMC7142977 DOI: 10.3390/microorganisms8030342] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/14/2020] [Accepted: 02/25/2020] [Indexed: 12/13/2022] Open
Abstract
Studies in plant-microbiome currently use diverse protocols, making their comparison difficult and biased. Research in human microbiome have faced similar challenges, but the scientific community proposed various recommendations which could also be applied to phytobiome studies. Here, we addressed the isolation of plant microbiota through apple carposphere and lettuce root microbiome. We demonstrated that the fraction of the culturable epiphytic microbiota harvested by a single wash might only represent one-third of the residing microbiota harvested after four successive washes. In addition, we observed important variability between the efficiency of washing protocols (up to 1.6-fold difference for apple and 1.9 for lettuce). QIIME2 analysis of 16S rRNA gene, showed a significant difference of the alpha and beta diversity between protocols in both cases. The abundance of 76 taxa was significantly different between protocols used for apple. In both cases, differences between protocols disappeared when sequences of the four washes were pooled. Hence, pooling the four successive washes increased the alpha diversity for apple in comparison to a single wash. These results underline the interest of repeated washing to leverage abundance of microbial cells harvested from plant epiphytic microbiota whatever the washing protocols, thus minimizing bias.
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Affiliation(s)
- Abdoul Razack Sare
- Laboratory of Integrated and Urban Phytopathology, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; (G.S.); (M.E.); (M.H.J.); (S.M.)
- Correspondence:
| | - Gilles Stouvenakers
- Laboratory of Integrated and Urban Phytopathology, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; (G.S.); (M.E.); (M.H.J.); (S.M.)
| | - Mathilde Eck
- Laboratory of Integrated and Urban Phytopathology, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; (G.S.); (M.E.); (M.H.J.); (S.M.)
| | - Amber Lampens
- VIB-UGent Center of Plant Systems Biology, 9052 Ghent, Belgium; (A.L.); (S.G.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Sofie Goormachtig
- VIB-UGent Center of Plant Systems Biology, 9052 Ghent, Belgium; (A.L.); (S.G.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - M. Haïssam Jijakli
- Laboratory of Integrated and Urban Phytopathology, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; (G.S.); (M.E.); (M.H.J.); (S.M.)
| | - Sebastien Massart
- Laboratory of Integrated and Urban Phytopathology, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; (G.S.); (M.E.); (M.H.J.); (S.M.)
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19
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Almeida OGG, Pinto UM, Matos CB, Frazilio DA, Braga VF, von Zeska-Kress MR, De Martinis ECP. Does Quorum Sensing play a role in microbial shifts along spontaneous fermentation of cocoa beans? An in silico perspective. Food Res Int 2020; 131:109034. [PMID: 32247478 DOI: 10.1016/j.foodres.2020.109034] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/20/2020] [Accepted: 01/24/2020] [Indexed: 12/20/2022]
Abstract
Cocoa fermentation is a spontaneous process shaped by a variable microbial ecosystem which is assembled due to cross-feeding relationship among yeasts and bacteria, resulting in a synchronized microbial succession started by yeasts, followed by lactic acid bacteria (LAB) and finalized by acetic acid bacteria (AAB). Several studies have indicated the effect of microbial interactions in food ecosystems highlighting the importance of quorum sensing (QS) in bacterial adaptation in harsh environments modulating several phenotypes such as biofilm formation, tolerance to acid stress, bacteriocin production, competence, morphological modifications, motility, among others. However, antagonic interactions also occur, and can be marked by Quorum Quenching (QQ) activity, negatively impacting QS regulated phenotypes. Our current knowledge regarding microbial cocoa composition and functioning is based on culture-based analysis and culture-independent PCR-based methods. Therefore, we set out to investigate the application of metagenomics analysis on a classical spontaneous cocoa fermentation in order to describe: (I) the microbial taxonomic composition; (II) the functional potential of the cocoa microbiome; (III) the microbiome putative QS potential; and (IV) the microbiome QQ potential. Both aims III and IV are related to the expression of effectors that may confer advantageous traits along fermentation which can explain their dominance in specific time zones during the entire process. We have observed a bacterial succession shaped by yeasts and filamentous fungi and then Enterobacteriaceales, LAB and AAB, as well as a diverse genetic metabolic potential related to proteins and carbohydrates metabolism associated to the yeast Saccharomyces cerevisiae and members of the Enterobacteriaceales order and LAB and AAB groups. In addition, in silico evidences of interspecific QS arsenal were found in members of the genera Enterobacter, Lactobacillus, Bacillus and Pantoea, while inferences of intraspecific QS potential were found in the members of the genera Bacillus, Enterobacter, Komagataeibacter, Lactobacillus and Pantoea. In addition, a QQ potential was detected in Lactobacillus and in AAB members. These findings indicate that QS and QQ may modulate bacterial dominance in different time points during fermentation, along with cross-feeding, being responsible for their maintenance in a large time range.
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Affiliation(s)
- O G G Almeida
- Universidade de São Paulo - Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Brazil
| | - U M Pinto
- Food Research Center, Universidade de São Paulo - Faculdade de Ciências Farmacêuticas, Brazil
| | - C B Matos
- Comissão Executiva do Plano da Lavoura Cacaueira- Centro de Pesquisas do Cacau (CEPLAC-CEPEC), Rod. Jorge Amado, 22 - Alto Mirante, Itabuna, BA, Brazil
| | - D A Frazilio
- Universidade de São Paulo - Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Brazil
| | - V F Braga
- Universidade de São Paulo - Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Brazil
| | - M R von Zeska-Kress
- Universidade de São Paulo - Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Brazil
| | - E C P De Martinis
- Universidade de São Paulo - Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Brazil.
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20
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Cruz AF, Barka GD, Blum LEB, Tanaka T, Ono N, Kanaya S, Reineke A. Evaluation of microbial communities in peels of Brazilian tropical fruits by amplicon sequence analysis. Braz J Microbiol 2019; 50:739-748. [PMID: 31073985 PMCID: PMC6863208 DOI: 10.1007/s42770-019-00088-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 03/20/2019] [Indexed: 10/26/2022] Open
Abstract
Elucidation of the distinctive microbial taxonomic profiles of tropical fruit peels is the indispensable component of investigations aimed at the detection of microorganisms responsible for the post-harvest loss. The objective of the present work was to dissect the bacterial and fungal community of five tropical fruit peels (banana, guava, mango, papaya, and passion fruit) in wild (non-cultivated) and conventionally produced samples from Brazil. To that end, 16S rRNA-encoding gene and ITS rDNA amplicon analysis of the five tropical fruit peels were performed to discriminate the bacterial and fungal communities, respectively. The result showed that bacterial communities of the five types of fruit peels were by far more diversified than that of fungal communities, independent of the type of production system involved. Among the investigated fruits, non-cultivated papaya peels hosted the most diversified bacterial community while the least bacterial community diversity was found in the conventionally produced papaya fruit peels. The gene amplicon analysis clearly discriminated the bacterial community into their respective classes, while fungal communities were better classified in their phyla, yet with clearer component discrimination of fungal community based on the type of cultivation system practiced. Conventionally produced banana and non-cultivated passion fruit peels were characteristically dominated by fungal and bacterial groups, respectively. Overall, in conventionally produced fruit peels, bacterial community was mainly composed of Proteobacteria, Actinobacteria, and Bacilli. The result provided a broad microbial diversity profile that could be used as an important input for seeking alternative fruit spoilage control and post-harvest treatments.
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Affiliation(s)
- André Freire Cruz
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - Geleta Dugassa Barka
- Applied Biology Department, Adama Science and Technology University, Adama, Oromia, Ethiopia.
| | | | - Tetsushi Tanaka
- Division of Information Science, Nara Institute of Science and Technology, Nara, Japan
| | - Naoaki Ono
- Division of Information Science, Nara Institute of Science and Technology, Nara, Japan
| | - Shigehiko Kanaya
- Division of Information Science, Nara Institute of Science and Technology, Nara, Japan
| | - Annette Reineke
- Department of Crop Protection, Geisenheim University, Geisenheim, Germany
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21
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Ghani MI, Ali A, Atif MJ, Ali M, Amin B, Anees M, Khurshid H, Cheng Z. Changes in the Soil Microbiome in Eggplant Monoculture Revealed by High-Throughput Illumina MiSeq Sequencing as Influenced by Raw Garlic Stalk Amendment. Int J Mol Sci 2019; 20:ijms20092125. [PMID: 31036790 PMCID: PMC6539610 DOI: 10.3390/ijms20092125] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/19/2019] [Accepted: 04/24/2019] [Indexed: 11/16/2022] Open
Abstract
The incorporation of plant residues into soil can be considered a keystone sustainability factor in improving soil structure function. However, the effects of plant residue addition on the soil microbial communities involved in biochemical cycles and abiotic stress phenomena are poorly understood. In this study, experiments were conducted to evaluate the role of raw garlic stalk (RGS) amendment in avoiding monoculture-related production constraints by studying the changes in soil chemical properties and microbial community structures. RGS was applied in four different doses, namely the control (RGS0), 1% (RGS1), 3% (RGS2), and 5% (RGS3) per 100 g of soil. The RGS amendment significantly increased soil electrical conductivity (EC), N, P, K, and enzyme activity. The soil pH significantly decreased with RGS application. High-throughput Illumina MiSeq sequencing revealed significant alterations in bacterial community structures in response to RGS application. Among the 23 major taxa detected, Anaerolineaceae, Acidobacteria, and Cyanobacteria exhibited an increased abundance level. RGS2 increased some bacteria reported to be beneficial including Acidobacteria, Bacillus, and Planctomyces (by 42%, 64%, and 1% respectively). Furthermore, internal transcribed spacer (ITS) fungal regions revealed significant diversity among the different treatments, with taxa such as Chaetomium (56.2%), Acremonium (4.3%), Fusarium (4%), Aspergillus (3.4%), Sordariomycetes (3%), and Plectosphaerellaceae (2%) showing much abundance. Interestingly, Coprinellus (14%) was observed only in RGS-amended soil. RGS treatments effectively altered soil fungal community structures and reduced certain known pathogenic fungal genera, i.e., Fusarium and Acremonium. The results of the present study suggest that RGS amendment potentially affects the microbial community structures that probably affect the physiological and morphological attributes of eggplant under a plastic greenhouse vegetable cultivation system (PGVC) in monoculture.
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Affiliation(s)
| | - Ahmad Ali
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Muhammad Jawaad Atif
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
- Vegetable Crops Program, National Agricultural Research Centre, Islamabad 44000, Pakistan.
| | - Muhammad Ali
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Bakht Amin
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Muhammad Anees
- Department of Microbiology, Kohat University of Science & Technology, Kohat 26000, Pakistan.
| | - Haris Khurshid
- Oilseeds Research Program, National Agricultural Research Centre, Islamabad 44000, Pakistan.
| | - Zhihui Cheng
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
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