1
|
Sivaprakasam N, Vaithiyanathan S, Gandhi K, Narayanan S, Kavitha PS, Rajasekaran R, Muthurajan R. Metagenomics approaches in unveiling the dynamics of Plant Growth-Promoting Microorganisms (PGPM) vis-à-vis Phytophthora sp. suppression in various crop ecological systems. Res Microbiol 2024:104217. [PMID: 38857835 DOI: 10.1016/j.resmic.2024.104217] [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: 02/29/2024] [Revised: 05/02/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
Phytophthora species are destructive pathogens causing yield losses in different ecological systems, such as potato, black pepper, pepper, avocado, citrus, and tobacco. The diversity of plant growth-promoting microorganisms (PGPM) plays a crucial role in disease suppression. Knowledge of metagenomics approaches is essential for assessing the dynamics of PGPM and Phytophthora species across various ecosystems, facilitating effective management strategies for better crop protection. This review discusses the dynamic interplay between PGPM and Phytophthora sp. using metagenomics approaches that sheds light on the potential of PGPM strains tailored to specific crop ecosystems to bolster pathogen suppressiveness.
Collapse
Affiliation(s)
- Navarasu Sivaprakasam
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | | | - Karthikeyan Gandhi
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Swarnakumari Narayanan
- Department of Nematology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - P S Kavitha
- School of Post Graduate Studies, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raghu Rajasekaran
- Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raveendran Muthurajan
- Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| |
Collapse
|
2
|
Wei G, Liang Y, Zhang G, Zhang Z, Zhang Y, Chen S, Dong L. Influence of sampling location and processing on the assembly and network of Polygoni Multiflori Radix surface microbiome. Int J Food Microbiol 2024; 410:110442. [PMID: 37984213 DOI: 10.1016/j.ijfoodmicro.2023.110442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 08/24/2023] [Accepted: 10/07/2023] [Indexed: 11/22/2023]
Abstract
The raw and processed roots of Polygonum multiflorum Thunb is a popular traditional Chinese medicine. However, Polygoni Multiflori Radix is easily contaminated by toxigenic fungi and mycotoxins during harvesting, processing, and transportation, thereby posing a health risk for consumers. This study aims to investigate the presence of fungi on the surface of raw and processed Polygoni Multiflori Radix collected from four producing areas using high-throughput sequencing. Results showed that the phyla Ascomycota and Basidiomycota, the genera Xeromyces, Cystofilobasidium, Eurotium, and Aspergillus were the dominant fungus, and significant differences are presented in four areas and two processed products. Three potential mycotoxin-producing fungi were detected, namely Trichosporon cutaneum, Aspergillus restrictus, and Fusarium oxysporum. The α-diversity and network complexity showed significant differences in four areas. Chao 1 and Shannon were highest in Yunnan (YN), then incrementally decreased from SC (Sichuan) to AH (Anhui) and GD (Guangdong) areas. Meanwhile, α-diversity was also strongly influenced by processing. Chao 1 and Shannon indices were higher in the raw group, however, the network complexity and connectivity were higher in the processed group. In conclusion, the assembly and network of the surface microbiome on Polygoni Multiflori Radix were influenced by sampling location and processing. This work provides details on the surface microbiome of Polygoni Multiflori Radix samples, which could ensure the drug and consumers' safety.
Collapse
Affiliation(s)
- Guangfei Wei
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Yichuan Liang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Guozhuang Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Zhaoyu Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Yongqing Zhang
- Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| |
Collapse
|
3
|
Kim MS, Park EJ. Composition and variability of core phyllosphere fungal mycobiota on field-grown broccoli. ENVIRONMENTAL MICROBIOME 2023; 18:15. [PMID: 36855218 PMCID: PMC9976476 DOI: 10.1186/s40793-023-00474-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Fresh vegetables harbor an assemblage of different microorganisms on their surfaces. The phyllosphere microbiota is important for maintaining plant health and managing crop quality before and after harvest. However, the diversity and ecology of fungal communities are largely unexplored in fresh vegetables. This study investigated the phyllosphere mycobiota of field-grown broccoli florets (n = 66) collected from 22 farms across four regions in Korea, using culturing, amplicon sequencing of the internal transcribed spacer region, and microbial network analysis. RESULTS Microbial network analysis identified core genera (Purpureocillium, Filobasidium, Cystofilobasidium, Papiliotrema, Aureobasidium, and unclassified genera of Capnodiales) specific to the broccoli phyllosphere. The composition and network complexity of core and unique populations varied among farming regions, and was associated with local agro-meteorological conditions. The complexity of microbial associations was higher in mature communities than in immature communities, but complexity was lost upon development of plant pathogenic disease. Broccoli mycobiota were classified according to the dominance of Purpurecillium. While Purpurecillium-type microbiota were prevalent in normal samples, Filobasidium-type microbiota were frequently observed in immature, damaged, or postharvest samples. CONCLUSIONS Together, fungal communities were important components of phyllosphere microbiota on fresh vegetables, and have substantial potential for exploitation to enhance and stabilize plant health and growth.
Collapse
Affiliation(s)
- Min-Soo Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, 99 Daehak-ro, Yuseon-gu, Daejeon, 34134, Republic of Korea.
| | - Eun-Jin Park
- Department of Food Bioengineering, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, Republic of Korea.
| |
Collapse
|
4
|
Liu J, Zhang X, Tian J, Li Y, Liu Q, Chen X, Feng F, Yu X, Yang C. Multiomics analysis reveals that peach gum colouring reflects plant defense responses against pathogenic fungi. Food Chem 2022; 383:132424. [PMID: 35182869 DOI: 10.1016/j.foodchem.2022.132424] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/22/2021] [Accepted: 02/08/2022] [Indexed: 11/29/2022]
Abstract
In the present study, the differences in the antioxidant capability, metabolite composition and fungal diversity in peach gum with various colours were investigated. Metabolomics revealed that peach gum comprised many small-molecule metabolites (including primary and secondary metabolites), and most polyphenols (such as flavonoids and phenolic acids) showed a significantly positive relationship with the colour deepening, total phenol content and antioxidant capability. Using fungal diversity analysis, the abundance of five fungi at the genus level increased with peach gum colour deepening, and these fungi demonstrated a significantly positive relationship with two defense hormones (salicylic acid and abscisic acid) and most polyphenols (particularly flavonoids). The gummosis pathogenic fungus Botryosphaeria was among the five fungi, suggesting that peach gum colouring may reflect plant defense responses against pathogenic fungi. Additionally, the concentrations of 12 flavonoids in peach gum samples were detected based on LC-QQQ/MS, among which hesperetin, naringenin and eriodictyol were the most abundant.
Collapse
Affiliation(s)
- Jia Liu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China; School of Food and Biological Engineering, Jiangsu University, 301 Zhenjiang City University Road, Zhenjiang 212001, China
| | - Xiping Zhang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Ju Tian
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Yong Li
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China; School of Food and Biological Engineering, Jiangsu University, 301 Zhenjiang City University Road, Zhenjiang 212001, China.
| | - Qiyue Liu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Xiaolong Chen
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Fayun Feng
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Xiangyang Yu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China.
| | - Chenye Yang
- Central Laboratory in Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| |
Collapse
|
5
|
The Microbiome of the ‘Williams’ Pear Variety Grown in the Organic Orchard and Antifungal Activity by the Autochthonous Bacterial and Yeast Isolates. Microorganisms 2022; 10:microorganisms10071282. [PMID: 35889000 PMCID: PMC9321879 DOI: 10.3390/microorganisms10071282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 01/04/2023] Open
Abstract
The total diversity of bacterial and fungal communities associated with the phyllosphere (fruits and leaves) of the ‘Williams’ pear variety was analyzed in two phenological stages during fruit development and maturation. The antagonistic potential of autochthonous bacterial and yeast isolates against phytopathogenic fungi was also evaluated. A metabarcoding approach revealed Pantoea, Sphingomonas, Hymenobacter, Massilia, and Pseudomonas as dominant bacterial constituents of the pear phyllosphere, whilst most abundant among the fungal representatives identified were Metschnikowia, Filobasidium, Aureobasidiumpullulans, Botrytis cinerea, and Taphrina. The traditional culturable approach revealed that the Pseudomonas genus with P. graminis, P. putida, and P. congelans was most prevalent. The most frequently cultivated fungal representatives belonged to the genus Fusarium with six identified species. A broad range of the antagonistic activity was detected for the Hannaella luteola and Metschnikowia pulcherrima yeasts, significantly affecting the growth of many fungal isolates in the range of 53–70%. Fusarium sporotrichioides was the most susceptible fungal isolate. The autochthonous antagonistic yeasts H. luteola and M. pulcherrima might be powerful biological control agents of postharvest diseases caused by Fusarium spp. and common pathogens like Monilinia laxa, Botrytis cinerea, Alternaria tenuissima, and Cladosporium cladosporioides.
Collapse
|
6
|
Zhang Y, Gao C, Masum MMI, Cheng Y, Wei C, Guan Y, Guan J. Dynamic Microbiome Changes Reveal the Effect of 1-Methylcyclopropene Treatment on Reducing Post-harvest Fruit Decay in "Doyenne du Comice" Pear. Front Microbiol 2021; 12:729014. [PMID: 34512605 PMCID: PMC8430257 DOI: 10.3389/fmicb.2021.729014] [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: 06/22/2021] [Accepted: 08/02/2021] [Indexed: 11/13/2022] Open
Abstract
Pathogen-induced decay is one of the most common causes of fruit loss, resulting in substantial economic loss and posing a health risk to humans. As an ethylene action inhibitor, 1-methylcyclopropene (1-MCP) can significantly reduce fruit decay, but its effect on fruit pathogens remains unclear. Herein, the change in microbial community structure was analyzed using the high-throughput sequencing technology, and characteristics related to fruit quality were determined after 1-MCP (1.0 M l L-1) treatment in "Doyenne du Comiceis" pear fruit during storage at ambient temperature. Overall, 1-MCP was highly effective in reducing disease incidence and induced multiple changes of the fungal and bacterial microbiota. At day 15, the microbial diversity of fungi or bacteria was reduced significantly in the control fruit (non-treated with 1-MCP), which had the most severe decay incidence. For fungi, in addition to Alternaria being the most abundant in both 1-MCP treatment (59.89%) and control (40.18%), the abundances of Botryosphaeria (16.75%), Penicillium (8.81%), and Fusarium (6.47%) increased significantly with the extension of storage time. They became the primary pathogens to cause fruit decay in control, but they were markedly decreased in 1-MCP treatment, resulting in reduced disease incidence. For bacteria, the abundance of Gluconobacter (50.89%) increased dramatically at day 15 in the control fruit, showing that it also played a crucial role in fruit decay. In addition, Botryosphaeria, Fusarium fungi, and Massilia, Kineococcus bacteria were identified as biomarkers to distinguish 1-MCP treatment and control using Random Forest analysis. The redundancy analysis (RDA) result showed that the amount of Botryosphaeria, Penicillium, and Fusarium were positively correlated with disease incidence and respiration rate of pear fruits while negatively correlated with fruit firmness. This investigation is the first comprehensive analysis of the microbiome response to 1-MCP treatment in post-harvest pear fruit, and reveals the relationship between fruit decay and microbial composition in pear fruit.
Collapse
Affiliation(s)
- Yang Zhang
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Congcong Gao
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Md. Mahidul Islam Masum
- Department of Plant Pathology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Yudou Cheng
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Chuangqi Wei
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Yeqing Guan
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Junfeng Guan
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| |
Collapse
|
7
|
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.
Collapse
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.)
| |
Collapse
|