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Xing B, Zheng Y, Zhang M, Liu X, Li L, Mou C, Wu Q, Guo H, Shao Q. Biocontrol: Endophytic bacteria could be crucial to fight soft rot disease in the rare medicinal herb, Anoectochilus roxburghii. Microb Biotechnol 2022; 15:2929-2941. [PMID: 36099393 PMCID: PMC9733646 DOI: 10.1111/1751-7915.14142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/21/2022] [Accepted: 08/26/2022] [Indexed: 12/14/2022] Open
Abstract
Microbial destabilization induced by pathogen infection has severely affected plant quality and output, such as Anoectochilus roxburghii, an economically important herb. Soft rot is the main disease that occurs during A. roxburghii culturing. However, the key members of pathogens and their interplay with non-detrimental microorganisms in diseased plants remain largely unsolved. Here, by utilizing a molecular ecological network approach, the interactions within bacterial communities in endophytic compartments and the surrounding soils during soft rot infection were investigated. Significant differences in bacterial diversity and community composition between healthy and diseased plants were observed, indicating that the endophytic communities were strongly influenced by pathogen invasion. Endophytic stem communities of the diseased plants were primarily derived from roots and the root endophytes were largely derived from rhizosphere soils, which depicts a possible pathogen migration image from soils to roots and finally the stems. Furthermore, interactions among microbial members indicated that pathogen invasion might be aided by positively correlated native microbial members, such as Enterobacter and Microbacterium, who may assist in colonization and multiplication through a mutualistic relationship in roots during the pathogen infection process. Our findings will help open new avenues for developing more accurate strategies for biological control of A. roxburghii bacterial soft rot disease.
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Affiliation(s)
- Bingcong Xing
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouChina,Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese MedicineZhejiang A&F UniversityHangzhouChina
| | - Ying Zheng
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouChina,Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese MedicineZhejiang A&F UniversityHangzhouChina
| | - Man Zhang
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese MedicineZhejiang A&F UniversityHangzhouChina
| | - Xinting Liu
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouChina,Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese MedicineZhejiang A&F UniversityHangzhouChina
| | - Lihong Li
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouChina,Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese MedicineZhejiang A&F UniversityHangzhouChina
| | - Chenhao Mou
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouChina,Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese MedicineZhejiang A&F UniversityHangzhouChina
| | - Qichao Wu
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouChina,Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese MedicineZhejiang A&F UniversityHangzhouChina
| | - Haipeng Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, School of Marine SciencesNingbo UniversityNingboChina
| | - Qingsong Shao
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouChina,Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese MedicineZhejiang A&F UniversityHangzhouChina
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Fernández Escámez PS, Maradona MP, Querol A, Suarez JE, Sundh I, Vlak J, Barizzone F, Correia S, Herman L. Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 11: suitability of taxonomic units notified to EFSA until September 2019. EFSA J 2020; 18:e05965. [PMID: 32874211 PMCID: PMC7448003 DOI: 10.2903/j.efsa.2020.5965] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Qualified presumption of safety (QPS) was developed to provide a generic safety evaluation for biological agents to support EFSA's Scientific Panels. The taxonomic identity, body of knowledge, safety concerns and antimicrobial resistance are assessed. Safety concerns identified for a taxonomic unit (TU) are where possible to be confirmed at strain or product level, reflected by 'qualifications'. No new information was found that would change the previously recommended QPS TUs and their qualifications. The list of microorganisms notified to EFSA was updated with 54 biological agents, received between April and September 2019; 23 already had QPS status, 14 were excluded from the QPS exercise (7 filamentous fungi, 6 Escherichia coli, Sphingomonas paucimobilis which was already evaluated). Seventeen, corresponding to 16 TUs, were evaluated for possible QPS status, fourteen of these for the first time, and Protaminobacter rubrum, evaluated previously, was excluded because it is not a valid species. Eight TUs are recommended for QPS status. Lactobacillus parafarraginis and Zygosaccharomyces rouxii are recommended to be included in the QPS list. Parageobacillus thermoglucosidasius and Paenibacillus illinoisensis can be recommended for the QPS list with the qualification 'for production purposes only' and absence of toxigenic potential. Bacillus velezensis can be recommended for the QPS list with the qualification 'absence of toxigenic potential and the absence of aminoglycoside production ability'. Cupriavidus necator, Aurantiochytrium limacinum and Tetraselmis chuii can be recommended for the QPS list with the qualification 'production purposes only'. Pantoea ananatis is not recommended for the QPS list due to lack of body of knowledge in relation to its pathogenicity potential for plants. Corynebacterium stationis, Hamamotoa singularis, Rhodococcus aetherivorans and Rhodococcus ruber cannot be recommended for the QPS list due to lack of body of knowledge. Kodamaea ohmeri cannot be recommended for the QPS list due to safety concerns.
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Asselin JAE, Bonasera JM, Beer SV. Center Rot of Onion (Allium cepa) Caused by Pantoea ananatis Requires pepM, a Predicted Phosphonate-Related Gene. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:1291-1300. [PMID: 29953334 DOI: 10.1094/mpmi-04-18-0077-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Pantoea ananatis, a cause of center rot of onion, is problematic in the United States and elsewhere. The bacterium lacks disease determinants common to most other bacterial pathogens of plants. A genomic island containing the gene pepM was detected within many onion-pathogenic strains of P. ananatis of diverse origins. The pepM gene of P. ananatis putatively encodes a protein that converts phosphoenolpyruvate to phosphonopyruvate, the first step in the biosynthesis of phosphonates and related molecules. This gene appears to be essential for center rot disease. Deletion of pepM rendered the mutant strain unable to cause lesions in leaves of growing onions and water-soaking of inoculated yellow onion bulbs. Furthermore, growth of the deletion mutant in onion leaves was significantly diminished compared with wild-type bacteria, and the mutant failed to cause cell death in tobacco. Complementation of the mutated strain with pepM restored the phenotype to wild-type capability. The pepM gene is the first pathogenicity factor identified that affects bacterial fitness as well as symptom development in both leaves and bulbs in a pathogen causing center rot of onion.
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Affiliation(s)
- Jo Ann E Asselin
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, U.S.A
| | - Jean M Bonasera
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, U.S.A
| | - Steven V Beer
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, U.S.A
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Genome Sequence of Pantoea ananatis SGAir0210, Isolated from Outdoor Air in Singapore. GENOME ANNOUNCEMENTS 2018; 6:6/27/e00643-18. [PMID: 29976614 PMCID: PMC6033981 DOI: 10.1128/genomea.00643-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pantoea ananatis SGAir0210 was isolated from outdoor air collected in Singapore. The genome was assembled from long reads generated by single-molecule real-time sequencing complemented with short reads. Pantoea ananatis SGAir0210 was isolated from outdoor air collected in Singapore. The genome was assembled from long reads generated by single-molecule real-time sequencing complemented with short reads. The genome size was approximately 4.81 Mb, with 4,303 protein-coding genes, 80 tRNAs, and 22 rRNAs identified.
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Weller‐Stuart T, De Maayer P, Coutinho T. Pantoea ananatis: genomic insights into a versatile pathogen. MOLECULAR PLANT PATHOLOGY 2017; 18:1191-1198. [PMID: 27880983 PMCID: PMC6638271 DOI: 10.1111/mpp.12517] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
UNLABELLED Pantoea ananatis, a bacterium that is well known for its phytopathogenic characteristics, has been isolated from a myriad of ecological niches and hosts. Infection of agronomic crops, such as maize and rice, can result in substantial economic losses. In the last few years, much of the research performed on P. ananatis has been based on the sequencing and analysis of the genomes of strains isolated from different environments and with different lifestyles. In this review, we summarize the advances made in terms of pathogenicity determinants of phytopathogenic strains of P. ananatis and how this bacterium is able to adapt and survive in such a wide variety of habitats. The diversity and adaptability of P. ananatis can largely be attributed to the plasticity of its genome and the integration of mobile genetic elements on both the chromosome and plasmid. Furthermore, we discuss the recent interest in this species in various biotechnological applications. TAXONOMY Domain Bacteria; Class Gammaproteobacteria; Family Enterobacteriaceae; genus Pantoea; species ananatis. DISEASE SYMPTOMS Pantoea ananatis causes disease on a wide range of plants, and symptoms can range from dieback and stunted growth in Eucalyptus seedlings to chlorosis and bulb rotting in onions. DISEASE CONTROL Currently, the only methods of control of P. ananatis on most plant hosts are the use of resistant clones and cultivars or the eradication of infected plant material. The use of lytic bacteriophages on certain host plants, such as rice, has also achieved a measure of success.
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Affiliation(s)
- Tania Weller‐Stuart
- Forestry and Agricultural Biotechnology Institute (FABI), Department of MicrobiologyUniversity of PretoriaPretoria0002South Africa
| | - Pieter De Maayer
- School of Molecular and Cell BiologyUniversity of the WitwatersrandJohannesburg2050South Africa
| | - Teresa Coutinho
- Forestry and Agricultural Biotechnology Institute (FABI), Department of MicrobiologyUniversity of PretoriaPretoria0002South Africa
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De Maayer P, Aliyu H, Vikram S, Blom J, Duffy B, Cowan DA, Smits THM, Venter SN, Coutinho TA. Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii. Front Microbiol 2017; 8:1755. [PMID: 28959245 PMCID: PMC5603701 DOI: 10.3389/fmicb.2017.01755] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/29/2017] [Indexed: 12/12/2022] Open
Abstract
Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart's wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes, has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis. While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range.
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Affiliation(s)
- Pieter De Maayer
- School of Molecular and Cell Biology, University of the WitwatersrandJohannesburg, South Africa
| | - Habibu Aliyu
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Jochen Blom
- Department of Bioinformatics and Systems Biology, Justus-Liebig-University GiessenGiessen, Germany
| | - Brion Duffy
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied SciencesWinterthur, Switzerland
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Theo H. M. Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied SciencesWinterthur, Switzerland
| | - Stephanus N. Venter
- Department of Microbiology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Teresa A. Coutinho
- Department of Microbiology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
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De Maayer P, Chan WY, Martin DAJ, Blom J, Venter SN, Duffy B, Cowan DA, Smits THM, Coutinho TA. Integrative conjugative elements of the ICEPan family play a potential role in Pantoea ananatis ecological diversification and antibiosis. Front Microbiol 2015; 6:576. [PMID: 26106378 PMCID: PMC4458695 DOI: 10.3389/fmicb.2015.00576] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/25/2015] [Indexed: 12/31/2022] Open
Abstract
Pantoea ananatis is a highly versatile enterobacterium isolated from diverse environmental sources. The ecological diversity of this species may be attributed, in part, to the acquisition of mobile genetic elements. One such element is an Integrative and Conjugative Element (ICE). By means of in silico analyses the ICE elements belonging to a novel family, ICEPan, were identified in the genome sequences of five P. ananatis strains and characterized. PCR screening showed that ICEPan is prevalent among P. ananatis strains isolated from different environmental sources and geographic locations. Members of the ICEPan family share a common origin with ICEs of other enterobacteria, as well as conjugative plasmids of Erwinia spp. Aside from core modules for ICEPan integration, maintenance and dissemination, the ICEPan contain extensive non-conserved islands coding for proteins that may contribute toward various phenotypes such as stress response and antibiosis, and the highly diverse ICEPan thus plays a major role in the diversification of P. ananatis. An island is furthermore integrated within an ICEPan DNA repair-encoding locus umuDC and we postulate its role in stress-induced dissemination and/or expression of the genes on this island.
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Affiliation(s)
- Pieter De Maayer
- Centre for Microbial Ecology and Genomics, University of Pretoria Pretoria, South Africa ; Department of Microbiology, University of Pretoria Pretoria, South Africa
| | - Wai-Yin Chan
- Department of Microbiology, University of Pretoria Pretoria, South Africa ; Forestry and Agricultural Biotechnology Institute, University of Pretoria Pretoria, South Africa
| | - Douglas A J Martin
- Department of Microbiology, University of Pretoria Pretoria, South Africa ; Forestry and Agricultural Biotechnology Institute, University of Pretoria Pretoria, South Africa
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen Giessen, Germany
| | - Stephanus N Venter
- Department of Microbiology, University of Pretoria Pretoria, South Africa ; Forestry and Agricultural Biotechnology Institute, University of Pretoria Pretoria, South Africa
| | - Brion Duffy
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zürich University of Applied Sciences Wädenswil, Switzerland
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria Pretoria, South Africa ; Department of Genetics, University of Pretoria Pretoria, South Africa
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zürich University of Applied Sciences Wädenswil, Switzerland
| | - Teresa A Coutinho
- Department of Microbiology, University of Pretoria Pretoria, South Africa ; Forestry and Agricultural Biotechnology Institute, University of Pretoria Pretoria, South Africa
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