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Paudel S, Zhao M, Stice SP, Dutta B, Kvitko BH. Thiosulfinate Tolerance Gene Clusters Are Common Features of Burkholderia Onion Pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:507-519. [PMID: 38489400 DOI: 10.1094/mpmi-01-24-0005-r] [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: 03/17/2024]
Abstract
Burkholderia gladioli pv. alliicola, B. cepacia, and B. orbicola are common bacterial pathogens of onion. Onions produce organosulfur thiosulfinate defensive compounds after cellular decompartmentalization. Using whole-genome sequencing and in silico analysis, we identified putative thiosulfinate tolerance gene (TTG) clusters in multiple onion-associated Burkholderia species similar to those characterized in other Allium-associated bacterial endophytes and pathogens. Sequence analysis revealed the presence of three Burkholderia TTG cluster types, with both Type A and Type B being broadly distributed in B. gladioli, B. cepacia, and B. orbicola in both the chromosome and plasmids. Based on isolate natural variation and generation of isogenic strains, we determined the in vitro and in vivo contribution of TTG clusters in B. gladioli, B. cepacia, and B. orbicola. The Burkholderia TTG clusters contributed to enhanced allicin tolerance and improved growth in filtered onion extracts by all three species. TTG clusters also made clear contributions to B. gladioli foliar necrosis symptoms and bacterial populations. Surprisingly, the TTG cluster did not contribute to bacterial populations in onion bulb scales by these three species. Based on our findings, we hypothesize onion-associated Burkholderia may evade or inhibit the production of thiosulfinates in onion bulb tissues. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Sujan Paudel
- Department of Plant Pathology, University of Georgia, Athens, GA, U.S.A
| | - Mei Zhao
- Department of Plant Pathology, University of Georgia, Tifton, GA, U.S.A
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Shaun P Stice
- Department of Plant Pathology, University of Georgia, Athens, GA, U.S.A
| | - Bhabesh Dutta
- Department of Plant Pathology, University of Georgia, Tifton, GA, U.S.A
| | - Brian H Kvitko
- Department of Plant Pathology, University of Georgia, Athens, GA, U.S.A
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Stice SP, Jan HH, Chen HC, Nwosu L, Shin GY, Weaver S, Coutinho T, Kvitko BH, Baltrus DA. Pantailocins: phage-derived bacteriocins from Pantoea ananatis and Pantoea stewartii subsp. indologenes. Appl Environ Microbiol 2023; 89:e0092923. [PMID: 37982620 PMCID: PMC10870728 DOI: 10.1128/aem.00929-23] [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: 06/02/2023] [Accepted: 09/15/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE Phage-derived bacteriocins (tailocins) are ribosomally synthesized structures produced by bacteria in order to provide advantages against competing strains under natural conditions. Tailocins are highly specific in their target range and have proven to be effective for the prevention and/or treatment of bacterial diseases under clinical and agricultural settings. We describe the discovery and characterization of a new tailocin locus encoded within genomes of Pantoea ananatis and Pantoea stewartii subsp. indologenes, which may enable the development of tailocins as preventative treatments against phytopathogenic infection by these species.
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Affiliation(s)
- Shaun P. Stice
- Department of Plant Pathology, University of Georgia, Athens, Georgia, USA
| | - Hsiao-Hsuan Jan
- Department of Plant Pathology, University of Georgia, Athens, Georgia, USA
| | - Hsiao-Chun Chen
- Department of Plant Pathology, University of Georgia, Athens, Georgia, USA
| | - Linda Nwosu
- Department of Plant Pathology, University of Georgia, Athens, Georgia, USA
| | - Gi Yoon Shin
- Department of Plant Pathology, University of Georgia, Athens, Georgia, USA
| | - Savannah Weaver
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, USA
| | - Teresa Coutinho
- The Plant Center, University of Georgia, Athens, Georgia, USA
| | - Brian H. Kvitko
- Department of Plant Pathology, University of Georgia, Athens, Georgia, USA
- Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria, South Africa
| | - David A. Baltrus
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, USA
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
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Zhao M, Gitaitis R, Dutta B. Characterization of Pseudomonas capsici strains from pepper and tomato. Front Microbiol 2023; 14:1267395. [PMID: 37886076 PMCID: PMC10599140 DOI: 10.3389/fmicb.2023.1267395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023] Open
Abstract
Disease outbreaks of bacterial leaf spot and blight of pepper and tomato often occur in both transplant- and field-production systems worldwide. In some cases, the outbreaks are caused by novel bacterial species. Characterization of these novel bacterial species are critical in developing diagnostic assays and identifying management options for pathogen monitoring and sustainable production, respectively. We characterized strains belonging to novel Pseudomonas species that are responsible for outbreaks in pepper and tomato both in transplant-houses and in production fields in Georgia, USA. Phylogenomic analyses and whole genome sequence indices demonstrated that the pepper and tomato strains belonged to P. capsici. The whole-genome comparison revealed that 13 Pseudomonas strains from diverse isolation sources that were curated in NCBI were indeed P. capsici indicating a potential wide-host range for this bacterial species. Our greenhouse-based host-range assay also indicated that P. capsici strains were pathogenic on pepper, tomato, eggplant, cabbage, lettuce, and watermelon corroborating a wide-host-range. A phylogenetic tree inferred from the whole genome sequence data showed that the P. capsici strains from Georgia (pepper and tomato) were genetically diverse, and were closely related to tomato P. capsici strains from Florida. Genomic presence of traditional bacterial virulence factors in P. capsici strains was also determined. Pseudomonascapsici strains encode one set of type I secretion system, two sets of type II secretion systems, one set of type III secretion system, two sets of type V secretion systems, three sets of type VI secretion systems, and various secondary metabolite gene clusters including lipopeptides. In in-vitro assays, it was demonstrated that six out of seven P. capsici strains (pepper and tomato strains from Georgia) were not sensitive to 0.8 mM CuSO4. When the genomes of copper-tolerant strains were compared with the copper-sensitive strains, it was observed that the former strains encode a cluster of genes related to copper tolerance, which were absent in the genomes of copper-sensitive strains. Considering the ability of P. capsici strains to infect a range of vegetable hosts and possession of a wide range of bacterial virulence factors, secondary metabolites, and copper-tolerance genes, we envision that the management of this pathogen might potentially be a challenge.
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Affiliation(s)
- Mei Zhao
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Ron Gitaitis
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Bhabesh Dutta
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
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Khanal M, Bhatta BP, Malla S. Isolation and Characterization of Bacteria Associated with Onion and First Report of Onion Diseases Caused by Five Bacterial Pathogens in Texas, U.S.A. PLANT DISEASE 2023:PDIS09222206SR. [PMID: 36451309 DOI: 10.1094/pdis-09-22-2206-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacterial diseases pose a severe challenge to growers and cause significant loss to the billion-dollar onion industry in the United States. Texas is the sixth largest onion producing state, yet the bacterial communities associated with short-day onion crops grown in Texas have not been studied. This study was conducted to identify, characterize, and understand the diversity of bacteria associated with onion production in Texas. In 2020, 190 foliar and 210 bulb samples were collected from onion crops in the Rio Grande Valley and Winter Garden regions of Texas. Sequencing of the 16s rRNA gene was used to identify each bacterial strains to a genus. The pathogenicity to onion of each bacterial strain was tested using three assays: a red onion scale assay, a yellow onion bulb assay, and a foliar assay. Whole genome sequencing was done to identify the onion-pathogenic strains to species. Collectively, isolates of 24 genera belonging to three phyla were detected, including 19 genera from foliar samples and nine genera from bulb samples. Isolates in the Phylum Proteobacteria, including 15 genera of Gram-negative bacteria, were the most abundant of the taxa, comprising 90.0% of the strains isolated. The diversity of foliar isolates was evenly distributed between Gram-positive and Gram-negative bacteria, while Gram-negative bacteria dominated the isolates from bulb samples. In total, 83.9% of the bacterial isolates were not pathogenic on onion, with only isolates of Pantoea, Pseudomonas, Burkholderia, Erwinia, Enterobacter, and Curtobacterium proving pathogenic. Strains of Burkholderia gladioli, Pseudomonas alliivorans, Pantoea agglomerans, P. ananatis, and P. allii are the first documented cases of these pathogens of onion in Texas. Identifying and characterizing the nature of onion microflora, including pathogens of onion, is vital to developing rapid disease detection techniques via pathogenomics and minimizing losses through the application of effective disease management measures.
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Affiliation(s)
- Manzeal Khanal
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801
| | - Bed Prakash Bhatta
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801
| | - Subas Malla
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801
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Zhao M, Shin GY, Stice S, Bown JL, Coutinho T, Metcalf WW, Gitaitis R, Kvitko B, Dutta B. A Novel Biosynthetic Gene Cluster Across the Pantoea Species Complex Is Important for Pathogenicity in Onion. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:176-188. [PMID: 36534063 PMCID: PMC10433531 DOI: 10.1094/mpmi-08-22-0165-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Onion center rot is caused by at least four species of genus Pantoea (P. ananatis, P. agglomerans, P. allii, and P. stewartii subsp. indologenes). Critical onion pathogenicity determinants for P. ananatis were recently described, but whether those determinants are common among other onion-pathogenic Pantoea species remains unknown. In this work, we report onion pathogenicity determinants in P. stewartii subsp. indologenes and P. allii. We identified two distinct secondary metabolite biosynthetic gene clusters present separately in different strains of onion-pathogenic P. stewartii subsp. indologenes. One cluster is similar to the previously described HiVir phosphonate biosynthetic cluster identified in P. ananatis and another is a novel putative phosphonate biosynthetic gene cluster, which we named Halophos. The Halophos gene cluster was also identified in P. allii strains. Both clusters are predicted to be phosphonate biosynthetic clusters based on the presence of a characteristic phosphoenolpyruvate phosphomutase (pepM) gene. The deletion of the pepM gene from either HiVir or Halophos clusters in P. stewartii subsp. indologenes caused loss of necrosis on onion leaves and red onion scales and resulted in significantly lower bacterial populations compared with the corresponding wild-type and complemented strains. Seven (halB to halH) of 11 genes (halA to halK) in the Halophos gene cluster are required for onion necrosis phenotypes. The onion nonpathogenic strain PNA15-2 (P. stewartii subsp. indologenes) gained the capacity to cause foliar necrosis on onion via exogenous expression of a minimal seven-gene Halophos cluster (genes halB to halH). Furthermore, cell-free culture filtrates of PNA14-12 expressing the intact Halophos gene cluster caused necrosis on onion leaves consistent with the presence of a secreted toxin. Based on the similarity of proteins to those with experimentally determined functions, we are able to predict most of the steps in Halophos biosynthesis. Together, these observations indicate that production of the toxin phosphonate seems sufficient to account for virulence of a variety of different Pantoea strains, although strains differ in possessing a single but distinct phosphonate biosynthetic cluster. Overall, this is the first report of onion pathogenicity determinants in P. stewartii subsp. indologenes and P. allii. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Mei Zhao
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, P. R. China
- Department of Plant Pathology, University of Georgia, Tifton GA USA
| | - Gi Yoon Shin
- Department of Plant Pathology, University of Georgia, Athens GA USA
| | - Shaun Stice
- Department of Plant Pathology, University of Georgia, Athens GA USA
| | - Jonathon Luke Bown
- Department of Microbiology, University of Illinois, Urbana-Champaign, IL
| | - Teresa Coutinho
- The Genomics Research Institute, University of Pretoria, Hatfield, South Africa
| | - William W. Metcalf
- Department of Microbiology, University of Illinois, Urbana-Champaign, IL
| | - Ron Gitaitis
- Department of Plant Pathology, University of Georgia, Tifton GA USA
| | - Brian Kvitko
- Department of Plant Pathology, University of Georgia, Athens GA USA
| | - Bhabesh Dutta
- Department of Plant Pathology, University of Georgia, Tifton GA USA
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Myers BK, Shin GY, Agarwal G, Stice SP, Gitaitis RD, Kvitko BH, Dutta B. Genome-wide association and dissociation studies in Pantoea ananatis reveal potential virulence factors affecting Allium porrum and Allium fistulosum × Allium cepa hybrid. Front Microbiol 2023; 13:1094155. [PMID: 36817114 PMCID: PMC9933511 DOI: 10.3389/fmicb.2022.1094155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/30/2022] [Indexed: 02/05/2023] Open
Abstract
Pantoea ananatis is a member of a Pantoea species complex that causes center rot of bulb onions (A. cepa) and also infects other Allium crops like leeks (Allium porrum), chives (Allium schoenoprasum), bunching onion or Welsh onion (Allium fistulosum), and garlic (Allium sativum). This pathogen relies on a chromosomal phosphonate biosynthetic gene cluster (HiVir) and a plasmid-borne thiosulfinate tolerance cluster (alt) for onion pathogenicity and virulence, respectively. However, pathogenicity and virulence factors associated with other Allium species remain unknown. We used phenotype-dependent genome-wide association (GWAS) and phenotype-independent gene-pair coincidence (GPC) analyses on a panel of diverse 92 P. ananatis strains, which were inoculated on A. porrum and A. fistulosum × A. cepa under greenhouse conditions. Phenotypic assays showed that, in general, these strains were more aggressive on A. fistulosum × A. cepa as opposed to A. porrum. Of the 92 strains, only six showed highly aggressive foliar lesions on A. porrum compared to A. fistulosum × A. cepa. Conversely, nine strains showed highly aggressive foliar lesions on A. fistulosum × A. cepa compared to A. porrum. These results indicate that there are underlying genetic components in P. ananatis that may drive pathogenicity in these two Allium spp. Based on GWAS for foliar pathogenicity, 835 genes were associated with P. ananatis' pathogenicity on A. fistulosum × A. cepa whereas 243 genes were associated with bacterial pathogenicity on A. porrum. The Hivir as well as the alt gene clusters were identified among these genes. Besides the 'HiVir' and the alt gene clusters that are known to contribute to pathogenicity and virulence from previous studies, genes annotated with functions related to stress responses, a potential toxin-antitoxin system, flagellar-motility, quorum sensing, and a previously described phosphonoglycan biosynthesis (pgb) cluster were identified. The GPC analysis resulted in the identification of 165 individual genes sorted into 39 significant gene-pair association components and 255 genes sorted into 50 significant gene-pair dissociation components. Within the coincident gene clusters, several genes that occurred on the GWAS outputs were associated with each other but dissociated with genes that did not appear in their respective GWAS output. To focus on candidate genes that could explain the difference in virulence between hosts, a comparative genomics analysis was performed on five P. ananatis strains that were differentially pathogenic on A. porrum or A. fistulosum × A. cepa. Here, we found a putative type III secretion system, and several other genes that occurred on both GWAS outputs of both Allium hosts. Further, we also demonstrated utilizing mutational analysis that the pepM gene in the HiVir cluster is important than the pepM gene in the pgb cluster for P. ananatis pathogenicity in A. fistulosum × A. cepa and A. porrum. Overall, our results support that P. ananatis may utilize a common set of genes or gene clusters to induce symptoms on A. fistulosum × A. cepa foliar tissue as well as A. cepa but implicates additional genes for infection on A. porrum.
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Affiliation(s)
- Brendon K. Myers
- Department of Plant Pathology, The University of Georgia, Tifton, GA, United States
| | - Gi Yoon Shin
- Department of Plant Pathology, The University of Georgia, Athens, GA, United States
| | - Gaurav Agarwal
- Department of Plant Pathology, The University of Georgia, Tifton, GA, United States
| | - Shaun P. Stice
- Department of Plant Pathology, The University of Georgia, Athens, GA, United States
| | - Ronald D. Gitaitis
- Department of Plant Pathology, The University of Georgia, Tifton, GA, United States
| | - Brian H. Kvitko
- Department of Plant Pathology, The University of Georgia, Athens, GA, United States
| | - Bhabesh Dutta
- Department of Plant Pathology, The University of Georgia, Tifton, GA, United States,*Correspondence: Bhabesh Dutta, ✉
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Bing XL, Wan YY, Liu HH, Ji R, Zhao DS, Niu YD, Li TP, Hong XY. Characterization of Pantoea ananatis from rice planthoppers reveals a clade of rice-associated P. ananatis undergoing genome reduction. Microb Genom 2022; 8:mgen000907. [PMID: 36748509 PMCID: PMC9837560 DOI: 10.1099/mgen.0.000907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Abstract
Pantoea ananatis is a bacterium that is found in many agronomic crops and agricultural pests. Here, we isolated a P. ananatis strain (Lstr) from the rice planthopper Laodelphax striatellus, a notorious pest that feeds on rice plant sap and transmits rice viruses, in order to examine its genome and biology. P. ananatis Lstr is an insect symbiont that is pathogenic to the host insect and appears to mostly inhabit the gut. Its pathogenicity thus raises the possibility of using the Lstr strain as a biological agent. To this end, we analysed the genome of the Lstr strain and compared it with the genomes of other Pantoea species. Our analysis of these genomes shows that P. ananatis can be divided into two mono-phylogenetic clades (clades one and two). The Lstr strain belongs to clade two and is grouped with P. ananatis strains that were isolated from rice or rice-associated samples. A comparative genomic analysis shows that clade two differs from clade one in many genomic characteristics including genome structures, mobile elements, and categories of coding proteins. The genomes of clade two P. ananatis are significantly smaller, have much fewer coding sequences but more pseudogenes than those of clade one, suggesting that clade two species are at the early stage of genome reduction. On the other hand, P. ananatis has a type VI secretion system that is highly variable but cannot be separated by clades. These results clarify our understanding of P. ananatis' phylogenetic diversity and provide clues to the interactions between P. ananatis, host insect, and plant that may lead to advances in rice protection and pest control.
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Affiliation(s)
- Xiao-Li Bing
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Yu-Ying Wan
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Huan-Huan Liu
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Rui Ji
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, PR China
| | - Dian-Shu Zhao
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Yue-Di Niu
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Tong-Pu Li
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China,*Correspondence: Xiao-Yue Hong,
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de Lima Ferreira JK, de Mello Varani A, Tótola MR, Fernandes Almeida M, de Sousa Melo D, Ferreira Silva E Batista C, Chalfun-Junior A, Pimenta de Oliveira KK, Wurdig Roesch LF, Satler Pylro V. Phylogenomic characterization and pangenomic insights into the surfactin-producing bacteria Bacillus subtilis strain RI4914. Braz J Microbiol 2022; 53:2051-2063. [PMID: 36083529 PMCID: PMC9679098 DOI: 10.1007/s42770-022-00815-0] [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: 04/29/2022] [Accepted: 08/22/2022] [Indexed: 01/13/2023] Open
Abstract
Bacillus subtilis is a versatile bacterial species able to produce surfactin, a lipopeptide biosurfactant. We carried out the phylogenomic characterization and pangenomic analyses using available B. subtilis complete genomes. Also, we report the whole genome of the biosurfactant-producing B. subtilis strain RI4914 that was isolated from effluent water from an oil exploration field. We applied a hybrid sequencing approach using both long- and short-read sequencing technologies to generate a highly accurate, single-chromosome genome. The pangenomics analysis of 153 complete genomes classified as B. subtilis retrieved from the NCBI shows an open pangenome composed of 28,511 accessory genes, which agrees with the high genetic plasticity of the species. Also, this analysis suggests that surfactin production is a common trait shared by members of this species since the srfA operon is highly conserved among the B. subtilis strains found in most of the assemblies available. Finally, increased surfactin production corroborates the higher srfAA gene expression in B. subtilis strain RI4914.
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Affiliation(s)
| | - Alessandro de Mello Varani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias E Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, Sao Paulo, Brazil
| | - Marcos Rogério Tótola
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Minas Gerais, Viçosa, Brazil
| | - Michelle Fernandes Almeida
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Minas Gerais, Viçosa, Brazil
| | - Dirceu de Sousa Melo
- Department of Biology, Federal University of Lavras - UFLA, Lavras, Minas Gerais, Brazil
| | | | - Antonio Chalfun-Junior
- Department of Biology, Federal University of Lavras - UFLA, Lavras, Minas Gerais, Brazil
| | | | | | - Victor Satler Pylro
- Department of Biology, Federal University of Lavras - UFLA, Lavras, Minas Gerais, Brazil.
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9
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Zhao M, Tyson C, Gitaitis R, Kvitko B, Dutta B. Rouxiella badensis, a new bacterial pathogen of onion causing bulb rot. Front Microbiol 2022; 13:1054813. [DOI: 10.3389/fmicb.2022.1054813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022] Open
Abstract
Onion bulb rot can be caused by multiple plant pathogens including bacterial pathogens. During our routine survey of commercial onion farms in 2014, 2020, and 2021, seven putative Rouxiella spp. strains were isolated from symptomatic onion samples in Georgia, United States. Upon fulfilling Koch’s postulates on onion, a genome analysis was conducted. Whole-genome indices (ANI and dDDH) showed that the strains belonged to Rouxiella badensis. Although the seven R. badensis strains were not pathogenic on onion foliage, the strains were able to cause bulb rot and could also produce necrotic lesions in a red onion scale assay. R. badensis populations increased significantly and to a level comparable to P. ananatis PNA 97-1R in a red onion scale infection assay. The core-genome analysis grouped all onion R. badensis strains from Georgia together, and distinct from R. badensis strains isolated from other sources and locations. Based on the genome analysis of strains (from the current study and available genomes in the repository), type I, III (Ssa-Esc and Inv-Mxi-Spa types), and V secretion systems are present in R. badensis genomes, while type II, IV, and VI secretion systems are absent. However, various secondary metabolite gene clusters were identified from R. badensis genomes, and a thiol/redox-associated enzyme gene cluster similar to the Pantoea alt cluster mediating thiosulfinate tolerance was also present in onion strains of R. badensis. This is the first report of R. badensis as a plant pathogen.
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Usuda Y, Nishio Y, Nonaka G, Hara Y. Microbial Production Potential of Pantoea ananatis: From Amino Acids to Secondary Metabolites. Microorganisms 2022; 10:microorganisms10061133. [PMID: 35744651 PMCID: PMC9231021 DOI: 10.3390/microorganisms10061133] [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: 03/25/2022] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 11/16/2022] Open
Abstract
Pantoea ananatis, a gram-negative bacterium belonging to the Erwiniaceae family, is a well-known phytopathogen isolated from many ecological niches and plant hosts. However, this bacterium also provides us with various beneficial characteristics, such as the growth promotion of their host plants and increased crop yield. Some isolated non-pathogenic strains are promising for the microbial production of useful substances. P. ananatis AJ13355 was isolated as an acidophilic bacterium and was used as an excellent host to produce L-glutamic acid under acidic conditions. The genome sequence of P. ananatis AJ13355 was determined, and specific genome-engineering technologies were developed. As a result, P. ananatis was successfully used to construct a bacterial strain that produces cysteine, a sulfur-containing amino acid that has been difficult to produce through fermentation because of complex regulation. Furthermore, by heterologous expression including plant-derived genes, construction of a strain that produces isoprenoids such as isoprene and linalool as secondary metabolites was achieved. P. ananatis is shown to be a useful host for the production of secondary metabolites, as well as amino acids, and is expected to be used as a platform for microbial production of bioactive substances, aromatic substances, and other high-value-added substances of plant origin in the future.
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Affiliation(s)
- Yoshihiro Usuda
- Research and Business Planning Department, Ajinomoto Co., Inc., Tokyo 104-8315, Japan
- Correspondence: ; Tel.: +81-70-4361-3762; Fax: +81-3-5250-8352
| | - Yousuke Nishio
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8681, Japan; (Y.N.); (Y.H.)
| | - Gen Nonaka
- Ajinomoto-Genetika Research Institute, Moscow 117545, Russia;
| | - Yoshihiko Hara
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8681, Japan; (Y.N.); (Y.H.)
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De Armas S, Galván GA, Lapaz MI, González-Barrios P, Vicente E, Pianzzola MJ, Siri MI. Phylogeny and Identification of Pantoea Species Associated with Bulb Rot and Bacterial Leaf Blight of Onion Crops in Uruguay. PLANT DISEASE 2022; 106:1216-1225. [PMID: 34818920 DOI: 10.1094/pdis-06-21-1140-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: 06/13/2023]
Abstract
Onion is among the most consumed vegetables in Uruguay, grown in the northwestern and southern regions of the country. The onion supply presents interannual variations associated with significant postharvest losses, mainly caused by bacterial rots. Besides bulb rotting, onion leaf lesions as well as infections on seed-stalks during seed production may be devastating for some varieties under conducive conditions. This research aimed to identify the causal agents of bulb rots and leaf blight of onion crops in Uruguay. Symptomatic bulbs, seeds-stalks, and leaves were collected from commercial fields from 2015 to 2020. Bacterial colonies were isolated and identified at genera level using physiological tests and 16S rRNA gene sequence analysis. A collection of 59 Pantoea spp. isolates was obtained (11 from bulbs and 48 from leaves and seeds-stalks). Multilocus sequence analysis using four housekeeping genes (rpoB, gyrB, leuS, and fusA) allowed the assignment of the isolates to five Pantoea species: P. ananatis, P. agglomerans, P. allii, P. eucalypti, and P. vagans. The last two species were not previously reported as onion pathogens elsewhere. The ability to cause disease symptoms was tested by leaf inoculation and red onion scale assays. P. ananatis isolates showed the highest aggressiveness in both assays. Specific isolates from P. allii (MAI 6022), P. eucalypti (MAI 6036), P. vagans (MAI 6050), and Pantoea sp. (MAI 6049) ranked second in aggressiveness on onion leaves, whereas only three isolates belonging to P. eucalypti (MAI 6036 and MAI 6058) and P. agglomerans (MAI 6045) exhibited the same scale-clearing phenotype as P. ananatis. Leaf inoculation assays were also performed on a set of eight onion cultivars and breeding lines. Overall, P. ananatis MAI 6032 showed the highest aggressiveness in all tested cultivars, followed by P. eucalypti MAI 6036. The presence of new reported bacterial species leads to complex disease management and highlights the need for further studies on virulence factors and the epidemiology of these pathogens.
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Affiliation(s)
- Stefanie De Armas
- Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo 11800, Uruguay
- Programa de Desarrollo de las Ciencias Básicas (PEDECIBA), Montevideo 11800, Uruguay
| | - Guillermo A Galván
- Programa de Desarrollo de las Ciencias Básicas (PEDECIBA), Montevideo 11800, Uruguay
- Departamento de Producción Vegetal, Centro Regional Sur (CRS), Facultad de Agronomía, Universidad de la República, Canelones 90100, Uruguay
| | - María I Lapaz
- Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo 11800, Uruguay
- Programa de Desarrollo de las Ciencias Básicas (PEDECIBA), Montevideo 11800, Uruguay
| | - Pablo González-Barrios
- Departamento de Biometría, Estadística y Computación. Facultad de Agronomía, Universidad de la República, Montevideo 12900, Uruguay
| | - Esteban Vicente
- Salto Grande Experimental Station, Instituto Nacional de Investigación Agropecuaria (INIA), Salto 50000, Uruguay
| | - María J Pianzzola
- Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo 11800, Uruguay
- Programa de Desarrollo de las Ciencias Básicas (PEDECIBA), Montevideo 11800, Uruguay
| | - María I Siri
- Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo 11800, Uruguay
- Programa de Desarrollo de las Ciencias Básicas (PEDECIBA), Montevideo 11800, Uruguay
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12
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Khanal M, Timilsina S, Bhatta BP, Bophela K, Coutinho T, Cochran K, Malla S. Pseudomonas uvaldensis sp. nov., a bacterial pathogen causing onion bulb rot. Int J Syst Evol Microbiol 2022; 72. [PMID: 35442877 DOI: 10.1099/ijsem.0.005311] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic and non-spore-forming bacterial strain, designated 20TX0172T, was isolated from a rotting onion bulb in Texas, USA. The results of phylogenetic analysis based on the 16S rRNA sequence indicated that the novel strain represented a member of the genus Pseudomonas and had the greatest sequence similarities with Pseudomonas kilonensis 520-20T (99.3 %), Pseudomonas corrugata CFBP 2431T (99.2 %), and Pseudomonas viciae 11K1T (99.2 %) but the 16S rRNA phylogenetic tree displayed a monophyletic clade with Pseudomonas mediterranea CFBP 5447T. In the phylogenetic trees based on sequences of four housekeeping genes (gap1, gltA, gyrB and rpoD), the novel strain formed a separate branch, indicating that the strain was distinct phylogenetically from known species of the genus Pseudomonas. The genome-sequence-derived average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the novel isolate and P. mediterranea DSM 16733T were 86.7 and 32.7 %, respectively. These values were below the accepted species cutoff threshold of 96 % ANI and 70 % dDDH, affirming that the strain represented a novel species. The genome size of the novel species was 5.98 Mbp with a DNA G+C content of 60.8 mol%. On the basis of phenotypic and genotypic characteristics, strain 20TX0172T represents a novel species of the genus Pseudomonas. The name Pseudomonas uvaldensis sp. nov. is proposed. The type strain is 20TX0172T (=NCIMB 15426T=CIP 112022T).
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Affiliation(s)
- Manzeal Khanal
- Department of Horticultural Sciences, Texas A&M University, College Station, Texas 77843, USA.,Texas A&M AgriLife Research and Extension Center, Uvalde, Texas 78801, USA
| | - Sujan Timilsina
- Department of Plant Pathology, University of Florida, Gainesville, Florida 32611, USA.,Present address: Charles River Laboratories, Newark, DE, USA
| | - Bed Prakash Bhatta
- Department of Horticultural Sciences, Texas A&M University, College Station, Texas 77843, USA.,Texas A&M AgriLife Research and Extension Center, Uvalde, Texas 78801, USA
| | - Khumbuzile Bophela
- Department of Plant and Soil Sciences, University of Pretoria, 0002 Pretoria, South Africa
| | - Teresa Coutinho
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics/Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa
| | - Kimberly Cochran
- Texas A&M AgriLife Research and Extension Center, Uvalde, Texas 78801, USA.,Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA
| | - Subas Malla
- Department of Horticultural Sciences, Texas A&M University, College Station, Texas 77843, USA.,Texas A&M AgriLife Research and Extension Center, Uvalde, Texas 78801, USA
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13
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Negatively regulated aerobactin and desferrioxamine E by Fur in Pantoea ananatis are required for full siderophore production and antibacterial activity, but not for virulence. Appl Environ Microbiol 2022; 88:e0240521. [PMID: 35108090 DOI: 10.1128/aem.02405-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pantoea ananatis is an emerging plant pathogen that causes disease in economically important crops such as rice, corn, onion, melon, and pineapple, and it also infects humans and insects. In this study, we identified biosynthetic gene clusters of aerobactin and desferrioxamine E (DFO-E) siderophores using the complete genome of P. ananatis PA13 isolated from rice sheath rot. P. ananatis PA13 exhibited the strongest antibacterial activity against Erwinia amylovora and Yersinia enterocolitica (Enterobacterales). Mutants of aerobactin or DFO-E maintained antibacterial activity against E. amylovora and Y. enterocolitica, as well as in a siderophore activity assay. However, double aerobactin- and DFO-E-gene-deletion mutants completely lost siderophore and antibacterial activity. These results reveal that both siderophore biosynthetic gene clusters are essential for siderophore production and antibacterial activity in P. ananatis PA13. A ferric uptake regulator protein (Fur) mutant exhibited a significant increase in siderophore production, and a Fur-overexpressing strain completely lost antibacterial activity. Expression of the iucA, dfoJ, and foxA genes was significantly increased in the Δfur mutant background, and expression of these genes returned to wild type levels after fur compensation. These results indicate that Fur negatively regulates aerobactin and DFO-E siderophores. However, siderophore production was not required for P. ananatis virulence in plants, but it appears to be involved in the microbial ecology surrounding the plant environment. This study is the first to report the regulation and functional characteristics of siderophore biosynthetic genes in P. ananatis. IMPORTANCE Pantoea ananatis is a bacterium that causes diseases in several economically important crops, as well as in insects and humans. This bacterium has been studied extensively as a potentially dangerous pathogen due to its saprophytic ability. Recently, the types, biosynthetic gene clusters, and origin of the siderophores in the Pantoea genus were determined using genome comparative analyses. However, few genetic studies have investigated the characteristics and functions of siderophores in P. ananatis. The results of this study revealed that the production of aerobactin and desferrioxamine E in the rice pathogen P. ananatis PA13 is negatively regulated by Fur, and that these siderophores are essential for antibacterial activity against Erwinia amylovora and Yersinia enterocolitica (Enterobacterales). However, siderophore production was not required for P. ananatis virulence in plants, but it appears to be involved in the microbial ecology surrounding the plant environment.
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14
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Aspergillus sp. A31 and Curvularia geniculata P1 mitigate mercury toxicity to Oryza sativa L. Arch Microbiol 2021; 203:5345-5361. [PMID: 34387704 DOI: 10.1007/s00203-021-02481-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/29/2022]
Abstract
Aspergillus sp. A31 and Curvularia geniculata P1 are endophytes that colonize the roots of Aeschynomene fluminensis Vell. and Polygonum acuminatum Kunth. in humid environments contaminated with mercury. The two strains mitigated mercury toxicity and promoted Oryza sativa L growth. C. geniculata P1 stood out for increasing the host biomass by fourfold and reducing the negative effects of the metal on photosynthesis. Assembling and annotation of Aspergillus sp. A31 and C. geniculata P1 genomes resulted in 28.60 Mb (CG% 53.1; 10,312 coding DNA sequences) and 32.92 Mb (CG% 50.72; 8,692 coding DNA sequences), respectively. Twelve and 27 genomes of Curvularia/Bipolaris and Aspergillus were selected for phylogenomic analyzes, respectively. Phylogenetic analysis inferred the separation of species from the genus Curvularia and Bipolaris into different clades, and the separation of species from the genus Aspergillus into three clades; the species were distinguished by occupied niche. The genomes had essential gene clusters for the adaptation of microorganisms to high metal concentrations, such as proteins of the phytoquelatin-metal complex (GO: 0090423), metal ion binders (GO: 0046872), ABC transporters (GO: 0042626), ATPase transporters (GO: 0016887), and genes related to response to reactive oxygen species (GO: 0000302) and oxidative stress (GO: 0006979). The results reported here help to understand the unique regulatory mechanisms of mercury tolerance and plant development.
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15
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Asselin JAE, Bonasera JM, Helmann TC, Beer SV, Stodghill PV. Complete Genome Sequence Resources for the Onion Pathogen, Pantoea ananatis OC5a. PHYTOPATHOLOGY 2021; 111:1885-1888. [PMID: 33724871 DOI: 10.1094/phyto-09-20-0416-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Here, we report on the genomic sequence and annotation for Pantoea ananatis OC5a, a strain that was isolated from an onion bulb grown in New York and that is pathogenic to onion, causing center rot of onion. OC5a is the first P. ananatis strain pathogenic to onion from New York to be completely assembled and sequenced. Having been assembled using long PacBio reads and high-fidelity Illumina reads, this genome is closed, complete, and of high quality.
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Affiliation(s)
- Jo Ann E Asselin
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY
| | - Jean M Bonasera
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY
| | - Tyler C Helmann
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY
| | - Steven V Beer
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY
| | - Paul V Stodghill
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY
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16
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Agarwal G, Choudhary D, Stice SP, Myers BK, Gitaitis RD, Venter SN, Kvitko BH, Dutta B. Pan-Genome-Wide Analysis of Pantoea ananatis Identified Genes Linked to Pathogenicity in Onion. Front Microbiol 2021; 12:684756. [PMID: 34489883 PMCID: PMC8417944 DOI: 10.3389/fmicb.2021.684756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
Pantoea ananatis, a gram negative and facultative anaerobic bacterium is a member of a Pantoea spp. complex that causes center rot of onion, which significantly affects onion yield and quality. This pathogen does not have typical virulence factors like type II or type III secretion systems but appears to require a biosynthetic gene-cluster, HiVir/PASVIL (located chromosomally comprised of 14 genes), for a phosphonate secondary metabolite, and the 'alt' gene cluster (located in plasmid and comprised of 11 genes) that aids in bacterial colonization in onion bulbs by imparting tolerance to thiosulfinates. We conducted a deep pan-genome-wide association study (pan-GWAS) to predict additional genes associated with pathogenicity in P. ananatis using a panel of diverse strains (n = 81). We utilized a red-onion scale necrosis assay as an indicator of pathogenicity. Based on this assay, we differentiated pathogenic (n = 51)- vs. non-pathogenic (n = 30)-strains phenotypically. Pan-genome analysis revealed a large core genome of 3,153 genes and a flexible accessory genome. Pan-GWAS using the presence and absence variants (PAVs) predicted 42 genes, including 14 from the previously identified HiVir/PASVIL cluster associated with pathogenicity, and 28 novel genes that were not previously associated with pathogenicity in onion. Of the 28 novel genes identified, eight have annotated functions of site-specific tyrosine kinase, N-acetylmuramoyl-L-alanine amidase, conjugal transfer, and HTH-type transcriptional regulator. The remaining 20 genes are currently hypothetical. Further, a core-genome SNPs-based phylogeny and horizontal gene transfer (HGT) studies were also conducted to assess the extent of lateral gene transfer among diverse P. ananatis strains. Phylogenetic analysis based on PAVs and whole genome multi locus sequence typing (wgMLST) rather than core-genome SNPs distinguished red-scale necrosis inducing (pathogenic) strains from non-scale necrosis inducing (non-pathogenic) strains of P. ananatis. A total of 1182 HGT events including the HiVir/PASVIL and alt cluster genes were identified. These events could be regarded as a major contributing factor to the diversification, niche-adaptation and potential acquisition of pathogenicity/virulence genes in P. ananatis.
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Affiliation(s)
- Gaurav Agarwal
- Department of Plant Pathology, Coastal Plain Experimental Station, University of Georgia, Tifton, GA, United States
| | - Divya Choudhary
- Department of Plant Pathology, Coastal Plain Experimental Station, University of Georgia, Tifton, GA, United States
| | - Shaun P Stice
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Brendon K Myers
- Department of Plant Pathology, Coastal Plain Experimental Station, University of Georgia, Tifton, GA, United States
| | - Ronald D Gitaitis
- Department of Plant Pathology, Coastal Plain Experimental Station, University of Georgia, Tifton, GA, United States
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Brian H Kvitko
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Bhabesh Dutta
- Department of Plant Pathology, Coastal Plain Experimental Station, University of Georgia, Tifton, GA, United States
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17
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Khoiri AN, Cheevadhanarak S, Jirakkakul J, Dulsawat S, Prommeenate P, Tachaleat A, Kusonmano K, Wattanachaisaereekul S, Sutheeworapong S. Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management. Front Microbiol 2021; 12:623799. [PMID: 33828538 PMCID: PMC8019924 DOI: 10.3389/fmicb.2021.623799] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/01/2021] [Indexed: 12/21/2022] Open
Abstract
Converting conventional farms to organic systems to improve ecosystem health is an emerging trend in recent decades, yet little is explored to what extent and how this process drives the taxonomic diversity and functional capacity of above-ground microbes. This study was, therefore, conducted to investigate the effects of agricultural management, i.e., organic, transition, and conventional, on the structure and function of sugarcane phyllosphere microbial community using the shotgun metagenomics approach. Comparative metagenome analysis exhibited that farming practices strongly influenced taxonomic and functional diversities, as well as co-occurrence interactions of phyllosphere microbes. A complex microbial network with the highest connectivity was observed in organic farming, indicating strong resilient capabilities of its microbial community to cope with the dynamic environmental stressors. Organic farming also harbored genus Streptomyces as the potential keystone species and plant growth-promoting bacteria as microbial signatures, including Mesorhizobium loti, Bradyrhizobium sp. SG09, Lactobacillus plantarum, and Bacillus cellulosilyticus. Interestingly, numerous toxic compound-degrading species were specifically enriched in transition farming, which might suggest their essential roles in the transformation of conventional to organic farming. Moreover, conventional practice diminished the abundance of genes related to cell motility and energy metabolism of phyllosphere microbes, which could negatively contribute to lower microbial diversity in this habitat. Altogether, our results demonstrated the response of sugarcane-associated phyllosphere microbiota to specific agricultural managements that played vital roles in sustainable sugarcane production.
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Affiliation(s)
- Ahmad Nuruddin Khoiri
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Supapon Cheevadhanarak
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Jiraporn Jirakkakul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Sudarat Dulsawat
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Peerada Prommeenate
- Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Anuwat Tachaleat
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Kanthida Kusonmano
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Songsak Wattanachaisaereekul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Faculty of Food Industry, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Sawannee Sutheeworapong
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
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18
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Allicin, the Odor of Freshly Crushed Garlic: A Review of Recent Progress in Understanding Allicin's Effects on Cells. Molecules 2021; 26:molecules26061505. [PMID: 33801955 PMCID: PMC8001868 DOI: 10.3390/molecules26061505] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 12/14/2022] Open
Abstract
The volatile organic sulfur compound allicin (diallyl thiosulfinate) is produced as a defense substance when garlic (Allium sativum) tissues are damaged, for example by the activities of pathogens or pests. Allicin gives crushed garlic its characteristic odor, is membrane permeable and readily taken up by exposed cells. It is a reactive thiol-trapping sulfur compound that S-thioallylates accessible cysteine residues in proteins and low molecular weight thiols including the cellular redox buffer glutathione (GSH) in eukaryotes and Gram-negative bacteria, as well as bacillithiol (BSH) in Gram-positive firmicutes. Allicin shows dose-dependent antimicrobial activity. At higher doses in eukaryotes allicin can induce apoptosis or necrosis, whereas lower, biocompatible amounts can modulate the activity of redox-sensitive proteins and affect cellular signaling. This review summarizes our current knowledge of how bacterial and eukaryotic cells are specifically affected by, and respond to, allicin.
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19
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Stice SP, Shin GY, De Armas S, Koirala S, Galván GA, Siri MI, Severns PM, Coutinho T, Dutta B, Kvitko BH. The Distribution of Onion Virulence Gene Clusters Among Pantoea spp. FRONTIERS IN PLANT SCIENCE 2021; 12:643787. [PMID: 33777079 PMCID: PMC7988079 DOI: 10.3389/fpls.2021.643787] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/18/2021] [Indexed: 05/31/2023]
Abstract
Pantoea ananatis is a gram-negative bacterium and the primary causal agent of center rot of onions in Georgia. Previous genomic studies identified two virulence gene clusters, HiVir and alt, associated with center rot. The HiVir gene cluster is required to induce necrosis on onion tissues via synthesis of pantaphos, (2-hydroxy[phosphono-methyl)maleate), a phosphonate phytotoxin. The alt gene cluster aids in tolerance to thiosulfinates generated during onion tissue damage. Whole genome sequencing of other Pantoea species suggests that these gene clusters are present outside of P. ananatis. To assess the distribution of these gene clusters, two PCR primer sets were designed to detect the presence of HiVir and alt. Two hundred fifty-two strains of Pantoea spp. were phenotyped using the red onion scale necrosis (RSN) assay and were genotyped using PCR for the presence of these virulence genes. A diverse panel of strains from three distinct culture collections comprised of 24 Pantoea species, 41 isolation sources, and 23 countries, collected from 1946-2019, was tested. There is a significant association between the alt PCR assay and Pantoea strains recovered from symptomatic onion (P < 0.001). There is also a significant association of a positive HiVir PCR and RSN assay among P. ananatis strains but not among Pantoea spp., congeners. This may indicate a divergent HiVir cluster or different pathogenicity and virulence mechanisms. Last, we describe natural alt positive [RSN+/HiVir+/alt +] P. ananatis strains, which cause extensive bulb necrosis in a neck-to-bulb infection assay compared to alt negative [RSN+/HiVir+/alt -] P. ananatis strains. A combination of assays that include PCR of virulence genes [HiVir and alt] and an RSN assay can potentially aid in identification of onion-bulb-rotting pathogenic P. ananatis strains.
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Affiliation(s)
- Shaun P. Stice
- Department of Plant Pathology, University of Georgia College of Agricultural and Environmental Sciences, Athens, GA, United States
| | - Gi Yoon Shin
- Centre for Microbial Ecology and Genomics, Forestry and Agriculture Biotechnology Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Stefanie De Armas
- Área de Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Santosh Koirala
- Department of Plant Pathology, University of Georgia College of Agricultural and Environmental Sciences, Athens, GA, United States
| | - Guillermo A. Galván
- Departamento de Producción Vegetal, Centro Regional Sur (CRS), Facultad de Agronomía, Universidad de la República, Canelones, Uruguay
| | - María Inés Siri
- Área de Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Paul M. Severns
- Department of Plant Pathology, University of Georgia College of Agricultural and Environmental Sciences, Athens, GA, United States
| | - Teresa Coutinho
- Centre for Microbial Ecology and Genomics, Forestry and Agriculture Biotechnology Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Bhabesh Dutta
- Department of Plant Pathology, University of Georgia College of Agricultural and Environmental Sciences, Athens, GA, United States
| | - Brian H. Kvitko
- Department of Plant Pathology, University of Georgia College of Agricultural and Environmental Sciences, Athens, GA, United States
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20
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Pantoea ananatis, A New Bacterial Pathogen Affecting Wheat Plants ( Triticum L.) in Poland. Pathogens 2020; 9:pathogens9121079. [PMID: 33371529 PMCID: PMC7767503 DOI: 10.3390/pathogens9121079] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 12/14/2022] Open
Abstract
Wheat (Triticum aestivum) is one of the most economically important crops in the world. During the routine monitoring of wheat pest, the cereal leaf beetle (CLB, Oulema melanopus, Coleoptera, Chrysomelidae), in the Greater Poland region, it was observed that some leaves wounded by CLB also displayed brownish lesions with clear margins and yellow halo, disease symptoms resembling a bacterial infection. The aim of this study was therefore to investigate those symptoms to establish a causal agent of the disease. The identification based on the results of the Biolog’s Gen III system, 16S rRNA, and gyrB genes sequencing, revealed the presence of eight strains of Pantoea ananatis bacteria. Four strains were derived from wheat leaves (Ta024, Ta027, Ta030, Ta046), and four from the CLB’s oral secretion (OUC1, OUD2, OUF2, and OUG1). They shared the nucleotide identity ranging from 99 to 100% to P. ananatis strains deposited in the GenBank database. Additionally, the multi-locus sequence analysis (MLSA) of concatenated sequences of partial atpD, fusA, gyrB, rplB, and rpoB genes was performed. All P. ananatis strains isolated in Poland, grouped into one cluster supported with high bootstrap value. Pathogenicity tests performed on four varieties of wheat plants have identified P. ananatis strains as a causal agent of wheat disease. To our knowledge, this is the first report of P. ananatis affecting wheat plants.
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21
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Kini K, Lefeuvre P, Poulin L, Silué D, Koebnik R. Genome Resources of Three West African Strains of Pantoea ananatis Causing Bacterial Blight and Grain Discoloration of Rice. PHYTOPATHOLOGY 2020; 110:1500-1502. [PMID: 32338197 DOI: 10.1094/phyto-03-20-0091-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Members of the genus Pantoea have been reported as pathogens for many economically important crops, including rice. Little is known about their host-pathogen interactions at the molecular level and the lack of comprehensive genome data impedes targeted breeding strategies toward resistant rice cultivars. Here, we describe the structural and functional annotation of the draft genome sequences of three rice-pathogenic Pantoea ananatis strains, ARC272, ARC310, and ARC311, which were isolated in Burkina Faso, Togo, and Benin, respectively. The genome sequences of these strains will help in developing molecular diagnostic tools and provide new insight into common traits that may enable P. ananatis to infect rice.
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Affiliation(s)
- Kossi Kini
- AfricaRice, Plant Pathology, Africa Rice Center, B.P. 2031, Cotonou, Benin
- IRD, Cirad, Université de Montpellier, IPME, 34394 Montpellier, France
| | | | - Lucie Poulin
- IRD, Cirad, Université de Montpellier, IPME, 34394 Montpellier, France
| | - Drissa Silué
- AfricaRice, Plant Pathology, Africa Rice Center, B.P. 2031, Cotonou, Benin
| | - Ralf Koebnik
- IRD, Cirad, Université de Montpellier, IPME, 34394 Montpellier, France
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22
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Thiosulfinate Tolerance Is a Virulence Strategy of an Atypical Bacterial Pathogen of Onion. Curr Biol 2020; 30:3130-3140.e6. [PMID: 32619480 DOI: 10.1016/j.cub.2020.05.092] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/07/2020] [Accepted: 05/29/2020] [Indexed: 01/01/2023]
Abstract
Unlike most characterized bacterial plant pathogens, the broad-host-range plant pathogen Pantoea ananatis lacks both the virulence-associated type III and type II secretion systems. In the absence of these typical pathogenicity factors, P. ananatis induces necrotic symptoms and extensive cell death in onion tissue dependent on the HiVir proposed secondary metabolite synthesis gene cluster. Onion (Allium. cepa L), garlic (A. sativum L.), and other members of the Allium genus produce volatile antimicrobial thiosulfinates upon cellular damage. However, the roles of endogenous thiosulfinate production in host-bacterial pathogen interactions have not been described. We found a strong correlation between the genetic requirements for P. ananatis to colonize necrotized onion tissue and its capacity for tolerance to the thiosulfinate "allicin" based on the presence of an eleven-gene, plasmid-borne, virulence cluster of sulfur redox genes. We have designated them "alt" genes for allicin tolerance. We show that allicin and onion thiosulfinates restrict bacterial growth with similar kinetics. The alt gene cluster is sufficient to confer allicin tolerance and protects the glutathione pool during allicin treatment. Independent alt genes make partial phenotypic contributions indicating that they function as a collective cohort to manage thiol stress. Our work implicates endogenous onion thiosulfinates produced during cellular damage as major mediators of interactions with bacteria. The P. ananatis-onion pathosystem can be modeled as a chemical arms race of pathogen attack, host chemical counterattack, and pathogen defense.
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23
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Borlinghaus J, Bolger A, Schier C, Vogel A, Usadel B, Gruhlke MC, Slusarenko AJ. Genetic and molecular characterization of multicomponent resistance of Pseudomonas against allicin. Life Sci Alliance 2020; 3:e202000670. [PMID: 32234751 PMCID: PMC7119367 DOI: 10.26508/lsa.202000670] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/14/2020] [Accepted: 03/16/2020] [Indexed: 01/05/2023] Open
Abstract
The common foodstuff garlic produces the potent antibiotic defense substance allicin after tissue damage. Allicin is a redox toxin that oxidizes glutathione and cellular proteins and makes garlic a highly hostile environment for non-adapted microbes. Genomic clones from a highly allicin-resistant Pseudomonas fluorescens (PfAR-1), which was isolated from garlic, conferred allicin resistance to Pseudomonas syringae and even to Escherichia coli Resistance-conferring genes had redox-related functions and were on core fragments from three similar genomic islands identified by sequencing and in silico analysis. Transposon mutagenesis and overexpression analyses revealed the contribution of individual candidate genes to allicin resistance. Taken together, our data define a multicomponent resistance mechanism against allicin in PfAR-1, achieved through horizontal gene transfer.
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Affiliation(s)
- Jan Borlinghaus
- Department of Plant Physiology, Rheinisch-Westfälische Technische Hochschule Aachen (RWTH Aachen University), Aachen, Germany
| | - Anthony Bolger
- Department of Botany, Rheinisch-Westfälische Technische Hochschule Aachen (RWTH Aachen University), Aachen, Germany
| | - Christina Schier
- Department of Plant Physiology, Rheinisch-Westfälische Technische Hochschule Aachen (RWTH Aachen University), Aachen, Germany
| | - Alexander Vogel
- Department of Botany, Rheinisch-Westfälische Technische Hochschule Aachen (RWTH Aachen University), Aachen, Germany
| | - Björn Usadel
- Department of Botany, Rheinisch-Westfälische Technische Hochschule Aachen (RWTH Aachen University), Aachen, Germany
| | - Martin Ch Gruhlke
- Department of Plant Physiology, Rheinisch-Westfälische Technische Hochschule Aachen (RWTH Aachen University), Aachen, Germany
| | - Alan J Slusarenko
- Department of Plant Physiology, Rheinisch-Westfälische Technische Hochschule Aachen (RWTH Aachen University), Aachen, Germany
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24
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Newberry E, Bhandari R, Kemble J, Sikora E, Potnis N. Genome-resolved metagenomics to study co-occurrence patterns and intraspecific heterogeneity among plant pathogen metapopulations. Environ Microbiol 2020; 22:2693-2708. [PMID: 32207218 DOI: 10.1111/1462-2920.14989] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/09/2020] [Accepted: 03/18/2020] [Indexed: 01/12/2023]
Abstract
Assessment of pathogen diversity in agricultural fields is essential for informing management decisions and the development of resistant plant varieties. However, many population genomic studies have relied on culture-based approaches that do not provide quantitative assessment of pathogen populations at the field-level or the associated host microbiome. Here, we applied whole-genome shotgun sequencing of microbial DNA extracted directly from the washings of pooled leaf samples, collected from individual tomato and pepper fields in Alabama that displayed the classical symptoms of bacterial spot disease caused by Xanthomonas spp. Our results revealed that while the occurrence of both X. perforans and X. euvesicatoria within fields was limited, evidence of co-occurrence of up to three distinct X. perforans genotypes was obtained in 7 of 10 tomato fields sampled. These population dynamics were accompanied by the corresponding type 3 secreted effector repertoires associated with the co-occurring X. perforans genotypes, indicating that metapopulation structure within fields should be considered when assessing the adaptive potential of X. perforans. Finally, analysis of microbial community composition revealed that co-occurrence of the bacterial spot pathogens Pseudomonas cichorii and Xanthomonas spp. is common in Alabama fields and provided evidence for the non-random association of several other human and plant opportunists.
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Affiliation(s)
- Eric Newberry
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Rishi Bhandari
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Joseph Kemble
- Department of Horticulture, Auburn University, Auburn, AL, USA
| | - Edward Sikora
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA.,Alabama Cooperative Extension System, Auburn, AL, USA
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
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25
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Shin GY, Schachterle JK, Shyntum DY, Moleleki LN, Coutinho TA, Sundin GW. Functional Characterization of a Global Virulence Regulator Hfq and Identification of Hfq-Dependent sRNAs in the Plant Pathogen Pantoea ananatis. Front Microbiol 2019; 10:2075. [PMID: 31572315 PMCID: PMC6749038 DOI: 10.3389/fmicb.2019.02075] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/22/2019] [Indexed: 12/26/2022] Open
Abstract
To successfully infect plant hosts, the collective regulation of virulence factors in a bacterial pathogen is crucial. Hfq is an RNA chaperone protein that facilitates the small RNA (sRNA) regulation of global gene expression at the post-transcriptional level. In this study, the functional role of Hfq in a broad host range phytopathogen Pantoea ananatis was determined. Inactivation of the hfq gene in P. ananatis LMG 2665T resulted in the loss of pathogenicity and motility. In addition, there was a significant reduction of quorum sensing signal molecule acyl-homoserine lactone (AHL) production and biofilm formation. Differential sRNA expression analysis between the hfq mutant and wild-type strains of P. ananatis revealed 276 sRNAs affected in their abundance by the loss of hfq at low (OD600 = 0.2) and high cell (OD600 = 0.6) densities. Further analysis identified 25 Hfq-dependent sRNAs, all showing a predicted Rho-independent terminator of transcription and mapping within intergenic regions of the P. ananatis genome. These included known sRNAs such as ArcZ, FnrS, GlmZ, RprA, RyeB, RyhB, RyhB2, Spot42, and SsrA, and 16 novel P. ananatis sRNAs. The current study demonstrated that Hfq is an important component of the collective regulation of virulence factors and sets a foundation for understanding Hfq-sRNA mediated regulation in the phytopathogen P. ananatis.
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Affiliation(s)
- Gi Yoon Shin
- Centre for Microbial Ecology and Genomics, Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.,Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Jeffrey K Schachterle
- Department of Plant, Soil and Microbial Sciences, College of Agriculture & Natural Resources, Michigan State University, East Lansing, MI, United States
| | - Divine Y Shyntum
- Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Lucy N Moleleki
- Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Teresa A Coutinho
- Centre for Microbial Ecology and Genomics, Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.,Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - George W Sundin
- Department of Plant, Soil and Microbial Sciences, College of Agriculture & Natural Resources, Michigan State University, East Lansing, MI, United States
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Gutiérrez-Barranquero JA, Cazorla FM, Torés JA, de Vicente A. Pantoea agglomerans as a New Etiological Agent of a Bacterial Necrotic Disease of Mango Trees. PHYTOPATHOLOGY 2019; 109:17-26. [PMID: 30102576 DOI: 10.1094/phyto-06-18-0186-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Bacterial apical necrosis of mango trees, a disease elicited by Pseudomonas syringae pv. syringae, is a primary limiting factor of mango crop production in the Mediterranean region. In this study, a collection of bacterial isolates associated with necrotic symptoms in mango trees similar to those produced by bacterial apical necrosis disease were isolated over five consecutive years in orchards from the Canary Islands. The bacterial isolates were characterized and identified as Pantoea agglomerans. Pathogenicity tests conducted on onion bulbs and mango plants confirmed that P. agglomerans strains isolated from mango trees are a new etiological agent of a bacterial necrotic disease in the Canary Islands. Pathogenicity plasmids of the pPATH family have been previously reported in P. agglomerans. The majority of putatively pathogenic (n = 23) and pathogenic (n = 4) P. agglomerans strains isolated from mango trees harbored four plasmids, one of which was close in size to the 135-kb pPATH pathogenicity plasmid. The analysis of the presence of two major genes in pPATH plasmids (repA and hrpJ) was undertaken in P. agglomerans strains isolated from mango trees. The hrpJ gene was detected in the 140-kb plasmid of pathogenic P. agglomerans strains isolated from mango trees but it showed differences in nucleotide sequences compared with other pathogenic strains. In contrast, the repA gene was not detected in any of the putatively pathogenic and pathogenic P. agglomerans strains isolated from mango trees. Finally, genetic characterization and phylogenetic analysis using the hrpJ gene and the housekeeping genes gyrB and rpoB showed that almost all P. agglomerans strains that were putatively pathogenic and pathogenic on mango trees clustered together, forming a differentiated phylogroup with respect to the other pathogenic P. agglomerans strains described from other hosts.
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Affiliation(s)
- José A Gutiérrez-Barranquero
- First, second, and fourth authors: Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain; and third author: IHSM-UMA-CSIC, Estación Experimental "La Mayora", 29750 Algarrobo-Costa (Málaga), Spain
| | - Francisco M Cazorla
- First, second, and fourth authors: Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain; and third author: IHSM-UMA-CSIC, Estación Experimental "La Mayora", 29750 Algarrobo-Costa (Málaga), Spain
| | - Juan Antonio Torés
- First, second, and fourth authors: Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain; and third author: IHSM-UMA-CSIC, Estación Experimental "La Mayora", 29750 Algarrobo-Costa (Málaga), Spain
| | - Antonio de Vicente
- First, second, and fourth authors: Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain; and third author: IHSM-UMA-CSIC, Estación Experimental "La Mayora", 29750 Algarrobo-Costa (Málaga), Spain
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