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Pathogens
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Plant Pathogenic Bacteria in Crops
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Plant Pathogenic Bacteria in Crops

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Bacterial Pathogens".

Deadline for manuscript submissions: closed (30 September 2022) | Viewed by 21043

Special Issue Editor

Prof. Jong Hyun Ham

E-Mail Website
Guest Editor
Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70808, USA
Interests: virulence mechanisms of plant pathogenic bacteria; genetics and genomics of plant disease resistance; microbiome structure and function for plant growth promotion

Special Issue Information

Dear Colleagues,

Stable crop production is frequently challenged by outbreaks of various plant diseases. In particular, numerous species of emerging and established bacterial pathogens cause serious economic losses not only from direct damages to crops but from quarantine practices including trading restriction. In most cases, it is not practical to use antibiotic chemicals for managing bacterial diseases in crops due to legal restriction and rapid generation of antibiotic resistance. Therefore, it is very imperative to develop alternative strategies for effective management of major bacterial diseases in crops based on better understanding of bacterial pathogens, plant disease resistance and environmental factors affecting disease severity.      

Study of plant pathogenic bacteria includes diagnostics, etiology, molecular genetics, population genetics, plant-bacterial interactions, disease management, epidemiology, and the recently emerging microbiomics. Integrated information obtained from these study areas is the foundation for developing innovative and sustainable strategies to manage bacterial crop diseases. In particular, recently emerging multi-omics studies provide new insights into the development of novel approaches for sustainable management of bacterial diseases.     

This Special Issue will publish original research articles and/or review articles covering current topics in all the aforementioned study areas of bacterial plant diseases. 

Prof. Jong Hyun Ham
Guest Editor

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Keywords

  • virulence mechanism of plant pathogenic bacteria
  • plant resistance to bacterial diseases
  • innovative strategies to manage bacterial plant diseases
  • plant-bacterial interactions
  • major and emerging bacterial diseases in crops

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Published Papers (6 papers)

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Research

17 pages, 3645 KiB  
Article
Next Generation Sequencing and Comparative Genomic Analysis Reveal Extreme Plasticity of Two Burkholderia glumae Strains HN1 and HN2
by Sai Wang, Wenhan Nie, Ayizekeranmu Yiming, Peihong Wang, Yan Wu, Jin Huang, Iftikhar Ahmad, Gongyou Chen, Longbiao Guo and Bo Zhu
Pathogens 2022, 11(11), 1265; https://doi.org/10.3390/pathogens11111265 - 30 Oct 2022
Cited by 1 | Viewed by 1960
Abstract
Burkholderia glumae is an important rice pathogen, thus the genomic and evolutionary history may be helpful to control this notorious pathogen. Here, we present two complete genomes of the B. glumae strains HN1 and HN2, which were isolated from diseased rice seed in [...] Read more.
Burkholderia glumae is an important rice pathogen, thus the genomic and evolutionary history may be helpful to control this notorious pathogen. Here, we present two complete genomes of the B. glumae strains HN1 and HN2, which were isolated from diseased rice seed in China. Average nucleotide identity (ANI) analysis shows greater than 99% similarity of the strains HN1 and HN2 with other published B. glumae genomes. Genomic annotation revealed that the genome of strain HN1 consists of five replicons (6,680,415 bp) with an overall G + C content of 68.06%, whereas the genome of strain HN2 comprises of three replicons (6,560,085 bp) with an overall G + C content of 68.34%. The genome of HN1 contains 5434 protein-coding genes, 351 pseudogenes, and 1 CRISPR, whereas the genome of HN2 encodes 5278 protein-coding genes, 357 pseudogenes, and 2 CRISPR. Both strains encode many pathogenic-associated genes (143 genes in HN1 vs. 141 genes in HN2). Moreover, comparative genomic analysis shows the extreme plasticity of B. glumae, which may contribute to its pathogenicity. In total, 259 single-copy genes were affected by positive selection. These genes may contribute to the adaption to different environments. Notably, six genes were characterized as virulence factors which may be an additional way to assist the pathogenicity of B. glumae. Full article
(This article belongs to the Special Issue Plant Pathogenic Bacteria in Crops)
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28 pages, 2253 KiB  
Article
The International Trade of Ware Vegetables and Orna-Mental Plants—An Underestimated Risk of Accelerated Spreading of Phytopathogenic Bacteria in the Era of Globalisation and Ongoing Climatic Changes
by Magdalena Smoktunowicz, Joanna Jonca, Aneta Stachowska, Michal May, Michal Mateusz Waleron, Malgorzata Waleron and Krzysztof Waleron
Pathogens 2022, 11(7), 728; https://doi.org/10.3390/pathogens11070728 - 26 Jun 2022
Cited by 6 | Viewed by 2096
Abstract
Bacteria of the genus Pectobacterium are globally occurring pathogens that infect a broad spectrum of plants. The plant cell wall degrading enzymes allow them to cause diseases like soft rot and blackleg. Worldwide trade and exchange of plant material together with the accompanying [...] Read more.
Bacteria of the genus Pectobacterium are globally occurring pathogens that infect a broad spectrum of plants. The plant cell wall degrading enzymes allow them to cause diseases like soft rot and blackleg. Worldwide trade and exchange of plant material together with the accompanying microorganisms contributed to the rapid spread and consequently the acquisition of new traits by bacteria. The 161 pectinolytic strains were isolated from symptomless vegetables and ornamental plants acquired from Polish and foreign local food markets. All strains except four Dickeya isolates were identified as belonging to the Pectobacterium genus by PCR with species-specific primers and recA gene sequencing. The newly isolated bacteria were assigned to eight species, P. versatile (50 strains), P. carotovorum (33), P. brasiliense (27), P. atrosepticum (19), P. parmentieri (12), P. polaris (11), P. parvum (3) and P. odoriferum (2). ERIC PCR and phenotypic characteristics revealed high heterogeneity among P. carotovorum, P. brasiliense and P. versatile isolates. Moreover, a subset of the newly isolated strains was characterised by high tolerance to changing environmental conditions such as salinity, pH and water availability. These bacteria can effectively macerate the tissues of various plants, including potato, chicory and orchid. Our results indicate that Pectobacterium strains isolated from internationally traded, symptomless vegetables and ornamental plants have high potential for adaptation to adverse environmental conditions and to infect various host plants. These features may contribute to the success of the genus Pectobacterium in spreading between different climatic zones and facilitate the colonisation of different ecological niches. Full article
(This article belongs to the Special Issue Plant Pathogenic Bacteria in Crops)
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17 pages, 3177 KiB  
Article
Phylogenetic Characterization and Genome Sequence Analysis of Burkholderia glumae Strains Isolated in Thailand as the Causal Agent of Rice Bacterial Panicle Blight
by Nootjarin Jungkhun, Antonio Roberto Gomes de Farias, Jutatape Watcharachaiyakup, Nuttima Kositcharoenkul, Jong Hyun Ham and Sujin Patarapuwadol
Pathogens 2022, 11(6), 676; https://doi.org/10.3390/pathogens11060676 - 11 Jun 2022
Cited by 6 | Viewed by 3747
Abstract
Burkholderia glumae is one of the most critical rice-pathogenic bacteria, and it causes bacterial panicle blight (BPB) in rice plants. In 2017, BPB symptoms were observed from rice fields in Chiang Rai, Northern Thailand. Sixty-one isolates obtained from the symptomatic panicles of rice [...] Read more.
Burkholderia glumae is one of the most critical rice-pathogenic bacteria, and it causes bacterial panicle blight (BPB) in rice plants. In 2017, BPB symptoms were observed from rice fields in Chiang Rai, Northern Thailand. Sixty-one isolates obtained from the symptomatic panicles of rice were initially identified as B. glumae by polymerase chain reaction (PCR) using species-specific primers. Among them, six selected strains isolated from the susceptible japonica rice cultivar DOA2 were characterized in terms of morpho-physiology, pathology, phylogenetics, and genomics. Our genome sequence analysis of the six selected strains revealed the presence of multiple prophages, which may reflect the high level of diversity in this bacterial species through dynamic horizontal gene transfer processes, including phage infection. This notion was supported by the results of phylogenetic and phylogenomic analyses, which showed the formation of several subgroups not related to the years of isolation or the geographical origins. This study reports the isolation of B. glumae as the causal pathogen of BPB disease in japonica rice in Thailand and provides genomic resources to better understand the biology and diversity of this plant pathogenic bacterium. Further studies with a vast collection of B. glumae strains from various rice-growing regions around the world are needed to elucidate the evolution, variability, and lifestyle of the pathogen. Full article
(This article belongs to the Special Issue Plant Pathogenic Bacteria in Crops)
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11 pages, 5651 KiB  
Article
Detection of Rhodococcus fascians, the Causative Agent of Lily Fasciation in South Korea
by Joon Moh Park, Jachoon Koo, Se Won Kang, Sung Hee Jo and Jeong Mee Park
Pathogens 2021, 10(2), 241; https://doi.org/10.3390/pathogens10020241 - 20 Feb 2021
Cited by 2 | Viewed by 3326
Abstract
Rhodococcus fascians is an important pathogen that infects various herbaceous perennials and reduces their economic value. In this study, we examined R. fascians isolates carrying a virulence gene from symptomatic lily plants grown in South Korea. Phylogenetic analysis using the nucleotide sequences of [...] Read more.
Rhodococcus fascians is an important pathogen that infects various herbaceous perennials and reduces their economic value. In this study, we examined R. fascians isolates carrying a virulence gene from symptomatic lily plants grown in South Korea. Phylogenetic analysis using the nucleotide sequences of 16S rRNA, vicA, and fasD led to the classification of the isolates into four different strains of R. fascians. Inoculation of Nicotiana benthamiana with these isolates slowed root growth and resulted in symptoms of leafy gall. These findings elucidate the diversification of domestic pathogenic R. fascians and may lead to an accurate causal diagnosis to help reduce economic losses in the bulb market. Full article
(This article belongs to the Special Issue Plant Pathogenic Bacteria in Crops)
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14 pages, 4913 KiB  
Article
Genome Sequence and Adaptation Analysis of the Human and Rice Pathogenic Strain Burkholderia glumae AU6208
by Zhouqi Cui, Sai Wang, Kaleem Ullah Kakar, Guanglin Xie, Bin Li, Gongyou Chen and Bo Zhu
Pathogens 2021, 10(2), 87; https://doi.org/10.3390/pathogens10020087 - 20 Jan 2021
Cited by 8 | Viewed by 2477
Abstract
Burkholderia glumae causes rice (Oryza sativa) bacterial panicle blight, which is an increasingly economically important disease worldwide. As the first B. glumae strain isolated from patients with chronic infections, AU6208 has been reported as an opportunistic clinic pathogen. However, our understanding [...] Read more.
Burkholderia glumae causes rice (Oryza sativa) bacterial panicle blight, which is an increasingly economically important disease worldwide. As the first B. glumae strain isolated from patients with chronic infections, AU6208 has been reported as an opportunistic clinic pathogen. However, our understanding of the molecular mechanism underlying human pathogenesis by B. glumae remains rudimentary. In this study, we report the complete genome sequence of the human-isolated B. glumae strain AU6208 and compare this to the genome of the rice-pathogenic B. glumae type strain LMG 2196T. Analysis of the average nucleotide identity demonstrated 99.4% similarity between the human- and plant-pathogenic strains. However, the phenotypic results from this study suggest a history of niche adaptation and divergence. In particular, we found 44 genes were predicted to be horizontally transferred into AU6208, and most of these genes were upregulated in conditions that mimic clinical conditions. In these, the gene pair sbnAB encodes key enzymes in antibiotic biosynthesis. These results suggest that horizontal gene transfer in AU6208 may be responsible for selective advantages in its pathogenicity in humans. Our analysis of the AU6208 genome and comparison with that of LMG 2196T reveal the evolutionary signatures of B. glumae in the process of switching niches from plants to humans. Full article
(This article belongs to the Special Issue Plant Pathogenic Bacteria in Crops)
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13 pages, 1811 KiB  
Article
Pantoea ananatis, A New Bacterial Pathogen Affecting Wheat Plants (Triticum L.) in Poland
by Krzysztof Krawczyk, Beata Wielkopolan and Aleksandra Obrępalska-Stęplowska
Pathogens 2020, 9(12), 1079; https://doi.org/10.3390/pathogens9121079 - 21 Dec 2020
Cited by 19 | Viewed by 5866
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Plant Pathogenic Bacteria in Crops)
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