Plant Pathogenic Bacteria: Genetics, Genomics and Molecular Biology

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Plant Microbe Interactions".

Deadline for manuscript submissions: closed (15 April 2023) | Viewed by 11538

Special Issue Editors


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Faculty of Health and Applied Sciences, Harper Adams University, Newport, Shropshire TF10 8NB, UK
Interests: plant pathology; Pseudomonas plant pathogens; bacterial plant pathogens; evolution of virulence in plant pathogens; bacterial tree diseases
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Department of Agriculture, Food and Environment, University of Catania, 95125 Catania, Italy
Interests: plant pathology; bacterial plant pathogens; diagnosis; plant-microbiome interaction; characterization of biocontrol bacteria

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The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
Interests: plant-microbe interactions; bacterial pathogen evolution; effector biology; bacterial population genomics

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School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
Interests: plant-microbe interaction; tree bacterial diseases; biological control; bacteriophage-bacteria coevolution
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant pathogenic bacteria cause a number of devastating diseases that have serious consequences in areas such as global food security. Plant pathogenic bacteria cause disease on a wide range of plants from crops to trees. These bacteria can cause serious infections individually or working in consortium with other bacteria or other biotic and abiotic factors. The recent example of Xylella fastidiosa, which causes serious disease on a number of different plants and is spreading within mainland Europe, has led to increased concern about bacterial pathogens.  

Advances in research into the genetics, genomics and molecular biology of plant pathogenic bacteria are helping to unravel their lifestyle and mechanisms used to cause disease, leading to improved detection, prevention of infection and control of disease.

The aim of this Special Issue of Microorganisms is to present a collection of articles that provide a current snapshot of the research on bacterial plant pathogens. Manuscripts covering the genetics, genomics and molecular biology of plant pathogenic bacteria are welcome, including work from an applied angle (e.g., novel diagnostics) through to more fundamental questions relating to the biology of bacteria and their pathogenesis and epidemiology.

Prof. Dawn L. Arnold
Dr. Vittoria Catara
Dr. Michelle Hulin
Dr. Mojgan Rabiey
Guest Editors

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Keywords

  • plant pathogenic bacteria
  • plant pathology
  • molecular genetics of pathogenic bacteria
  • molecular plant-pathogenic bacteria interaction
  • molecular biology of pathogenic bacteria

Published Papers (6 papers)

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Research

14 pages, 1944 KiB  
Article
Regulation of corA, the Magnesium, Nickel, Cobalt Transporter, and Its Role in the Virulence of the Soft Rot Pathogen, Pectobacterium versatile Strain Ecc71
by Caleb M. Kersey and C. Korsi Dumenyo
Microorganisms 2023, 11(7), 1747; https://doi.org/10.3390/microorganisms11071747 - 04 Jul 2023
Viewed by 953
Abstract
Pectobacterium versatile (formally P. carotovorum) causes disease on diverse plant species by synthesizing and secreting copious amount of plant-cell-wall-degrading exoenzymes including pectate lyases, polygalacturonases, cellulases, and proteases. Exoenzyme production and virulence are controlled by many factors of bacterial, host, and environmental origin. [...] Read more.
Pectobacterium versatile (formally P. carotovorum) causes disease on diverse plant species by synthesizing and secreting copious amount of plant-cell-wall-degrading exoenzymes including pectate lyases, polygalacturonases, cellulases, and proteases. Exoenzyme production and virulence are controlled by many factors of bacterial, host, and environmental origin. The ion channel forming the magnesium, nickel, and cobalt transporter CorA is required for exoenzyme production and full virulence in strain Ecc71. We investigated CorA’s role as a virulence factor and its expression in P. versatile. Inhibiting the transport function of CorA by growing a CorA+ strain in the presence of specific CorA inhibitor, cobalt (III) hexaammine (Co (III)Hex), has no effect on exoenzyme production. Transcription of pel-1, encoding a pectate lyase isozyme, is decreased in the absence of CorA, suggesting that CorA influences exoenzyme production at the transcriptional level, although apparently not through its transport function. CorA and CorA+ strains grown in the presence of Co (III)Hex transcriptionally express corA at higher levels than CorA+ strains in the absence of an inhibitor, suggesting the transport role of corA contributes to autorepression. The expression of corA is about four-fold lower in HrpL strains lacking the hrp-specific extracytoplasmic sigma factor. The corA promoter region contains a sequence with a high similarity to the consensus Hrp box, suggesting that corA is part of Hrp regulon. Our data suggest a complex role, possibly requiring the physical presence of the CorA protein in the virulence of the Pectobacterium versatile strain Ecc71. Full article
(This article belongs to the Special Issue Plant Pathogenic Bacteria: Genetics, Genomics and Molecular Biology)
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15 pages, 3279 KiB  
Article
ntrC Contributes to Nitrogen Utilization, Stress Tolerance, and Virulence in Acidovorax citrulli
by Dehua Liu, Mei Zhao, Pei Qiao, Zhanhong Li, Gong Chen, Wei Guan, Qingrong Bai, Ron Walcott, Yuwen Yang and Tingchang Zhao
Microorganisms 2023, 11(3), 767; https://doi.org/10.3390/microorganisms11030767 - 16 Mar 2023
Cited by 5 | Viewed by 1247
Abstract
Bacterial fruit blotch (BFB), caused by Acidovorax citrulli, severely damages watermelon, melon, and other cucurbit crops worldwide. Nitrogen, one of the most important limiting elements in the environment, is necessary for the growth and reproduction of bacteria. As a nitrogen-regulating gene, ntrC [...] Read more.
Bacterial fruit blotch (BFB), caused by Acidovorax citrulli, severely damages watermelon, melon, and other cucurbit crops worldwide. Nitrogen, one of the most important limiting elements in the environment, is necessary for the growth and reproduction of bacteria. As a nitrogen-regulating gene, ntrC plays an important role in maintaining bacterial nitrogen utilization and biological nitrogen fixation. However, the role of ntrC has not been determined for A. citrulli. In this study, we constructed a ntrC deletion mutant and a corresponding complementary strain in the background of the A. citrulli wild-type strain, Aac5. Through phenotype assays and qRT-PCR analysis, we investigated the role of ntrC in A. citrulli in nitrogen utilization, stress tolerance, and virulence against watermelon seedlings. Our results showed that the A. citrulli Aac5 ntrC deletion mutant lost the ability to utilize nitrate. The ntrC mutant strain also exhibited significantly decreased virulence, in vitro growth, in vivo colonization ability, swimming motility, and twitching motility. In contrast, it displayed significantly enhanced biofilm formation and tolerance to stress induced by oxygen, high salt, and copper ions. The qRT-PCR results showed that the nitrate utilization gene nasS; the Type III secretion system-related genes hrpE, hrpX, and hrcJ; and the pili-related gene pilA were significantly downregulated in the ntrC deletion mutant. The nitrate utilization gene nasT, and the flagellum-related genes flhD, flhC, fliA, and fliC were significantly upregulated in the ntrC deletion mutant. The expression levels of ntrC gene in the MMX-q and XVM2 media were significantly higher than in the KB medium. These results suggest that the ntrC gene plays a pivotal role in the nitrogen utilization, stress tolerance, and virulence of A. citrulli. Full article
(This article belongs to the Special Issue Plant Pathogenic Bacteria: Genetics, Genomics and Molecular Biology)
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16 pages, 2744 KiB  
Article
Characterization of the Asian Citrus Psyllid-‘Candidatus Liberibacter Asiaticus’ Pathosystem in Saudi Arabia Reveals Two Predominant CLas Lineages and One Asian Citrus Psyllid Vector Haplotype
by Yasser E. Ibrahim, Jorge R. Paredes-Montero, Mohammed A. Al-Saleh, Arya Widyawan, Ruifeng He, Mahmoud H. El Komy, Hathal M. Al Dhafer, Noel Kitchen, David R. Gang and Judith K. Brown
Microorganisms 2022, 10(10), 1991; https://doi.org/10.3390/microorganisms10101991 - 08 Oct 2022
Viewed by 1618
Abstract
In Saudi Arabia (SA), the citrus greening disease is caused by ‘Candidatus Liberibacter asiaticus’ (CLas) transmitted by the Asian citrus psyllid (ACP) Diaphorina citri. The origin and route(s) of the ACP-CLas pathosystem invasion in SA have not been studied. Adult ACP [...] Read more.
In Saudi Arabia (SA), the citrus greening disease is caused by ‘Candidatus Liberibacter asiaticus’ (CLas) transmitted by the Asian citrus psyllid (ACP) Diaphorina citri. The origin and route(s) of the ACP-CLas pathosystem invasion in SA have not been studied. Adult ACP were collected from citrus trees in SA and differentiated by analysis of the mitochondrial cytochrome oxidase I (mtCOI) and nuclear copper transporting protein (atox1) genes. A phylogenetic analysis of the Wolbachia spp. surface protein (wsp) gene was used to identify the ACP-associated Wolbachia spp. A phylogenetic analysis of the atox1 and mtCOI gene sequences revealed one predominant ACP haplotype most closely related to the Indian subcontinent founder populations. The detection and identification of CLas in citrus trees were carried out by polymerase chain reaction (PCR) amplification and sequencing of the 16S rDNA gene. The CLas-integrated prophage genomes were sequenced, annotated, and used to differentiate CLas populations. The ML and ASTRAL trees reconstructed with prophages type 1 and 2 genome sequences, separately and concatenated, resolved two major lineages, CLas-1 and -2. The CLas-1 clade, reported here for the first time, consisted of isolates from SA isolates and Pakistan. The CLas-2 sequences formed two groups, CLas-2-1 and -2-2, previously the ‘Asiatic’ and ‘Floridian’ strains, respectively. Members of CLas-2-1 originated from Southeast Asia, the USA, and other worldwide locations, while CLas-2-2 was identified only in Florida. This study provides the first snapshot into the status of the ACP-CLas pathosystem in SA. In addition, the results provide new insights into the pathosystem coevolution and global invasion histories of two ACP-CLas lineages with a predicted center of origin in South and Southeast Asia, respectively. Full article
(This article belongs to the Special Issue Plant Pathogenic Bacteria: Genetics, Genomics and Molecular Biology)
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15 pages, 7893 KiB  
Article
Development of Droplet Digital PCR Assay for Detection of Seed-Borne Burkholderia glumae and B. gladioli Causing Bacterial Panicle Blight Disease of Rice
by Jiannan Zhang, Jinyan Luo, Lei Chen, Temoor Ahmed, Saqer S. Alotaibi, Yanli Wang, Guochang Sun, Bin Li and Qianli An
Microorganisms 2022, 10(6), 1223; https://doi.org/10.3390/microorganisms10061223 - 15 Jun 2022
Cited by 4 | Viewed by 2151
Abstract
Bacterial panicle blight of rice or bacterial grain rot of rice is a worldwide rice disease. Burkholderia glumae and B. gladioli are the causal agents. The early and accurate detection of seed-borne B. glumae and B. gladioli is critical for domestic and international [...] Read more.
Bacterial panicle blight of rice or bacterial grain rot of rice is a worldwide rice disease. Burkholderia glumae and B. gladioli are the causal agents. The early and accurate detection of seed-borne B. glumae and B. gladioli is critical for domestic and international quarantine and effective control of the disease. Here, genomic analyses revealed that B. gladioli contains five phylogroups and the BG1 primer pair designed to target the 3’-end sequence of a gene encoding a Rhs family protein is specific to B. glumae and two phylogroups within B. gladioli. Using the BG1 primer pair, a 138-bp DNA fragment was amplified only from the tested panicle blight pathogens B. glumae and B. gladioli. An EvaGreen droplet digital PCR (dPCR) assay on detection and quantification of the two pathogens was developed from a SYBR Green real-time quantitative PCR (qPCR). The detection limits of the EvaGreen droplet dPCR on the two pathogens were identical at 2 × 103 colony forming units (CFU)∙mL−1 from bacterial suspensions and 2 × 102 CFU∙seed−1 from rice seeds. The EvaGreen droplet dPCR assay showed 10-fold detection sensitivity of the SYBR Green qPCR and could detect a single copy of the target gene in a 20-μL assay. Together, the SYBR Green qPCR assay allows for routine high-throughput detection of the panicle blight pathogens and the EvaGreen droplet dPCR assay provides a high-sensitive and high-accurate diagnostic method for quarantine of the pathogens. Full article
(This article belongs to the Special Issue Plant Pathogenic Bacteria: Genetics, Genomics and Molecular Biology)
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18 pages, 3381 KiB  
Article
The GDSL-Lipolytic Enzyme Lip1 Is Required for Full Virulence of the Cucurbit Pathogenic Bacterium Acidovorax citrulli
by Tally Rosenberg, Irene Jiménez-Guerrero, Dafna Tamir-Ariel, Tali Yarnitzky and Saul Burdman
Microorganisms 2022, 10(5), 1016; https://doi.org/10.3390/microorganisms10051016 - 12 May 2022
Cited by 2 | Viewed by 1698
Abstract
Bacterial fruit blotch caused by Acidovoraxcitrulli is a serious disease of cucurbit crops. Here we report characterization of a mutant strain of A. citrulli M6 defective in lip1, a gene encoding a lipolytic enzyme. The M6-lip1- mutant was detected [...] Read more.
Bacterial fruit blotch caused by Acidovoraxcitrulli is a serious disease of cucurbit crops. Here we report characterization of a mutant strain of A. citrulli M6 defective in lip1, a gene encoding a lipolytic enzyme. The M6-lip1- mutant was detected in a mutant library screen aimed at identifying M6 mutants with altered levels of twitching motility. In this screen M6-lip1- was the only mutant that showed significantly larger twitching motility haloes around colonies than wild-type M6. Sequence analyses indicated that lip1 encodes a member of the GDSL family of secreted lipolytic enzymes. In line with this finding, lipolytic assays showed that the supernatants of M6-lip1- had lower lipolytic activity as compared with those of wild-type M6 and a lip1-complemented strain. The mutant was also affected in swimming motility and had compromised virulence on melon seedlings and on Nicotiana benthamiana leaves relative to wild-type and complemented strains. Lip1 contains a predicted N-terminal signal sequence for type II secretion. Evidence from our study confirms Lip1 is indeed secreted in a type II secretion-dependent manner, and this is required for full virulence of A. citrulli. To the best of our knowledge this is the first study reporting contribution of lipolytic activity to virulence of a plant-pathogenic Acidovorax species. Full article
(This article belongs to the Special Issue Plant Pathogenic Bacteria: Genetics, Genomics and Molecular Biology)
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18 pages, 3435 KiB  
Article
XAC4296 Is a Multifunctional and Exclusive Xanthomonadaceae Gene Containing a Fusion of Lytic Transglycosylase and Epimerase Domains
by Amanda C. P. de Oliveira, Rafael M. Ferreira, Maria Inês T. Ferro, Jesus A. Ferro, Caio Zamuner, Henrique Ferreira and Alessandro M. Varani
Microorganisms 2022, 10(5), 1008; https://doi.org/10.3390/microorganisms10051008 - 11 May 2022
Viewed by 1678
Abstract
Microorganisms have a limited and highly adaptable repertoire of genes capable of encoding proteins containing single or variable multidomains. The phytopathogenic bacteria Xanthomonas citri subsp. citri (X. citri) (Xanthomonadaceae family), the etiological agent of Citrus Canker (CC), presents a collection [...] Read more.
Microorganisms have a limited and highly adaptable repertoire of genes capable of encoding proteins containing single or variable multidomains. The phytopathogenic bacteria Xanthomonas citri subsp. citri (X. citri) (Xanthomonadaceae family), the etiological agent of Citrus Canker (CC), presents a collection of multidomain and multifunctional enzymes (MFEs) that remains to be explored. Recent studies have shown that multidomain enzymes that act on the metabolism of the peptidoglycan and bacterial cell wall, belonging to the Lytic Transglycosylases (LTs) superfamily, play an essential role in X. citri biology. One of these LTs, named XAC4296, apart from the Transglycosylase SLT_2 and Peptidoglycan binding-like domains, contains an unexpected aldose 1-epimerase domain linked to the central metabolism; therefore, resembling a canonical MFE. In this work, we experimentally characterized XAC4296 revealing its role as an MFE and demonstrating its probable gene fusion origin and evolutionary history. The XAC4296 is expressed during plant-pathogen interaction, and the Δ4296 mutant impacts CC progression. Moreover, Δ4296 exhibited chromosome segregation and cell division errors, and sensitivity to ampicillin, suggesting not only LT activity but also that the XAC4296 may also contribute to resistance to β-lactams. However, both Δ4296 phenotypes can be restored when the mutant is supplemented with sucrose or glutamic acid as a carbon and nitrogen source, respectively; therefore, supporting the epimerase domain’s functional relationship with the central carbon and cell wall metabolism. Taken together, these results elucidate the role of XAC4296 as an MFE in X. citri, also bringing new insights into the evolution of multidomain proteins and antimicrobial resistance in the Xanthomonadaceae family. Full article
(This article belongs to the Special Issue Plant Pathogenic Bacteria: Genetics, Genomics and Molecular Biology)
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