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Microorganisms
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Molecular Analysis of Plant Pathogenic Bacteria
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Molecular Analysis of Plant Pathogenic Bacteria

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

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 13519

Special Issue Editor

Dr. Toni A. Chapman

E-Mail Website
Guest Editor
Elizabeth Macarthur Agricultural Institute, Menangle 2568, Australia
Interests: plant bacteriology; diagnostics for plant pathogenic bacteria; microbial ecosystems; biosecurity; bacterial diagnostics and genomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Bacterial taxonomy is currently in a state of flux. As we learn more about bacteria through the application of molecular techniques, the accuracy of taxonomic identification can come into question. What type of analysis will suffice for an identification down to the subspecies level? What techniques are being used to separate species and subspecies within the different plant genera? What are we using to investigate pathogenicity and is this translating to disease severity in plants? How is the use of molecular techniques helping us to understand bacterial pathogens more? In this special edition, we plan to explore the use of molecular techniques to correctly identify bacterial pathogens and pathogenicity.

Dr. Toni A. Chapman
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • bacterial taxonomy
  • pathogenicity
  • bacterial pathogens

Related Special Issue

Published Papers (6 papers)

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Research

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11 pages, 7900 KiB  
Article
Analysis of the Diversity of Xylophilus ampelinus Strains Held in CIRM-CFBP Reveals a Strongly Homogenous Species
by Perrine Portier, Géraldine Taghouti, Paul-Emile Bertrand, Martial Briand, Cécile Dutrieux, Audrey Lathus and Marion Fischer-Le Saux
Microorganisms 2022, 10(8), 1531; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10081531 - 28 Jul 2022
Cited by 2 | Viewed by 1498
Abstract
Xylophilus ampelinus is the causal agent of blight and canker on grapevine. Only a few data are available on this species implying that the occurrence of this pathogen may be underestimated, and its actual ecological niche may not be understood. Moreover, its genetic [...] Read more.
Xylophilus ampelinus is the causal agent of blight and canker on grapevine. Only a few data are available on this species implying that the occurrence of this pathogen may be underestimated, and its actual ecological niche may not be understood. Moreover, its genetic diversity is not well known. To improve our knowledge of this species, an analysis of the complete genome sequences available in NCBI was performed. It appeared that several sequences are misidentified. The complete genome sequence of the type strain was obtained and primers designed in order to sequence gyrB and rpoD genes for the strains held in CIRM-CFBP. The genetic barcoding data were obtained for 93 strains, isolated over 35 years and from several geographical origins. The species revealed to be strongly homogenous, displaying nearly identical sequences for all strains. However, the oldest strains of this collection were isolated in 2001 therefore, a new isolation campaign and epidemiological surveys are necessary, along with the obtention of new complete genome sequences for this species. Full article
(This article belongs to the Special Issue Molecular Analysis of Plant Pathogenic Bacteria)
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7 pages, 246 KiB  
Communication
Using Genomics to Design a Pathovar-Specific Loop-Mediated Isothermal Amplification (LAMP) Assay, for the Improved Detection of Xanthomonas citri pv. citri
by John Webster, Monica A. Kehoe, Elisse Nogarotto, Linda Falconer, Nerida Jane Donovan and Toni A. Chapman
Microorganisms 2022, 10(6), 1153; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10061153 - 02 Jun 2022
Viewed by 1576
Abstract
The ability to swiftly respond to pathogen incursions relies heavily on fast and accurate diagnostics. Current published assays for citrus bacterial canker do not target Xanthomonas citri pv. citri, the causative agent, with high specificity when testing Australian samples. While the current [...] Read more.
The ability to swiftly respond to pathogen incursions relies heavily on fast and accurate diagnostics. Current published assays for citrus bacterial canker do not target Xanthomonas citri pv. citri, the causative agent, with high specificity when testing Australian samples. While the current diagnostics are useful in countries where canker is endemic, the detection of canker in Australia requires an emergency response. Close relatives to X. citri pv. citri found in Australia may generate false positives with the current recommended diagnostic assays. Therefore, we developed a more specific detection tool for citrus bacterial canker to provide greater diagnostic confidence for surveillance and eradication efforts. We used genomic comparisons of 161 Xanthomonad genomes and identified and confirmed genomic regions specific for X. citri pv. citri by performing local alignments of unique regions to reference genomes. We then developed loop-mediated isothermal amplification primers and validated them against a panel of 190 isolates to confirm specificity. Our diagnostic assay showed 100% corroboration with the concurrently developed multiplex primers and represents an improved diagnostic method capable of effective citrus bacterial canker identification. Full article
(This article belongs to the Special Issue Molecular Analysis of Plant Pathogenic Bacteria)
15 pages, 2299 KiB  
Article
The Only Chemoreceptor Encoded by che Operon Affects the Chemotactic Response of Agrobacterium to Various Chemoeffectors
by Jingyang Ye, Miaomiao Gao, Qingxuan Zhou, Hao Wang, Nan Xu and Minliang Guo
Microorganisms 2021, 9(9), 1923; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091923 - 10 Sep 2021
Cited by 5 | Viewed by 2354
Abstract
Chemoreceptor (also called methyl-accepting chemotaxis protein, MCP) is the leading signal protein in the chemotaxis signaling pathway. MCP senses and binds chemoeffectors, specifically, and transmits the sensed signal to downstream proteins of the chemotaxis signaling system. The genome of Agrobacterium fabrum (previously, tumefaciens [...] Read more.
Chemoreceptor (also called methyl-accepting chemotaxis protein, MCP) is the leading signal protein in the chemotaxis signaling pathway. MCP senses and binds chemoeffectors, specifically, and transmits the sensed signal to downstream proteins of the chemotaxis signaling system. The genome of Agrobacterium fabrum (previously, tumefaciens) C58 predicts that a total of 20 genes can encode MCP, but only the MCP-encoding gene atu0514 is located inside the che operon. Hence, the identification of the exact function of atu0514-encoding chemoreceptor (here, named as MCP514) will be very important for us to understand more deeply the chemotaxis signal transduction mechanism of A. fabrum. The deletion of atu0514 significantly decreased the chemotactic migration of A. fabrum in a swim plate. The test of atu0514-deletion mutant (Δ514) chemotaxis toward single chemicals showed that the deficiency of MCP514 significantly weakened the chemotactic response of A. fabrum to four various chemicals, sucrose, valine, citric acid and acetosyringone (AS), but did not completely abolish the chemotactic response. MCP514 was localized at cell poles although it lacks a transmembrane (TM) region and is predicted to be a cytoplasmic chemoreceptor. The replacement of residue Phe328 showed that the helical structure in the hairpin subdomain of MCP514 is a direct determinant for the cellular localization of MCP514. Single respective replacements of key residues indicated that residues Asn336 and Val353 play a key role in maintaining the chemotactic function of MCP514. Full article
(This article belongs to the Special Issue Molecular Analysis of Plant Pathogenic Bacteria)
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14 pages, 1940 KiB  
Article
Analyses of Virulence Genes of Clavibacter michiganensis subsp. michiganensis Strains Reveal Heterogeneity and Deletions That Correlate with Pathogenicity
by Miryam Valenzuela, Marianela González, Alexis Velásquez, Fernando Dorta, Iván Montenegro, Ximena Besoain, Francisco Salvà-Serra, Daniel Jaén-Luchoro, Edward R. B. Moore and Michael Seeger
Microorganisms 2021, 9(7), 1530; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071530 - 18 Jul 2021
Cited by 4 | Viewed by 2847
Abstract
Clavibacter michiganensis subsp. michiganensis (Cmm) is the causal agent of bacterial canker of tomato. Differences in virulence between Cmm strains have been reported. The aim of this study was the characterization of nine Cmm strains isolated in Chile to reveal the [...] Read more.
Clavibacter michiganensis subsp. michiganensis (Cmm) is the causal agent of bacterial canker of tomato. Differences in virulence between Cmm strains have been reported. The aim of this study was the characterization of nine Cmm strains isolated in Chile to reveal the causes of their differences in virulence. The virulence assays in tomato seedlings revealed different levels of severity associated with the strains, with two highly virulent strains and one causing only mild symptoms. The two most virulent showed increased cellulase activity, and no cellulase activity was observed in the strain causing mild symptoms. In three strains, including the two most virulent strains, PCR amplification of the 10 virulence genes analyzed was observed. In the strain causing mild symptoms, no amplification was observed for five genes, including celA. Sequence and cluster analyses of six virulence genes grouped the strains, as has been previously reported, except for gene pelA1. Gene sequence analysis from the genomes of five Chilean strains revealed the presence of deletions in the virulence genes, celB, xysA, pat-1, and phpA. The results of this study allow us to establish correlations between the differences observed in disease severity and the presence/absence of genes and deletions not previously reported. Full article
(This article belongs to the Special Issue Molecular Analysis of Plant Pathogenic Bacteria)
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15 pages, 2612 KiB  
Article
The Divergent Key Residues of Two Agrobacterium fabrum (tumefaciens) CheY Paralogs Play a Key Role in Distinguishing Their Functions
by Dawei Gao, Renjie Zong, Zhiwei Huang, Jingyang Ye, Hao Wang, Nan Xu and Minliang Guo
Microorganisms 2021, 9(6), 1134; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9061134 - 24 May 2021
Cited by 2 | Viewed by 1918
Abstract
The chemotactic response regulator CheY, when phosphorylated by the phosphoryl group from phosphorylated CheA, can bind to the motor switch complex to control the flagellar motor rotation. Agrobacterium fabrum (previous name: Agrobacterium tumefaciens), a phytopathogen, carries two paralogous cheY genes, cheY1 and [...] Read more.
The chemotactic response regulator CheY, when phosphorylated by the phosphoryl group from phosphorylated CheA, can bind to the motor switch complex to control the flagellar motor rotation. Agrobacterium fabrum (previous name: Agrobacterium tumefaciens), a phytopathogen, carries two paralogous cheY genes, cheY1 and cheY2. The functional difference of two paralogous CheYs remains unclear. Three cheY-deletion mutants were constructed to test the effects of two CheYs on the chemotaxis of A.fabrum. Phenotypes of three cheY-deletion mutants show that deletion of each cheY significantly affects the chemotactic response, but cheY2-deletion possesses more prominent effects on the chemotactic migration and swimming pattern of A. fabrum than does cheY1-deletion. CheA-dependent cellular localization of two CheY paralogs and in vitro pull-down of two CheY paralogs by FliM demonstrate that the distinct roles of two CheY paralogs arise mainly from the differentiation of their binding affinities for the motor switch component FliM, agreeing with the divergence of the key residues on the motor-binding surface involved in the interaction with FliM. The single respective replacements of key residues R93 and A109 on the motor-binding surface of CheY2 by alanine (A) and valine (V), the corresponding residues of CheY1, significantly enhanced the function of CheY2 in regulating the chemotactic response of A. fabrum CheY-deficient mutant Δy to nutrient substances and host attractants. These results conclude that the divergence of the key residues in the functional subdomain is the decisive factor of functional differentiation of these two CheY homologs and protein function may be improved by the substitution of the divergent key residues in the functional domain for the corresponding residues of its paralogs. This finding will help us to better understand how paralogous proteins sub-functionalize. In addition, the acquirement of two CheY2 variants, whose chemotactic response functions are significantly improved, will be very useful for us to further explore the mechanism of CheY to bind and regulate the flagellar motor and the role of chemotaxis in the pathogenicity of A. fabrum. Full article
(This article belongs to the Special Issue Molecular Analysis of Plant Pathogenic Bacteria)
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Review

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16 pages, 2515 KiB  
Review
Building More Resilient Culture Collections: A Call for Increased Deposits of Plant-Associated Bacteria
by Kirk Broders, Andrew Aspin, Jordan Bailey, Toni Chapman, Perrine Portier and Bevan S. Weir
Microorganisms 2022, 10(4), 741; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10040741 - 30 Mar 2022
Cited by 4 | Viewed by 2488
Abstract
Biological collections preserve our past, while helping protect our future and increase future knowledge. Plant bacterial culture collections are our security for domestic and global biosecurity. This feature article will provide an introduction to the global position of plant bacterial collections. The role [...] Read more.
Biological collections preserve our past, while helping protect our future and increase future knowledge. Plant bacterial culture collections are our security for domestic and global biosecurity. This feature article will provide an introduction to the global position of plant bacterial collections. The role of collections in monitoring plant pathogenic bacteria will be explored through the presentation of five cases studies. These case studies demonstrate why culture collections were imperative for the outcome in each situation. We discuss what we believe should be the best practices to improve microbial preservation and accessioning rates, and why plant bacterial culture collections must increase deposits to be prepared for future emerging pathogens. This is not only the case for global culture collections, but on a much bigger scale, our future scientific successes, our biosecurity decisions and responses, and our knowledge are contingent upon preserving our valuable bacterial strains. It is hoped that once you read this article, you will see the need to deposit your strains in registered public collections and make a concerted effort to build better bacterial culture collections with us. Full article
(This article belongs to the Special Issue Molecular Analysis of Plant Pathogenic Bacteria)
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