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Brochu AS, Dumonceaux TJ, Valenzuela M, Bélanger R, Pérez-López E. A New Multiplex TaqMan qPCR for Precise Detection and Quantification of Clavibacter michiganensis in Seeds and Plant Tissue. PLANT DISEASE 2024:PDIS06231194SR. [PMID: 38381965 DOI: 10.1094/pdis-06-23-1194-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Bacterial canker of tomato caused by Clavibacter michiganensis (Cm) is one of the most devastating bacterial diseases affecting the tomato industry worldwide. As the result of Cm colonization of the xylem, the susceptible host shows typical symptoms of wilt, marginal leaf necrosis, stem cankers, and ultimately plant death. However, what makes Cm an even more dangerous pathogen is its ability to infect seeds and plants without causing symptoms. Unfortunately, there are no resistant cultivars or effective chemical or biological control methods available to growers against Cm. Its control relies heavily on prevention. The implementation of a rapid and accurate detection tool is imperative to monitor the presence of Cm and prevent its spread. In this study, we developed a specific and sensitive multiplex TaqMan qPCR assay to detect Cm and distinguish it from related bacterial species that affect tomato plants. Two Cm chromosomal virulence-related genes, rhuM and tomA, were used as specific targets. The plant internal control tubulin alpha-3 was included in each of the multiplexes to improve the reliability of the assay. Specificity was evaluated with 37 bacterial strains including other Clavibacter spp. and related and unrelated bacterial pathogens from different geographic locations affecting a wide variety of hosts. Results showed that the assay is able to discriminate Cm strains from other related bacteria. The assay was validated on tissue and seed samples following artificial infection, and all tested samples accurately detected the presence of Cm. The tool described here is highly specific, sensitive, and reliable for the detection of Cm and allows the quantification of Cm in seeds, roots, stems, and leaves. The diagnostic assay can also be adapted for multiple purposes such as seed certification programs, surveillance, biosafety, the effectiveness of control methods, border protection, and epidemiological studies.[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)
- Anne-Sophie Brochu
- Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Québec City, Canada
- Centre de Recherche et d'Innovation sur les Végétaux (CRIV), Université Laval, Québec City, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Canada
- L'Institute EDS, Université Laval, Québec City, Canada
| | - Tim J Dumonceaux
- Agriculture and Agri-Food Canada Saskatoon Research and Development Centre, Saskatoon, SK, Canada
| | - Miryam Valenzuela
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry & Center of Biotechnology Dr. Daniel Alkalay Lowitt, Universidad Tecnica Federico Santa Maria, Valparaiso 2390123, Chile
| | - Richard Bélanger
- Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Québec City, Canada
- Centre de Recherche et d'Innovation sur les Végétaux (CRIV), Université Laval, Québec City, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Canada
| | - Edel Pérez-López
- Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Québec City, Canada
- Centre de Recherche et d'Innovation sur les Végétaux (CRIV), Université Laval, Québec City, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Canada
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Verma RK, Roman-Reyna V, Raanan H, Coaker G, Jacobs JM, Teper D. Allelic variations in the chpG effector gene within Clavibacter michiganensis populations determine pathogen host range. PLoS Pathog 2024; 20:e1012380. [PMID: 39028765 PMCID: PMC11290698 DOI: 10.1371/journal.ppat.1012380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 07/31/2024] [Accepted: 06/27/2024] [Indexed: 07/21/2024] Open
Abstract
Plant pathogenic bacteria often have a narrow host range, which can vary among different isolates within a population. Here, we investigated the host range of the tomato pathogen Clavibacter michiganensis (Cm). We determined the genome sequences of 40 tomato Cm isolates and screened them for pathogenicity on tomato and eggplant. Our screen revealed that out of the tested isolates, five were unable to cause disease on any of the hosts, 33 were exclusively pathogenic on tomato, and two were capable of infecting both tomato and eggplant. Through comparative genomic analyses, we identified that the five non-pathogenic isolates lacked the chp/tomA pathogenicity island, which has previously been associated with virulence in tomato. In addition, we found that the two eggplant-pathogenic isolates encode a unique allelic variant of the putative serine hydrolase chpG (chpGC), an effector that is recognized in eggplant. Introduction of chpGC into a chpG inactivation mutant in the eggplant-non-pathogenic strain Cm101, failed to complement the mutant, which retained its ability to cause disease in eggplant and failed to elicit hypersensitive response (HR). Conversely, introduction of the chpG variant from Cm101 into an eggplant pathogenic Cm isolate (C48), eliminated its pathogenicity on eggplant, and enabled C48 to elicit HR. Our study demonstrates that allelic variation in the chpG effector gene is a key determinant of host range plasticity within Cm populations.
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Affiliation(s)
- Raj Kumar Verma
- Dept. of Plant Pathology and Weed Research, Agricultural Research Organization—Volcani Institute, Rishon LeZion, Israel
| | - Veronica Roman-Reyna
- Dept. Of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Hagai Raanan
- Dept. of Plant Pathology and Weed Research, Agricultural Research Organization—Gilat Research Center, Negev, Israel
| | - Gitta Coaker
- Dept. of Plant Pathology, University of California Davis, Davis, California, United States of America
| | - Jonathan M. Jacobs
- Dept. of Plant Pathology, The Ohio State University, Columbus, Ohio, United States of America
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Doron Teper
- Dept. of Plant Pathology and Weed Research, Agricultural Research Organization—Volcani Institute, Rishon LeZion, Israel
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Deletion of pbpC Enhances Bacterial Pathogenicity on Tomato by Affecting Biofilm Formation, Exopolysaccharides Production, and Exoenzyme Activities in Clavibacter michiganensis. Int J Mol Sci 2023; 24:ijms24065324. [PMID: 36982399 PMCID: PMC10049144 DOI: 10.3390/ijms24065324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 02/14/2023] [Accepted: 03/07/2023] [Indexed: 03/18/2023] Open
Abstract
Penicillin-binding proteins (PBPs) are considered essential for bacterial peptidoglycan biosynthesis and cell wall assembly. Clavibacter michiganensis is a representative Gram-positive bacterial species that causes bacterial canker in tomato. pbpC plays a significant role in maintaining cell morphological characteristics and stress responses in C. michiganensis. The current study demonstrated that the deletion of pbpC commonly enhances bacterial pathogenicity in C. michiganensis and revealed the mechanisms through which this occurs. The expression of interrelated virulence genes, including celA, xysA, xysB, and pelA, were significantly upregulated in △pbpC mutants. Compared with those in wild-type strains, exoenzyme activities, the formation of biofilm, and the production of exopolysaccharides (EPS) were significantly increased in △pbpC mutants. It is noteworthy that EPS were responsible for the enhancement in bacterial pathogenicity, with the degree of necrotic tomato stem cankers intensifying with the injection of a gradient of EPS from C. michiganensis. These findings highlight new insights into the role of pbpC affecting bacterial pathogenicity, with an emphasis on EPS, advancing the current understanding of phytopathogenic infection strategies for Gram-positive bacteria.
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Park IW, Hwang IS, Oh EJ, Kwon CT, Oh CS. Nicotiana benthamiana, a Surrogate Host to Study Novel Virulence Mechanisms of Gram-Positive Bacteria, Clavibacter michiganensis, and C. capsici in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:876971. [PMID: 35620684 PMCID: PMC9127732 DOI: 10.3389/fpls.2022.876971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/25/2022] [Indexed: 06/11/2023]
Abstract
Clavibacter michiganensis is a Gram-positive bacterium that causes bacterial canker and wilting in host plants like tomato. Two major virulence genes encoding a cellulase (celA) and a putative serine protease (pat-1) have been reported. Here we show that Nicotiana benthamiana, a commonly used model plant for studying molecular plant-pathogen interactions, is a surrogate host of C. michiganensis and C. capsici. When a low concentration of two Clavibacter species, C. michiganensis and C. capsici, were infiltrated into N. benthamiana leaves, they caused blister-like lesions closely associated with cell death and the generation of reactive oxygen species and proliferated significantly like a pathogenic bacterium. By contrast, they did not cause any disease symptoms in N. tabacum leaves. The celA and pat-1 mutants of C. michiganensis still caused blister-like lesions and cankers like the wild-type strain. When a high concentration of two Clavibacter species and two mutant strains were infiltrated into N. benthamiana leaves, all of them caused strong and rapid necrosis. However, only C. michiganensis strains, including the celA and pat-1 mutants, caused wilting symptoms when it was injected into stems. When two Clavibacter species and two mutants were infiltrated into N. tabacum leaves at the high concentration, they (except for the pat-1 mutant) caused a strong hypersensitive response. These results indicate that C. michiganensis causes blister-like lesions, canker, and wilting in N. benthamiana, and celA and pat-1 genes are not necessary for the development of these symptoms. Overall, N. benthamiana is a surrogate host of Clavibacter species, and their novel virulence factors are responsible for disease development in this plant.
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Affiliation(s)
- In Woong Park
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin, South Korea
| | - In Sun Hwang
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Eom-Ji Oh
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Choon-Tak Kwon
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Chang-Sik Oh
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin, South Korea
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, South Korea
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Advances in the Characterization of the Mechanism Underlying Bacterial Canker Development and Tomato Plant Resistance. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8030209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Bacterial canker caused by the Gram-positive actinobacterium Clavibacter michiganensis is one of the most serious bacterial diseases of tomatoes, responsible for 10–100% yield losses worldwide. The pathogen can systemically colonize tomato vascular bundles, leading to wilting, cankers, bird’s eye lesions, and plant death. Bactericidal agents are insufficient for managing this disease, because the pathogen can rapidly migrate through the vascular system of plants and induce systemic symptoms. Therefore, the use of resistant cultivars is necessary for controlling this disease. We herein summarize the pathogenicity of C. michiganensis in tomato plants and the molecular basis of bacterial canker pathogenesis. Moreover, advances in the characterization of resistance to this pathogen in tomatoes are introduced, and the status of genetics-based research is described. Finally, we propose potential future research on tomato canker resistance. More specifically, there is a need for a thorough analysis of the host–pathogen interaction, the accelerated identification and annotation of resistance genes and molecular mechanisms, the diversification of resistance resources or exhibiting broad-spectrum disease resistance, and the production of novel and effective agents for control or prevention. This review provides researchers with the relevant information for breeding tomato cultivars resistant to bacterial cankers.
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Stevens DM, Tang A, Coaker G. A Genetic Toolkit for Investigating Clavibacter Species: Markerless Deletion, Permissive Site Identification, and an Integrative Plasmid. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1336-1345. [PMID: 34890250 DOI: 10.1094/mpmi-07-21-0171-ta] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The development of knockout mutants and expression variants are critical for understanding genotype-phenotype relationships. However, advances in these techniques in gram-positive actinobacteria have stagnated over the last decade. Actinobacteria in the Clavibacter genus are composed of diverse crop pathogens that cause a variety of wilt and cankering diseases. Here, we present a suite of tools for genetic manipulation in the tomato pathogen Clavibacter michiganensis including a markerless deletion system, an integrative plasmid, and an R package for identification of permissive sites for plasmid integration. The vector pSelAct-KO is a recombination-based, markerless knockout system that uses dual selection to engineer seamless deletions of a region of interest, providing opportunities for repeated higher-order genetic knockouts. The efficacy of pSelAct-KO was demonstrated in C. michiganensis and was confirmed using whole-genome sequencing. We developed permissR, an R package to identify permissive sites for chromosomal integration, which can be used in conjunction with pSelAct-Express, a nonreplicating integrative plasmid that enables recombination into a permissive genomic location. Expression of enhanced green fluorescent protein by pSelAct-Express was verified in two candidate permissive regions predicted by permissR in C. michiganensis. These molecular tools are essential advances for investigating gram-positive actinobacteria, particularly for important pathogens in the Clavibacter genus.[Formula: see text] Copyright © 2021 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)
- Danielle M Stevens
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, Davis, CA 95616, U.S.A
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, U.S.A
| | - Andrea Tang
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, U.S.A
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, U.S.A
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Yokotani N, Hasegawa Y, Sato M, Hirakawa H, Kouzai Y, Nishizawa Y, Yamamoto E, Naito Y, Isobe S. Transcriptome analysis of Clavibacter michiganensis subsp. michiganensis-infected tomatoes: a role of salicylic acid in the host response. BMC PLANT BIOLOGY 2021; 21:476. [PMID: 34666675 PMCID: PMC8524973 DOI: 10.1186/s12870-021-03251-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 10/05/2021] [Indexed: 05/05/2023]
Abstract
Bacterial canker of tomato (Solanum lycopersicon) caused by the Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis (Cmm) is an economically important disease. To understand the host defense response to Cmm infection, transcriptome sequences in tomato cotyledons were analyzed by RNA-seq. Overall, 1788 and 540 genes were upregulated and downregulated upon infection, respectively. Gene Ontology enrichment analysis revealed that genes involved in the defense response, phosphorylation, and hormone signaling were over-represented by the infection. Induced expression of defense-associated genes suggested that the tomato response to Cmm showed similarities to common plant disease responses. After infection, many resistance gene analogs (RGAs) were transcriptionally upregulated, including the expressions of some receptor-like kinases (RLKs) involved in pattern-triggered immunity. The expressions of WRKYs, NACs, HSFs, and CBP60s encoding transcription factors (TFs) reported to regulate defense-associated genes were induced after infection with Cmm. Tomato genes orthologous to Arabidopsis EDS1, EDS5/SID1, and PAD4/EDS9, which are causal genes of salicylic acid (SA)-deficient mutants, were upregulated after infection with Cmm. Furthermore, Cmm infection drastically stimulated SA accumulation in tomato cotyledons. Genes involved in the phenylalanine ammonia lyase pathway were upregulated, whereas metabolic enzyme gene expression in the isochorismate synthase pathway remained unchanged. Exogenously applied SA suppressed bacterial growth and induced the expression of WRKYs, suggesting that some Cmm-responsive genes are regulated by SA signaling, and SA signaling activation should improve tomato immunity against Cmm.
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Affiliation(s)
- Naoki Yokotani
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan.
| | - Yoshinori Hasegawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Masaru Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Yusuke Kouzai
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Yoko Nishizawa
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Eiji Yamamoto
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Yoshiki Naito
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
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Schlechter RO, Kear EJ, Remus DM, Remus-Emsermann MNP. Fluorescent Protein Expression as a Proxy for Bacterial Fitness in a High-Throughput Assay. Appl Environ Microbiol 2021; 87:e0098221. [PMID: 34260309 PMCID: PMC8388834 DOI: 10.1128/aem.00982-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/04/2021] [Indexed: 11/20/2022] Open
Abstract
Bacterial growth is classically assessed by measuring the increases in optical density of pure cultures in shaken liquid media. Measuring growth using optical density has severe limitations when studying multistrain interactions, as it is not possible to measure the growth of individual strains within mixed cultures. Here, we demonstrated that constitutively expressed fluorescent proteins can be used to track the growth of individual strains in different liquid media. Fluorescence measurements were highly correlated with optical density measurements and cell counts. This allowed us to assess bacterial growth not only in pure cultures but also in mixed bacterial cultures and determine the impact of a competitor on a focal strain, thereby assessing relative fitness. Furthermore, we were able to track the growth of two different strains simultaneously by using fluorescent proteins with differential excitation and emission wavelengths. Bacterial densities measured by fluorescence yielded more consistent data between technical replicates than optical density measurements. Our setup employs fluorescence microplate readers that allow high throughput and replication. IMPORTANCE We expand on an important limitation of the concept of measuring bacterial growth, which is classically limited to one strain at a time. By adopting our approach, it is possible to measure the growth of several bacterial strains simultaneously with high temporal resolution and in a high-throughput manner. This is important to investigate bacterial interactions, such as competition and facilitation.
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Affiliation(s)
- Rudolf O. Schlechter
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Bioprotection Research Core, University of Canterbury, Christchurch, New Zealand
| | - Evan J. Kear
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Daniela M. Remus
- Protein Science and Engineering, Callaghan Innovation, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Mitja N. P. Remus-Emsermann
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Bioprotection Research Core, University of Canterbury, Christchurch, New Zealand
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
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Peritore-Galve FC, Tancos MA, Smart CD. Bacterial Canker of Tomato: Revisiting a Global and Economically Damaging Seedborne Pathogen. PLANT DISEASE 2021; 105:1581-1595. [PMID: 33107795 DOI: 10.1094/pdis-08-20-1732-fe] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The gram-positive actinobacterium Clavibacter michiganensis is the causal agent of bacterial canker of tomato, an economically impactful disease with a worldwide distribution. This seedborne pathogen systemically colonizes tomato xylem leading to unilateral leaflet wilt, marginal leaf necrosis, stem and petiole cankers, and plant death. Additionally, splash dispersal of the bacterium onto fruit exteriors causes bird's-eye lesions, which are characterized as necrotic centers surrounded by white halos. The pathogen can colonize developing seeds systemically through xylem and through penetration of fruit tissues from the exterior. There are currently no commercially available resistant cultivars, and bactericidal sprays have limited efficacy for managing the disease once the pathogen is in the vascular system. In this review, we summarize research on epidemiology, host colonization, the bacterial genetics underlying virulence, and management of bacterial canker. Finally, we highlight important areas of research into this pathosystem that have the potential to generate new strategies for prevention and mitigation of bacterial canker.
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Affiliation(s)
- F Christopher Peritore-Galve
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
| | - Matthew A Tancos
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service, Frederick, MD 21702
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
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Basim H, Basim E, Tombuloglu H, Unver T. Comparative transcriptome analysis of resistant and cultivated tomato lines in response to Clavibacter michiganensis subsp. michiganensis. Genomics 2021; 113:2455-2467. [PMID: 34052318 DOI: 10.1016/j.ygeno.2021.05.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/19/2021] [Accepted: 05/26/2021] [Indexed: 11/28/2022]
Abstract
Clavibacter michiganensis subsp. michiganensis (Cmm) is a gram-positive bacterium causing destructive bacterial wilt and canker disease in tomato. Herein, a comparative transcriptome analysis was performed on Cmm-resistant and -susceptible tomato lines. Tomato seedlings were inoculated with Cmm and harvested for transcriptome analysis after 4 and 8 day time-points. Twenty-four transcriptome libraries were profiled by RNA sequencing approach. Total of 545 million clean reads was generated. 1642 and 2715 differentially expressed genes (DEG) were identified in susceptible lines within 4 and 8 days after inoculation (DAI), respectively. In resistant lines, 1731 and 1281 DEGs were found following 4 and 8 DAI, respectively. Gene Ontology analysis resulted in a higher number of genes involved in biological processes and molecular functions in susceptible lines. On the other hand, such biological processes, "defense response", and "response to stress" were distinctly indicated in resistant lines which were not found in susceptible ones upon inoculation, according to the gene set enrichment analyses. Upon Cmm-inoculation, several defense responsive genes were found to be differentially expressed. Of which 26 genes were in the resistant line and three were in the susceptible line. This study helps to understand the transcriptome response of Cmm-resistant and -susceptible tomato lines. The results provide comprehensive data for molecular breeding studies, for the purpose to control of the pathogen in tomato.
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Affiliation(s)
- Huseyin Basim
- Department of Plant Protection, Faculty of Agriculture, Akdeniz University, 07070 Antalya, Turkey.
| | - Esin Basim
- Department of Organic Agriculture, Technical Sciences Vocational School, Akdeniz University, 07070 Antalya, Turkey
| | - Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Turgay Unver
- Ficus Biotechnology, Ostim OSB Mah, 100. Yil Blv, No:55, Yenimahalle, Ankara, Turkey
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Chesneau G, Torres-Cortes G, Briand M, Darrasse A, Preveaux A, Marais C, Jacques MA, Shade A, Barret M. Temporal dynamics of bacterial communities during seed development and maturation. FEMS Microbiol Ecol 2021; 96:5910485. [PMID: 32966572 DOI: 10.1093/femsec/fiaa190] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 09/17/2020] [Indexed: 12/20/2022] Open
Abstract
Seed microbiota acts as a starting point for the assembly of the plant microbiota and contributes to successful plant establishment. To date, the order and timing of microbial taxa immigration during seed development and maturation remained unknown. We investigated the temporal dynamics of seed bacterial communities in bean and radish. A high phylogenetic turnover was observed for both plant species with few taxa associated with all seed developmental stages. Greater heterogeneity in communities structure within each stage was observed for radish. While, about one-third of radish seed bacterial taxa were detected in buds, flowers and fruits, very few taxa seem to be transmitted by the floral route in bean. In the latter species, bacterial populations belonging to the P. fluorescens species complex were found either in buds, flowers and fruits or in seeds. The relative phylogenetic proximity of these bacterial populations combined with their habitat specificity led us to explore the genetic determinants involved in successful seed transmission in bean. Comparative genomic analyses of representatives bacterial strains revealed dozens of coding sequences specifically associated with seed-transmitted strains. This study provided a first glimpse on processes involved in seed microbiota assembly, which could be used for designing plant-beneficial microbial consortia.
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Affiliation(s)
- Guillaume Chesneau
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Gloria Torres-Cortes
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Martial Briand
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Armelle Darrasse
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Anne Preveaux
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Coralie Marais
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Marie-Agnès Jacques
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Program in Ecology, Evolutionary Biology, and Behavior, The DOE Great Lakes Bioenergy Research Center, and The Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Matthieu Barret
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
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Ramachandran S, Dobhal S, Alvarez AM, Arif M. Improved multiplex TaqMan qPCR assay with universal internal control offers reliable and accurate detection of Clavibacter michiganensis. J Appl Microbiol 2021; 131:1405-1416. [PMID: 33484618 DOI: 10.1111/jam.15017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/16/2020] [Accepted: 01/21/2021] [Indexed: 11/27/2022]
Abstract
AIM Clavibacter michiganensis (Cm) is a seed-borne plant pathogen that significantly reduces tomato production worldwide. Due to repeated outbreaks and rapid spread of the disease, seeds/transplants need to be certified free of the pathogen before planting. To this end, we developed a multiplex TaqMan qPCR assay that can accurately detect Cm in infected samples. METHODS AND RESULTS A specific region of Cm (clvG gene) was selected for primer design using comparative genomics approach. A fully synthetic universal internal control (UIC) was also designed to detect PCR inhibitors and false-negative results in qPCRs. The Cm primers can be used alone or in a triplex TaqMan qPCR assay with UIC and previously described Clavibacter primers. The assay was specific for Cm and detected up to 10 fg of Cm DNA in sensitivity and spiked assays. Addition of the UIC did not change the specificity or sensitivity of the multiplex TaqMan qPCR assay. CONCLUSION The triplex TaqMan qPCR provides a specific and sensitive diagnostic assay for Cm. SIGNIFICANCE AND IMPACT OF THE STUDY This assay can be used for biosecurity surveillance, routine diagnostics, estimating bacterial titres in infected material and for epidemiological studies. The UIC is fully synthetic, efficiently amplified and multiplex compatible with any other qPCR assay.
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Affiliation(s)
- S Ramachandran
- Foreign Disease and Weed Science Research Unit, USDA-ARS, Fort Detrick, MD, USA.,ARS Research Participation Program, Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - S Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - A M Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - M Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
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Narváez-Barragán DA, Tovar-Herrera OE, Segovia L, Serrano M, Martinez-Anaya C. Expansin-related proteins: biology, microbe-plant interactions and associated plant-defense responses. MICROBIOLOGY-SGM 2020; 166:1007-1018. [PMID: 33141007 DOI: 10.1099/mic.0.000984] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Expansins, cerato-platanins and swollenins (which we will henceforth refer to as expansin-related proteins) are a group of microbial proteins involved in microbe-plant interactions. Although they share very low sequence similarity, some of their composing domains are near-identical at the structural level. Expansin-related proteins have their target in the plant cell wall, in which they act through a non-enzymatic, but still uncharacterized, mechanism. In most cases, mutagenesis of expansin-related genes affects plant colonization or plant pathogenesis of different bacterial and fungal species, and thus, in many cases they are considered virulence factors. Additionally, plant treatment with expansin-related proteins activate several plant defenses resulting in the priming and protection towards subsequent pathogen encounters. Plant-defence responses induced by these proteins are reminiscent of pattern-triggered immunity or hypersensitive response in some cases. Plant immunity to expansin-related proteins could be caused by the following: (i) protein detection by specific host-cell receptors, (ii) alterations to the cell-wall-barrier properties sensed by the host, (iii) displacement of cell-wall polysaccharides detected by the host. Expansin-related proteins may also target polysaccharides on the wall of the microbes that produced them under certain physiological instances. Here, we review biochemical, evolutionary and biological aspects of these relatively understudied proteins and different immune responses they induce in plant hosts.
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Affiliation(s)
- Delia A Narváez-Barragán
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62110 Cuernavaca Morelos, Mexico
| | - Omar E Tovar-Herrera
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Marcus Family Campus, BeerSheva, Israel
| | - Lorenzo Segovia
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62110 Cuernavaca Morelos, Mexico
| | - Mario Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62110 Cuernavaca Morelos, Mexico
| | - Claudia Martinez-Anaya
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62110 Cuernavaca Morelos, Mexico
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Orzali L, Valente MT, Scala V, Loreti S, Pucci N. Antibacterial Activity of Essential Oils and Trametes versicolor Extract against Clavibacter michiganensis subsp. michiganensis and Ralstonia solanacearum for Seed Treatment and Development of a Rapid In Vivo Assay. Antibiotics (Basel) 2020; 9:antibiotics9090628. [PMID: 32967338 PMCID: PMC7557780 DOI: 10.3390/antibiotics9090628] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/16/2020] [Accepted: 09/21/2020] [Indexed: 11/17/2022] Open
Abstract
Clavibacter michiganensis subsp. michiganensis (Smith) Davis et al. (Cmm) and Ralstonia solanacearum Yabuuchi et al. (Smith) (Rs) are important seed-borne bacterial pathogens of tomato (Solanum lycopersicum) listed as A2 pests in the EPPO (European and Mediterranean Plant Protection Organization) region. At present, there are few strategies to control these pathogens, and seed control with eco-compatible approaches is widely encouraged. In this work, the essential oils (EOs) of oregano (Origanum vulgare), garlic (Allium sativum), basil (Ocimum basilicum), cinnamon (Cinnamomum zeylanicum), clove buds (Syzygium aromaticum), thyme (Thymus vulgaris), and Trametes versicolor extract (Tve) were tested in vitro for their antimicrobial activity against Cmm and Rs (broth microdilution method). The tested EOs and the Tve extract caused a significant inhibition of bacterial growth, with very promising MBC (minimum bactericidal concentration) and MIC90 (minimum inhibitory concentration causing a 90% growth inhibition) values. Moreover, an in vivo germination test showed no major reduction in seed germination when the substances were applied as seed treatment. A rapid molecular screening method has been developed, through real-time PCR, for the specific quantification of Cmm in the presence of a vegetable matrix to test in vivo the antimicrobial efficacy of oregano and cinnamon oil on seed treatment without resorting to whole plant essays, which are time- and space-consuming.
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15
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New Insight into the Composition of Wheat Seed Microbiota. Int J Mol Sci 2020; 21:ijms21134634. [PMID: 32629754 PMCID: PMC7370184 DOI: 10.3390/ijms21134634] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/28/2020] [Accepted: 06/29/2020] [Indexed: 02/08/2023] Open
Abstract
Endophytes are associated with host plants throughout their life history from seed germination to fruit development. One of the most important plant organs colonized by endophytic microbiota is the seed. The aim of this study was to determine the structure of the seed core microbiome inhabiting the endosperms and embryos of eight wheat cultivars with the use of a culture-independent technique. The seeds of Triticum aestivum L. cv. Hondia, Wilejka, STH, Opcja, Tybalt, Euforia and Triticum spelta L. cv. Rokosz and Schwabencorn (producer: Plant Breeding Strzelce Sp. z o.o. Group IHAR) were studied. Rokosz and Hondia were cultured in vitro and in vivo to identify obligatory bacterial endophytes. A restrictive analysis of reads originating from the in vitro plants has demonstrated that the bacterial genera Paenibacillus and Propionibacterium inhabiting Rokosz and Hondia plants have a status of obligatory microorganisms. Greater biodiversity of seed-borne endophytes was found in the seed endosperms than in the embryos. The multiple comparison analysis of the OTU abundance indicated that the seed part significantly influenced the relative abundance. The seed-born microbiome is not statistically significantly dependent on the wheat cultivars; however, it cannot be claimed that every wheat seed is the same.
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16
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Qutb AM, Wei F, Dong W. Prediction and Characterization of Cationic Arginine-Rich Plant Antimicrobial Peptide SM-985 From Teosinte ( Zea mays ssp. mexicana). Front Microbiol 2020; 11:1353. [PMID: 32636825 PMCID: PMC7318549 DOI: 10.3389/fmicb.2020.01353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 05/26/2020] [Indexed: 12/17/2022] Open
Abstract
Antimicrobial peptides (AMPs) are effective against different plant pathogens and newly considered as part of plant defense systems. From prokaryotes to eukaryotes, AMPs can exist in all forms of life. SM-985 is a cationic AMP (CAMP) isolated from the cDNA library of Mexican teosinte (Zea mays ssp. mexicana). A computational prediction server running with different algorithms was used to screen the teosinte cDNA library for AMPs, and the SM-985 peptide was predicted as an AMP with high probability prediction values. SM-985 is an arginine-rich peptide and composed of 21 amino acids (MW: 2671.06 Da). The physicochemical properties of SM-985 are very promising as an AMP, including the net charge (+8), hydrophobicity ratio of 23%, Boman index of 5.19 kcal/mol, and isoelectric point of 12.95. The SM-985 peptide has amphipathic α-helix conformations. The antimicrobial activity of SM-985 was confirmed against six bacterial plant pathogens, and the MIC of SM-985 against Gram-positive indicators was 8 μM, while the MIC of SM-985 against Gram-negative indicators was 4 μM. The SM-985 interacting with the bacterial membrane and this interaction were examined by treatment of the bacterial indicators with FITC-SM-985 peptide, which showed a high binding affinity of SM-985 to the bacterial membrane (whether Gram-positive or Gram-negative). Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images of the treated bacteria with SM-985 demonstrated cell membrane damage and cell lysis. In vivo antimicrobial activity was examined, and SM-985 prevented leaf spot disease infection caused by Pst DC3000 on Solanum lycopersicum. Moreover, SM-985 showed sensitivity to calcium chloride salt, which is a common feature of CAMPs.
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Affiliation(s)
- Abdelrahman M. Qutb
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, China
- Department of Agricultural Botany, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Feng Wei
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wubei Dong
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, China
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17
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Peritore-Galve FC, Miller C, Smart CD. Characterizing Colonization Patterns of Clavibacter michiganensis During Infection of Tolerant Wild Solanum Species. PHYTOPATHOLOGY 2020; 110:574-581. [PMID: 31725349 DOI: 10.1094/phyto-09-19-0329-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Clavibacter michiganensis is the Gram-positive causal agent of bacterial canker of tomato, an economically devastating disease with a worldwide distribution. C. michiganensis colonizes the xylem, leading to unilateral wilt, stem canker, and plant death. C. michiganensis can also infect developing tomato fruit through splash dispersal, forming exterior bird's eye lesions. There are no documented sources of qualitative resistance in Solanum spp.; however, quantitative trait loci conferring tolerance in Solanum arcanum and Solanum habrochaites have been identified. Mechanisms of tolerance and C. michiganensis colonization patterns in wild tomato species remain poorly understood. This study describes differences in symptom development and colonization patterns of the wild type (WT) and a hypervirulent bacterial expansin knockout (ΔCmEXLX2) in wild and cultivated tomato genotypes. Overall, WT and ΔCmEXLX2 cause less severe symptoms in wild tomato species and are impeded in spread and colonization of the vascular system. Laser scanning confocal microscopy and scanning electron microscopy were used to observe preferential colonization of protoxylem vessels and reduced intravascular spread in wild tomatoes. Differences in C. michiganensis in vitro growth and aggregation were determined in xylem sap, which may suggest that responses to pathogen colonization are occurring, leading to reduced colonization density in wild tomato species. Finally, wild tomato fruit was determined to be susceptible to C. michiganensis through in vivo inoculations and assessing lesion numbers and size. Fruit symptom severity was in some cases unrelated to severity of symptoms during vascular infection, suggesting different mechanisms for colonization of different tissues.
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Affiliation(s)
- F Christopher Peritore-Galve
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
| | - Christine Miller
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27606
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
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18
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Cerutti A, Jauneau A, Laufs P, Leonhardt N, Schattat MH, Berthomé R, Routaboul JM, Noël LD. Mangroves in the Leaves: Anatomy, Physiology, and Immunity of Epithemal Hydathodes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:91-116. [PMID: 31100996 DOI: 10.1146/annurev-phyto-082718-100228] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Hydathodes are organs found on aerial parts of a wide range of plant species that provide almost direct access for several pathogenic microbes to the plant vascular system. Hydathodes are better known as the site of guttation, which is the release of droplets of plant apoplastic fluid to the outer leaf surface. Because these organs are only described through sporadic allusions in the literature, this review aims to provide a comprehensive view of hydathode development, physiology, and immunity by compiling a historic and contemporary bibliography. In particular, we refine the definition of hydathodes.We illustrate their important roles in the maintenance of plant osmotic balance, nutrient retrieval, and exclusion of deleterious chemicals from the xylem sap. Finally, we present our current understanding of the infection of hydathodes by adapted vascular pathogens and the associated plant immune responses.
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Affiliation(s)
- Aude Cerutti
- LIPM, Université de Toulouse, INRA and CNRS and Université Paul Sabatier, F-31326 Castanet-Tolosan, France;
| | - Alain Jauneau
- Plateforme Imagerie, Institut Fédératif de Recherche 3450, Pôle de Biotechnologie Végétale, F-31326 Castanet-Tolosan, France
| | - Patrick Laufs
- Institut Jean-Pierre Bourgin, INRA and AgroParisTech and CNRS, Université Paris-Saclay, F-78000 Versailles, France
| | - Nathalie Leonhardt
- Laboratoire de Biologie du Développement des Plantes, Institut de Biosciences et Biotechnologies d'Aix-Marseille, Aix-Marseille Université and Commissariat à l'Energie Atomique et aux Energies Alternatives and CNRS, UMR 7265, F-13108 Saint Paul-Les-Durance, France
| | - Martin H Schattat
- Department of Plant Physiology, Institute for Biology, Martin-Luther-University Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Richard Berthomé
- LIPM, Université de Toulouse and INRA and CNRS, F-31326 Castanet-Tolosan, France;
| | - Jean-Marc Routaboul
- LIPM, Université de Toulouse and INRA and CNRS, F-31326 Castanet-Tolosan, France;
| | - Laurent D Noël
- LIPM, Université de Toulouse and INRA and CNRS, F-31326 Castanet-Tolosan, France;
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19
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Mohammad HB, Lee SE, Kim MS. Refining a Pathogen's Genome to Know the Enemy Better for the Winning Battles. Proteomics 2019; 19:e1900005. [PMID: 30884182 DOI: 10.1002/pmic.201900005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 02/17/2019] [Indexed: 11/06/2022]
Abstract
Clavibacter michiganensis, subsp. michiganens is a gram positive bacterial pathogen infecting tomato, resulting in the great losses of yield and quality worldwide. Despite its great impact on economics, we do not fully understand the virulence factors from its genome probably due to imperfect genome annotation. Peritore-Galve et al. utilized proteogenomic approach to identify 26 novel protein-coding regions, to extend 59 annotated open reading frames and to confirm protein expression for ≈70% of predicted gene models of Clavibacter michiganensis subsp. michiganensis. New findings by the proteogenomics technique were further confirmed using reverse transcription-polymerase chain reaction. To win battles with pathogens, it is advantageous to know about our enemies accurately which can be achieved by mass spectrometry-based identifications of novel protein-coding regions in genomes.
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Affiliation(s)
| | - Seung-Eun Lee
- Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Min-Sik Kim
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea
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20
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Peritore-Galve FC, Schneider DJ, Yang Y, Thannhauser TW, Smart CD, Stodghill P. Proteome Profile and Genome Refinement of the Tomato-Pathogenic Bacterium Clavibacter michiganensis subsp. michiganensis. Proteomics 2019; 19:e1800224. [PMID: 30648817 DOI: 10.1002/pmic.201800224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 11/29/2018] [Indexed: 11/07/2022]
Affiliation(s)
- F Christopher Peritore-Galve
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, 14456, USA
| | - David J Schneider
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada
| | - Yong Yang
- United States Department of Agriculture (USDA), Agricultural Research Service, Robert W. Holley Center, Ithaca, NY, 14853, USA
| | - Theodore W Thannhauser
- United States Department of Agriculture (USDA), Agricultural Research Service, Robert W. Holley Center, Ithaca, NY, 14853, USA
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, 14456, USA
| | - Paul Stodghill
- United States Department of Agriculture (USDA), Agricultural Research Service, Robert W. Holley Center, Ithaca, NY, 14853, USA
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21
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Tancos MA, Lowe‐Power TM, Peritore‐Galve FC, Tran TM, Allen C, Smart CD. Plant-like bacterial expansins play contrasting roles in two tomato vascular pathogens. MOLECULAR PLANT PATHOLOGY 2018; 19:1210-1221. [PMID: 28868644 PMCID: PMC5835177 DOI: 10.1111/mpp.12611] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/04/2017] [Accepted: 08/31/2017] [Indexed: 05/27/2023]
Abstract
Expansin proteins, which loosen plant cell walls, play critical roles in normal plant growth and development. The horizontal acquisition of functional plant-like expansin genes in numerous xylem-colonizing phytopathogenic bacteria suggests that bacterial expansins may also contribute to virulence. To investigate the role of bacterial expansins in plant diseases, we mutated the non-chimeric expansin genes (CmEXLX2 and RsEXLX) of two xylem-inhabiting bacterial pathogens, the Actinobacterium Clavibacter michiganensis ssp. michiganensis (Cmm) and the β-proteobacterium Ralstonia solanacearum (Rs), respectively. The Cmm ΔCmEXLX2 mutant caused increased symptom development on tomato, which was characterized by more rapid wilting, greater vascular necrosis and abundant atypical lesions on distant petioles. This increased disease severity correlated with larger in planta populations of the ΔCmEXLX2 mutant, even though the strains grew as well as the wild-type in vitro. Similarly, when inoculated onto tomato fruit, ΔCmEXLX2 caused significantly larger lesions with larger necrotic centres. In contrast, the Rs ΔRsEXLX mutant showed reduced virulence on tomato following root inoculation, but not following direct petiole inoculation, suggesting that the RsEXLX expansin contributes to early virulence at the root infection stage. Consistent with this finding, ΔRsEXLX attached to tomato seedling roots better than the wild-type Rs, which may prevent mutants from invading the plant's vasculature. These contrasting results demonstrate the diverse roles of non-chimeric bacterial expansins and highlight their importance in plant-bacterial interactions.
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Affiliation(s)
- Matthew A. Tancos
- Plant Pathology and Plant‐Microbe Biology Section, School of Integrative Plant SciencesCornell UniversityGenevaNY 14456USA
- Present address:
Foreign Disease‐Weed Science Research Unit, USDA‐ARSFort DetrickMD 21702USA
| | | | - F. Christopher Peritore‐Galve
- Plant Pathology and Plant‐Microbe Biology Section, School of Integrative Plant SciencesCornell UniversityGenevaNY 14456USA
| | - Tuan M. Tran
- Department of Plant PathologyUniversity of Wisconsin‐MadisonMadisonWI 53706USA
- Present address:
School of Biological SciencesNanyang Technological University639798Singapore
| | - Caitilyn Allen
- Department of Plant PathologyUniversity of Wisconsin‐MadisonMadisonWI 53706USA
| | - Christine D. Smart
- Plant Pathology and Plant‐Microbe Biology Section, School of Integrative Plant SciencesCornell UniversityGenevaNY 14456USA
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Baek KY, Lee HH, Son GJ, Lee PA, Roy N, Seo YS, Lee SW. Specific and Sensitive Primers Developed by Comparative Genomics to Detect Bacterial Pathogens in Grains. THE PLANT PATHOLOGY JOURNAL 2018; 34:104-112. [PMID: 29628816 PMCID: PMC5880354 DOI: 10.5423/ppj.oa.11.2017.0250] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/11/2018] [Accepted: 01/11/2018] [Indexed: 05/02/2023]
Abstract
Accurate and rapid detection of bacterial plant pathogen is the first step toward disease management and prevention of pathogen spread. Bacterial plant pathogens Clavibacter michiganensis subsp. nebraskensis (Cmn), Pantoea stewartii subsp. stewartii (Pss), and Rathayibacter tritici (Rt) cause Goss's bacterial wilt and blight of maize, Stewart's wilt of maize and spike blight of wheat and barley, respectively. The bacterial diseases are not globally distributed and not present in Korea. This study adopted comparative genomics approach and aimed to develop specific primer pairs to detect these three bacterial pathogens. Genome comparison among target pathogens and their closely related bacterial species generated 15-20 candidate primer pairs per bacterial pathogen. The primer pairs were assessed by a conventional PCR for specificity against 33 species of Clavibacter, Pantoea, Rathayibacter, Pectobacterium, Curtobacterium. The investigation for specificity and sensitivity of the primer pairs allowed final selection of one or two primer pairs per bacterial pathogens. In our assay condition, a detection limit of Pss and Cmn was 2 pg/μl of genomic DNA per PCR reaction, while the detection limit for Rt primers was higher. The selected primers could also detect bacterial cells up to 8.8 × 103 cfu to 7.84 × 104 cfu per gram of grain seeds artificially infected with corresponding bacterial pathogens. The primer pairs and PCR assay developed in this study provide an accurate and rapid detection method for three bacterial pathogens of grains, which can be used to investigate bacteria contamination in grain seeds and to ultimately prevent pathogen dissemination over countries.
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Affiliation(s)
- Kwang Yeol Baek
- Department of Applied Bioscience, Dong-A University, Busan 49315,
Korea
| | - Hyun-Hee Lee
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
| | - Geun Ju Son
- Department of Applied Bioscience, Dong-A University, Busan 49315,
Korea
| | - Pyeong An Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315,
Korea
| | - Nazish Roy
- Department of Applied Bioscience, Dong-A University, Busan 49315,
Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
- Co-corresponding authors. Young-Su Seo, Phone) +82-51-510-2267, FAX) +82-51-514-1778, E-mail) . Seon-Woo Lee, Phone) +82-51-200-7551, FAX) +82-51-200-7505, E-mail)
| | - Seon-Woo Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315,
Korea
- Co-corresponding authors. Young-Su Seo, Phone) +82-51-510-2267, FAX) +82-51-514-1778, E-mail) . Seon-Woo Lee, Phone) +82-51-200-7551, FAX) +82-51-200-7505, E-mail)
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23
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Nandi M, Macdonald J, Liu P, Weselowski B, Yuan Z. Clavibacter michiganensis ssp. michiganensis: bacterial canker of tomato, molecular interactions and disease management. MOLECULAR PLANT PATHOLOGY 2018; 19:2036-2050. [PMID: 29528201 PMCID: PMC6638088 DOI: 10.1111/mpp.12678] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 05/11/2023]
Abstract
Bacterial canker disease is considered to be one of the most destructive diseases of tomato (Solanum lycopersicum), and is caused by the seed-borne Gram-positive bacterium Clavibacter michiganensis ssp. michiganensis (Cmm). This vascular pathogen generally invades and proliferates in the xylem through natural openings or wounds, causing wilt and canker symptoms. The incidence of symptomless latent infections and the invasion of tomato seeds by Cmm are widespread. Pathogenicity is mediated by virulence factors and transcriptional regulators encoded by the chromosome and two natural plasmids. The virulence factors include serine proteases, cell wall-degrading enzymes (cellulases, xylanases, pectinases) and others. Mutational analyses of these genes and gene expression profiling (via quantitative reverse transcription-polymerase chain reaction, transcriptomics and proteomics) have begun to shed light on their roles in colonization and virulence, whereas the expression of tomato genes in response to Cmm infection suggests plant factors involved in the defence response. These findings may aid in the generation of target-specific bactericides or new resistant varieties of tomato. Meanwhile, various chemical and biological controls have been researched to control Cmm. This review presents a detailed investigation regarding the pathogen Cmm, bacterial canker infection, molecular interactions between Cmm and tomato, and current perspectives on improved disease management.
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Affiliation(s)
- Munmun Nandi
- Department of Microbiology & Immunology, Schulich School of Medicine & DentistryUniversity of Western OntarioLondonONCanada, N6A 5C1
| | - Jacqueline Macdonald
- Department of Microbiology & Immunology, Schulich School of Medicine & DentistryUniversity of Western OntarioLondonONCanada, N6A 5C1
| | - Peng Liu
- Department of Microbiology & Immunology, Schulich School of Medicine & DentistryUniversity of Western OntarioLondonONCanada, N6A 5C1
| | - Brian Weselowski
- London Research and Development Centre, Agriculture & Agri‐Food CanadaLondonONCanada, N5V 4T3
| | - Ze‐Chun Yuan
- Department of Microbiology & Immunology, Schulich School of Medicine & DentistryUniversity of Western OntarioLondonONCanada, N6A 5C1
- London Research and Development Centre, Agriculture & Agri‐Food CanadaLondonONCanada, N5V 4T3
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Shade A, Jacques MA, Barret M. Ecological patterns of seed microbiome diversity, transmission, and assembly. Curr Opin Microbiol 2017; 37:15-22. [PMID: 28437661 DOI: 10.1016/j.mib.2017.03.010] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 03/22/2017] [Indexed: 01/08/2023]
Abstract
Seeds are involved in the transmission of microorganisms from one plant generation to another and consequently act as the initial inoculum for the plant microbiota. The purpose of this mini-review is to provide an overview of current knowledge on the diversity, structure and role of the seed microbiota. The relative importance of the mode of transmission (vertical vs horizontal) of the microbial entities composing the seed microbiota as well as the potential connections existing between seed and other plant habitats such as the anthosphere and the spermosphere is discussed. Finally the governing processes (niche vs neutral) involved in the assembly and the dynamics of the seed microbiota are examined.
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Affiliation(s)
- Ashley Shade
- Department of Microbiology and Molecular Genetics, Program in Ecology, Evolutionary Biology, and Behavior, The DOE Great Lakes Bioenergy Research Center, The Plant Resilience Institute, Michigan State University, East Lansing MI 48824, United States
| | - Marie-Agnès Jacques
- INRA, UMR1345 Institut de Recherches en Horticulture et Semences, SFR4207 QUASAV, F-49071, Beaucouzé, France
| | - Matthieu Barret
- INRA, UMR1345 Institut de Recherches en Horticulture et Semences, SFR4207 QUASAV, F-49071, Beaucouzé, France.
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Nguyen TTX, Dehne HW, Steiner U. Maize leaf trichomes represent an entry point of infection for Fusarium species. Fungal Biol 2016; 120:895-903. [PMID: 27521623 DOI: 10.1016/j.funbio.2016.05.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 04/09/2016] [Accepted: 05/31/2016] [Indexed: 11/28/2022]
Abstract
Fifteen day old maize seedlings were inoculated with Fusarium graminearum, Fusarium proliferatum, and Fusarium verticillioides. More than 90 % F. proliferatum and F. verticillioides conidia and 50 % of F. graminearum formed one germ tube whereas the other 50 % of F. graminearum conidia formed two to three germ tubes. The germ tubes of F. graminearum conidia were longer than those of F. proliferatum and F. verticillioides. The three species of Fusarium infected bi-cellular trichomes by adhering and growing along the trichomes or by attaching to the cap cell of the trichomes 48 h after inoculation. Hyphae penetrated into the trichomes at the base, the side or at the top of the cap cells. The hyphae colonized the cap cells and then spread to base cells. Prickle trichomes were infected 72 h after inoculation. The hyphae either wrapped around prickle trichomes or formed a mass of hyphae around the top of prickle trichomes or formed appressorium. Macro trichomes were infected by F. graminearum 7 d after inoculation. Following penetration, the fungus spread to adjacent epidermal cells and to the subcuticle. This investigation provides the first assessment of F. graminearum, F. proliferatum, and F. verticillioides infection via trichomes of maize leaves.
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Affiliation(s)
- Thi Thanh Xuan Nguyen
- Institute of Crop Science and Resource Conservation, Division Phytomedicine, University of Bonn, Nussallee 9, 53115 Bonn, Germany; Faculty of Agriculture and Natural Resources, University of An Giang, 18 Ung Van Khiem, 880000 An Giang, Viet Nam.
| | - Heinz-Wilhelm Dehne
- Institute of Crop Science and Resource Conservation, Division Phytomedicine, University of Bonn, Nussallee 9, 53115 Bonn, Germany
| | - Ulrike Steiner
- Institute of Crop Science and Resource Conservation, Division Phytomedicine, University of Bonn, Nussallee 9, 53115 Bonn, Germany
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Rezki S, Campion C, Iacomi-Vasilescu B, Preveaux A, Toualbia Y, Bonneau S, Briand M, Laurent E, Hunault G, Simoneau P, Jacques MA, Barret M. Differences in stability of seed-associated microbial assemblages in response to invasion by phytopathogenic microorganisms. PeerJ 2016; 4:e1923. [PMID: 27077013 PMCID: PMC4830237 DOI: 10.7717/peerj.1923] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/21/2016] [Indexed: 11/20/2022] Open
Abstract
Seeds are involved in the vertical transmission of microorganisms from one plant generation to another and consequently act as reservoirs for the plant microbiota. However, little is known about the structure of seed-associated microbial assemblages and the regulators of assemblage structure. In this work, we have assessed the response of seed-associated microbial assemblages of Raphanus sativus to invading phytopathogenic agents, the bacterial strain Xanthomonas campestris pv. campestris (Xcc) 8004 and the fungal strain Alternaria brassicicola Abra43. According to the indicators of bacterial (16S rRNA gene and gyrB sequences) and fungal (ITS1) diversity employed in this study, seed transmission of the bacterial strain Xcc 8004 did not change the overall composition of resident microbial assemblages. In contrast seed transmission of Abra43 strongly modified the richness and structure of fungal assemblages without affecting bacterial assemblages. The sensitivity of seed-associated fungal assemblage to Abra43 is mostly related to changes in relative abundance of closely related fungal species that belong to the Alternaria genus. Variation in stability of the seed microbiota in response to Xcc and Abra43 invasions could be explained by differences in seed transmission pathways employed by these micro-organisms, which ultimately results in divergence in spatio-temporal colonization of the seed habitat.
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Affiliation(s)
- Samir Rezki
- Institut de Recherche en Horticulture et Semences, Institut National de la Recherche Agronomique , Beaucouzé , France
| | - Claire Campion
- Institut de Recherche en Horticulture et Semences, Université d'Angers , Beaucouzé , France
| | | | - Anne Preveaux
- Institut de Recherche en Horticulture et Semences, Institut National de la Recherche Agronomique , Beaucouzé , France
| | - Youness Toualbia
- Institut de Recherche en Horticulture et Semences, Université d'Angers , Beaucouzé , France
| | - Sophie Bonneau
- Institut de Recherche en Horticulture et Semences, Institut National de la Recherche Agronomique , Beaucouzé , France
| | - Martial Briand
- Institut de Recherche en Horticulture et Semences, Institut National de la Recherche Agronomique , Beaucouzé , France
| | - Emmanuelle Laurent
- Federation Nationale des Agriculteurs Multiplicateurs de Semences , Brain sur l'Authion , France
| | - Gilles Hunault
- Laboratoire d'Hémodynamique, Interaction Fibrose et Invasivité tumorale Hépatique, Université d'Angers , Angers , France
| | - Philippe Simoneau
- Institut de Recherche en Horticulture et Semences, Université d'Angers , Beaucouzé , France
| | - Marie-Agnès Jacques
- Institut de Recherche en Horticulture et Semences, Institut National de la Recherche Agronomique , Beaucouzé , France
| | - Matthieu Barret
- Institut de Recherche en Horticulture et Semences, Institut National de la Recherche Agronomique , Beaucouzé , France
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A Proteomic Study of Clavibacter Michiganensis Subsp. Michiganensis Culture Supernatants. Proteomes 2015; 3:411-423. [PMID: 28248277 PMCID: PMC5217389 DOI: 10.3390/proteomes3040411] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 10/30/2015] [Accepted: 11/10/2015] [Indexed: 11/23/2022] Open
Abstract
Clavibacter michiganensis, subsp. michiganensis is a Gram-positive plant pathogen infecting tomato (Solanum lycopersicum). Despite a considerable economic importance due to significant losses of infected plants and fruits, knowledge about virulence factors of C. michiganensis subsp. michiganensis and host-pathogen interactions on a molecular level are rather limited. In the study presented here, the proteome of culture supernatants from C. michiganensis subsp. michiganensis NCPPB382 was analyzed. In total, 1872 proteins were identified in M9 and 1766 proteins in xylem mimicking medium. Filtration of supernatants before protein precipitation reduced these to 1276 proteins in M9 and 976 proteins in the xylem mimicking medium culture filtrate. The results obtained indicate that C. michiganensis subsp. michiganensis reacts to a sucrose- and glucose-depleted medium similar to the xylem sap by utilizing amino acids and host cell polymers as well as their degradation products, mainly peptides, amino acids and various C5 and C6 sugars. Interestingly, the bacterium expresses the previously described virulence factors Pat-1 and CelA not exclusively after host cell contact in planta but already in M9 minimal and xylem mimicking medium.
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Tancos MA, Lange HW, Smart CD. Characterizing the Genetic Diversity of the Clavibacter michiganensis subsp. michiganensis Population in New York. PHYTOPATHOLOGY 2015; 105:169-179. [PMID: 25208240 DOI: 10.1094/phyto-06-14-0178-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
New York Clavibacter michiganensis subsp. michiganensis isolates, collected from disparate bacterial canker of tomato outbreaks over the past 11 years, were characterized with a multilocus sequence analysis (MLSA) scheme that differentiated the 51 isolates into 21 haplotypes with a discriminatory power of 0.944. The MLSA scheme consisted of five housekeeping genes (kdpA, sdhA, dnaA, ligA, and gyrB) and three putative pathogenicity genes (celA, tomA, and nagA). Repetitive polymerase chain reaction (PCR), with the BOX-A1R primer, confirmed the high diversity of C. michiganensis subsp. michiganensis isolates in New York by demonstrating that all six PCR patterns (A, B, 13C, 65C, 81C, and D) were present, with PCR patterns C and A being the most common. The MLSA scheme provided higher resolving power than the current repetitive-PCR approach. The plasmid profiles of New York isolates were diverse and differed from reference strain NCPPB382. PCR analysis indicated that the presence of putative pathogenicity genes varied between isolates and highlighted the ephemeral nature of pathogenicity genes in field populations of C. michiganensis subsp. michiganensis. Analysis of molecular variance between Serbian and New York C. michiganensis subsp. michiganensis isolates demonstrated that the two populations were not significantly different, with 98% genetic variation within each population and only 2% genetic variation between populations.
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Sen Y, van der Wolf J, Visser RGF, van Heusden S. Bacterial Canker of Tomato: Current Knowledge of Detection, Management, Resistance, and Interactions. PLANT DISEASE 2015; 99:4-13. [PMID: 30699746 DOI: 10.1094/pdis-05-14-0499-fe] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Clavibacter michiganensis subsp. michiganensis is the causal agent of bacterial canker of tomato. The disease was first described in 1910 in Michigan, USA. C. michiganensis subsp. michiganensis (from now on called clavibacter) was initially thought to be a phloem parasite, but was later found to be a xylem-invading bacterium. The host range comprises mainly solanaceous crops such as tomato, pepper, and eggplant. Strains show great variability in virulence and are usually described as being hypervirulent, hypovirulent, or nonvirulent. Clavibacter lacks a type III secretion system, and only a few virulence factors have been experimentally determined from the many putative virulence factors. As the molecular mode of infection by clavibacter is unknown, researchers have avoided intensive work on this organism. Genetic plant mechanisms conferring resistance to clavibacter are apparently complex, and breeders have yet to develop disease-resistant cultivars.
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Affiliation(s)
- Yusuf Sen
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands, and Graduate School Experimental Plant Sciences, Wageningen, The Netherlands
| | - Jan van der Wolf
- Plant Research International Biointeractions and Plant Health, Wageningen, The Netherlands
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Sjaak van Heusden
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
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Scientific Opinion on the pest categorisation of Clavibacter michiganensis subsp. michiganensis (Smith) Davis et al. EFSA J 2014. [DOI: 10.2903/j.efsa.2014.3721] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Kassem II, Splitter GA, Miller S, Rajashekara G. Let There Be Light! Bioluminescent Imaging to Study Bacterial Pathogenesis in Live Animals and Plants. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 154:119-45. [DOI: 10.1007/10_2014_280] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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