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Phytoplasmas: Molecular Characterization and Host-Pathogen Interactions

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A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: closed (18 November 2023) | Viewed by 25329

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Special Issue Editors

Dr. Wei Wei

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Guest Editor

USDA ARS Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
Interests: insect-transmissible plant pathogenic mollicutes; host-pathogen interactions; phytoplasma taxonomy and classification; phytoplasma database construction; high throughput omics studies; molecular diagnosis and epidemiology

Dr. Yan Zhao

E-Mail Website
Guest Editor

Molecular Plant Pathology Laboratory, USDA ARS, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
Interests: genetic diversity and systematics of phytoplasmas; mechanisms of phytoplasma-host interactions and pathogenicity; molecular targets for pathogen detection and disease control

Dr. Fabio Quaglino

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Guest Editor

Department of Agricultural and Environmental Sciences, Production, Landscape, Agroenergy, the University of Milan, 20133 Milan, Italy
Interests: phytoplasma taxonomy and evolution; phytoplasma genomics; phytoplasma-host interactions; phytoplasma population diversity in natural hosts (plants and insect vectors); molecular epidemiology of phytoplasma-associated diseases and integrated sustainable control strategies (selection of resistant crop varieties; recovery induction; biocontrol agents; antimicrobial molecules; management of agroecosystems)

Special Issue Information

Dear Colleagues,

Phytoplasmas are obligate intracellular bacteria that infect a wide variety of plant species and multiply in phloem-feeding insects in the order Hemiptera. The transkingdom life cycle of phytoplasma determines the complexity of its pathosystem and epidemiology in a broad range of ecological environments. Based on molecular characterization and database-guided identification and classification, significant advances have been achieved in phytoplasma studies in terms of genetic diversity and geographic distribution (in both managed agroecosystems and natural habitats), potential insect vectors, and new host plants, including symptomatic and asymptomatic weed reservoirs. The accumulating data on “phytoplasma–vector–plant” tripartite components provides a solid basis for understanding phytoplasma epidemiology and disease management.

In recent decades, studies on host–phytoplasma interactions have involved not only molecular analysis (“bottom-up approach” of systems biology at a small scale), but also high-throughput omics studies (“top-down approach” of systems biology at a large scale) such as genomics, transcriptomics, proteomics, and metabolomics. Combining “top-down” and “bottom-up” research approaches, host–phytoplasma interaction research has made tremendous progress in exploration from disease symptoms to underlying mechanisms, including the identification of virulence factors corresponding to symptoms and changes in host–response induced by phytoplasmas. These new advances contribute to a better understanding of the role of host–phytoplasma interactions in complex pathogenic processes and biological and physiological pathways involved in disease development and transmission.

For this Special Issue of Biology, we invite you to submit original research articles, reviews, opinions, and perspectives on molecular characterization of phytoplasmas and host–phytoplasma interactions in various aspects.

We look forward to your contribution.

Dr. Wei Wei
Dr. Yan Zhao
Dr. Fabio Quaglino
Guest Editors

Manuscript Submission Information

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Keywords

molecular diagnosis and epidemiology
host-phytoplasma interactions
genetic diversity
taxonomy and classification
ecology and evolution
insect vectors
disease management
phytoplasma genomics and other omics studies

Published Papers (10 papers)

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Research

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11 pages, 1241 KiB

Open AccessArticle

Investigation on Flavescence Dorée in North-Western Italy Identifies Map-M54 (16SrV-D/Map-FD2) as the Only Phytoplasma Genotype in Vitis vinifera L. and Reveals the Presence of New Putative Reservoir Plants

by Ivo Ercole Rigamonti, Martino Salvetti, Paola Girgenti, Piero Attilio Bianco and Fabio Quaglino

Biology 2023, 12(9), 1216; https://doi.org/10.3390/biology12091216 - 07 Sep 2023

Cited by 2 | Viewed by 958

Abstract

Flavescence dorée (FD) is the most important phytoplasma-associated disease of the grapevine yellows complex in Europe. Recent studies highlighted a great genetic diversity within FD phytoplasma (FDp) strains and demonstrated that their diffusion is not related exclusively to the pathosystem including Vitis vinifera L. and Scaphoideus titanus but involves additional vectors and reservoir plants. This study aimed to investigate FD epidemiology in north-western Italy, with a particular focus on FDp hosts. During field surveys, leaf samples were collected from symptomatic grapevines and other symptomless plant species, and insects were collected within and around vineyards. Phytoplasmas belonging to the ribosomal group 16SrV were detected and typed using nested-PCR-based amplification and nucleotide sequence analyses of the map gene. All symptomatic grapevines were found to be infected by the FDp genotype M54, prevalent in S. titanus and also identified in other known and newly reported hosts. Interestingly, other FDp strains (M38, M50, M51, M121) and FDp-related strains (M39, M43, M48), never detected in grapevines, were largely identified in several known and newly reported host plants and insects including S. titanus. Such evidence confirmed the complexity of FD ecology, expanding the knowledge on the range of FDp host plants putatively involved in the disease spread. Full article

(This article belongs to the Special Issue Phytoplasmas: Molecular Characterization and Host-Pathogen Interactions)

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22 pages, 1761 KiB

Open AccessArticle

Phylogenetic Triage and Risk Assessment: How to Predict Emerging Phytoplasma Diseases

by Katrin Janik, Bernd Panassiti, Christine Kerschbamer, Johannes Burmeister and Valeria Trivellone

Biology 2023, 12(5), 732; https://doi.org/10.3390/biology12050732 - 17 May 2023

Viewed by 1289

Abstract

Phytoplasma diseases pose a substantial threat to diverse crops of agricultural importance. Management measures are usually implemented only after the disease has already occurred. Early detection of such phytopathogens, prior to disease outbreak, has rarely been attempted, but would be highly beneficial for phytosanitary risk assessment, disease prevention and mitigation. In this study, we present the implementation of a recently proposed proactive disease management protocol (DAMA: Document, Assess, Monitor, Act) for a group of vector-borne phytopathogens. We used insect samples collected during a recent biomonitoring program in southern Germany to screen for the presence of phytoplasmas. Insects were collected with malaise traps in different agricultural settings. DNA was extracted from these mass trap samples and subjected to PCR-based phytoplasma detection and mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding. Phytoplasma DNA was detected in two out of the 152 insect samples analyzed. Phytoplasma identification was performed using iPhyClassifier based on 16S rRNA gene sequence and the detected phytoplasmas were assigned to ‘Candidatus Phytoplasma asteris’-related strains. Insect species in the sample were identified by DNA metabarcoding. By using established databases, checklists, and archives, we documented historical associations and records of phytoplasmas and its hosts in the study region. For the assessment in the DAMA protocol, phylogenetic triage was performed in order to determine the risk for tri-trophic interactions (plant–insect–phytoplasma) and associated disease outbreaks in the study region. A phylogenetic heat map constitutes the basis for risk assessment and was used here to identify a minimum number of seven leafhopper species suggested to be monitored by stakeholders in this region. A proactive stance in monitoring changing patterns of association between hosts and pathogens can be a cornerstone in capabilities to prevent future phytoplasma disease outbreaks. To the best of our knowledge, this is the first time that the DAMA protocol has been applied in the field of phytopathology and vector-borne plant diseases. Full article

(This article belongs to the Special Issue Phytoplasmas: Molecular Characterization and Host-Pathogen Interactions)

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14 pages, 6350 KiB

Open AccessArticle

Nested Real-Time PCR Assessment of Vertical Transmission of Sandalwood Spike Phytoplasma (‘Ca. Phytoplasma asteris’)

by Kiran Kirdat, Bhavesh Tiwarekar, Purushotham Swetha, Sodaliyandi Padma, Vipool Thorat, Kathiruguppe Nagappa Manjula, Narayan Kavya, Ramachandran Sundararaj and Amit Yadav

Biology 2022, 11(10), 1494; https://doi.org/10.3390/biology11101494 - 12 Oct 2022

Cited by 3 | Viewed by 1834

Abstract

The Sandalwood Spike disease (SSD)-related to ‘Ca. Phytoplasma asteris’ has threatened the existence of sandalwood in India. The epidemiology of SSD is still poorly understood despite the efforts to understand the involvement of insect vectors in SSD transmission and alternate plant hosts over the last two decades. Apart from the transmission of SSD phytoplasma through insect vectors, the information on vertical transmission is entirely unknown. Over 200 seeds from SSD-affected trees and over 500 seedlings generated using commercially purchased seeds were screened for the presence of SSD phytoplasma to understand the vertical transmission in an insect-free environment. The end-point nested PCR and real-time nested PCR-based screening revealed an alarming rate of 38.66% and 23.23% phytoplasma positivity in one-month and four-month-old seedlings, respectively. These results were further validated by visualizing the phytoplasma bodies in sandalwood tissues using scanning electron microscopy. The presence of phytoplasma DNA in the seeds and seedlings is a concern for the commercial distribution of sandalwood seedlings in the current setup. This also poses a fear of spreading the disease to newer areas and negatively affecting the economy. The seedling mortality was also suspected to be associated with isolated bacterial and fungal isolates such as Erwinia, Curtobacterium, Pseudomonas, Rhodococcus, Aspergillus, Fusarium, and Neofusicoccum isolated using a culture-dependent approach. These findings strongly recommend the accreditation of commercial production of sandalwood seedlings curtailing SSD phytoplasma’s menace. Additionally, a new nested end-point and qRT PCR assays developed in this study proved valuable for the rapid screening of phytoplasma in many plant samples to detect phytoplasmas. Full article

(This article belongs to the Special Issue Phytoplasmas: Molecular Characterization and Host-Pathogen Interactions)

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14 pages, 2576 KiB

Open AccessArticle

Impact of the “Flavescence Dorée” Phytoplasma on Xylem Growth and Anatomical Characteristics in Trunks of ‘Chardonnay’ Grapevines (Vitis vinifera)

by Attilio Rizzoli, Luca Jelmini, Gianni Boris Pezzatti, Mauro Jermini, Olivier Schumpp, Christophe Debonneville, Enrico Marcolin, Patrik Krebs and Marco Conedera

Biology 2022, 11(7), 978; https://doi.org/10.3390/biology11070978 - 28 Jun 2022

Cited by 4 | Viewed by 1669

Abstract

Flavescence dorée (FD) is a grapevine disease caused by ‘Candidatus Phytoplasma vitis’ (FDp), which is epidemically transmitted by the Nearctic leafhopper Scaphoideus titanus. In this study, we applied dendrochronological techniques to analyse the response to FDp infections in terms of wood ring widths and anatomical structures of the xylem and phloem tissues of the trunk of the susceptible grapevine cultivar ‘Chardonnay.’ As a rule, grapevines are susceptible to water shortage and reduce their growth in diameter in case of summer drought. In the season of the external expression of FD symptoms, however, the ring width reductions are extreme and supersede any drought-induced effects. In addition, the anatomy of the phloem tissue in the year of the FD symptom expression appears heavily disarranged. Moreover, in the most suffering individuals, the xylem formation remains incomplete and mostly limited to the early wood tissue. In conclusion, even though the FD phytoplasma does not inhabit and replicate inside the xylem tissue, our results confirm existing indirect inhibiting effects on the ring growth and the xylem tissue formation in FDp-infected grapevines. Full article

(This article belongs to the Special Issue Phytoplasmas: Molecular Characterization and Host-Pathogen Interactions)

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21 pages, 2301 KiB

Open AccessArticle

Comparison of Traditional and Next-Generation Approaches for Uncovering Phytoplasma Diversity, with Discovery of New Groups, Subgroups and Potential Vectors

by Valeria Trivellone, Yanghui Cao and Christopher H. Dietrich

Biology 2022, 11(7), 977; https://doi.org/10.3390/biology11070977 - 28 Jun 2022

Cited by 9 | Viewed by 2587

Abstract

Despite several decades’ effort to detect and identify phytoplasmas (Mollicutes) using PCR and Sanger sequencing focusing on diseased plants, knowledge of phytoplasma biodiversity and vector associations remains highly incomplete. To improve protocols for documenting phytoplasma diversity and ecology, we used DNA extracted from phloem-feeding insects and compared traditional Sanger sequencing with a next-generation sequencing method, Anchored Hybrid Enrichment (AHE) for detecting and characterizing phytoplasmas. Among 22 of 180 leafhopper samples that initially tested positive for phytoplasmas using qPCR, AHE yielded phytoplasma 16Sr sequences for 20 (19 complete and 1 partial sequence) while Sanger sequencing yielded sequences for 16 (11 complete and 5 partial). AHE yielded phytoplasma sequences for an additional 7 samples (3 complete and 4 partial) that did not meet the qPCR threshold for phytoplasma positivity or yielded non-phytoplasma sequences using Sanger sequencing. This suggests that AHE is more efficient for obtaining phytoplasma sequences. Twenty-three samples with sufficient data were classified into eight 16Sr subgroups (16SrI-B, I-F, I-AO, III-U, V-C, IX-J, XI-C, XXXVII-A), three new subgroups (designated as 16SrVI-L, XV-D, XI-G) and three possible new groups. Our results suggest that screening phloem-feeding insects using qPCR and AHE sequencing may be the most efficient method for discovering new phytoplasmas. Full article

(This article belongs to the Special Issue Phytoplasmas: Molecular Characterization and Host-Pathogen Interactions)

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24 pages, 3422 KiB

Open AccessArticle

Comparative DNA Methylome of Phytoplasma Associated Retrograde Metamorphosis in Sesame (Sesamum indicum L.)

by Pratima Verma, Amrita Singh, Supriya Purru, Kangila Venkataramana Bhat and Suman Lakhanpaul

Biology 2022, 11(7), 954; https://doi.org/10.3390/biology11070954 - 23 Jun 2022

Cited by 1 | Viewed by 1908

Abstract

Phytoplasma-associated diseases such as phyllody and little leaf are critical threats to sesame cultivation worldwide. The mechanism of the dramatic conversion of flowers to leafy structures leading to yield losses and the drastic reduction in leaf size due to Phytoplasma infection remains yet to be identified. Cytosine methylation profiles of healthy and infected sesame plants studied using Whole Genome Bisulfite Sequencing (WGBS) and Quantitative analysis of DNA methylation with the real-time PCR (qAMP) technique revealed altered DNA methylation patterns upon infection. Phyllody was associated with global cytosine hypomethylation, though predominantly in the CHH (where H = A, T or C) context. Interestingly, comparable cytosine methylation levels were observed between healthy and little leaf-affected plant samples in CG, CHG and CHH contexts. Among the different genomic fractions, the highest number of differentially methylated Cytosines was found in the intergenic regions, followed by promoter, exonic and intronic regions in decreasing order. Further, most of the differentially methylated genes were hypomethylated and were mainly associated with development and defense-related processes. Loci for STOREKEEPER protein-like, a DNA-binding protein and PP2-B15, an F-Box protein, responsible for plugging sieve plates to maintain turgor pressure within the sieve tubes were found to be hypomethylated by WGBS, which was confirmed by methylation-dependent restriction digestion and qPCR. Likewise, serine/threonine-protein phosphatase-7 homolog, a positive regulator of cryptochrome signaling involved in hypocotyl and cotyledon growth and probable O-methyltransferase 3 locus were determined to be hypermethylated. Phytoplasma infection-associated global differential methylation as well as the defense and development-related loci reported here for the first time significantly elucidate the mechanism of phytoplasma-associated disease development. Full article

(This article belongs to the Special Issue Phytoplasmas: Molecular Characterization and Host-Pathogen Interactions)

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17 pages, 3025 KiB

Open AccessArticle

The Complete Genome of the “Flavescence Dorée” Phytoplasma Reveals Characteristics of Low Genome Plasticity

by Christophe Debonneville, Léa Mandelli, Justine Brodard, Raphaël Groux, David Roquis and Olivier Schumpp

Biology 2022, 11(7), 953; https://doi.org/10.3390/biology11070953 - 23 Jun 2022

Cited by 12 | Viewed by 2931

Abstract

Members of the genus ‘Candidatus Phytoplasma’ are obligate intracellular bacteria restricted to phloem sieve elements and are able to colonize several tissues and the hemolymph in their insect vectors. The current unfeasibility of axenic culture and the low complexity of genomic sequences are obstacles in assembling complete chromosomes. Here, a method combining pathogen DNA enrichment from infected insects and dual deep-sequencing technologies was used to obtain the complete genome of a phytoplasma causing Grapevine Flavescence dorée. The de novo assembly generated a circular chromosome of 654,223 bp containing 506 protein-coding genes. Quality assessment of the draft showed a high degree of completeness. Comparative analysis with other phytoplasmas revealed the absence of potential mobile units and a reduced amount of putative phage-derived segments, suggesting a low genome plasticity. Phylogenetic analyses identified Candidatus Phytoplasma ziziphi as the closest fully sequenced relative. The “Flavescence dorée” phytoplasma strain CH genome also encoded for several putative effector proteins potentially playing a role in pathogen virulence. The availability of this genome provides the basis for the study of the pathogenicity mechanisms and evolution of the Flavescence dorée phytoplasma. Full article

(This article belongs to the Special Issue Phytoplasmas: Molecular Characterization and Host-Pathogen Interactions)

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14 pages, 2081 KiB

Open AccessArticle

Molecular Identification and Characterization of Two Groups of Phytoplasma and Candidatus Liberibacter Asiaticus in Single or Mixed Infection of Citrus maxima on Hainan Island of China

by Shao-Shuai Yu, An-Na Zhu, Wei-Wei Song and Wei Yan

Biology 2022, 11(6), 869; https://doi.org/10.3390/biology11060869 - 06 Jun 2022

Cited by 6 | Viewed by 3411

Abstract

The pathogens associated with citrus Huanglongbing symptoms, including yellowing and mottled leaves in Citrus maxima, an important economic crop on Hainan Island of China, were identified and characterized. In the study, detection, genetic variation and phylogenetic relationship analysis of the pathogens were performed based on 16S rRNA and β-operon gene fragments specific to phytoplasma and Candidatus Liberibacter asiaticus. The results indicated that the pathogens—such as phytoplasma strains of CmPII-hn belonging to the 16SrII-V subgroup and CmPXXXII-hn belonging to the 16SrXXXII-D subgroup, as well as Candidatus Liberibacter asiaticus strains CmLas-hn—were identified in the diseased plant samples, with numbers of 12, 2 and 6 out of 54, respectively. Among them, mixed infection with the 16SrII-V subgroup phytoplasma and Candidatus Liberibacter asiaticus was found in the study, accounting for 7.4% (four samples). The phytoplasma strains of CmPII-hn—Tephrosia purpurea witches’ broom, Melochia corchorifolia witches’ broom and Emilia sonchifolia witches’ broom—were clustered into one clade belonging to the 16SrII-V subgroup, with a 99% bootstrap value. The phytoplasma strains of CmPXXXII-hn and Trema tomentosa witches’ broom belonging to 16SrXXXII-D, and the other 16SrXXXII subgroup strains were clustered into one clade belonging to the 16SrXXXII group with a 99% bootstrap value. There were 16 variable loci in the 16S rRNA gene sequences of the tested 16SrXXXII group phytoplasma strains, of which two bases had an insertion/deletion. The strains of Candidatus Liberibacter asiaticus, identified in the study and the strains that had been deposited in GenBank, were in one independent cluster with a 99% bootstrap value. To our knowledge, this is the first report showing that Citrus maxima can be infected by 16SrII-V and16SrXXXII-D subgroup phytoplasmas in China. Moreover, this is also the first report in which the plants are co-infected by 16SrII-V subgroup phytoplasmas and Candidatus Liberibacter asiaticus. More comprehensive and detailed identification and characterization of the pathogens associated with the diseased symptoms in Citrus maxima on the island in China would be beneficial for epidemic monitoring and for the effective prevention and control of related plant diseases. Full article

(This article belongs to the Special Issue Phytoplasmas: Molecular Characterization and Host-Pathogen Interactions)

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9 pages, 1290 KiB

Open AccessArticle

Multilocus Genotyping of ‘Candidatus Phytoplasma Solani’ Associated with Grapevine Bois Noir in Iran

by Elham Jamshidi, Sergio Murolo, Sareh Baghaee Ravari, Mohammad Salehi and Gianfranco Romanazzi

Biology 2022, 11(6), 835; https://doi.org/10.3390/biology11060835 - 29 May 2022

Cited by 3 | Viewed by 1748

Abstract

Grapevine Bois noir (BN) is associated with ‘Candidatus Phytoplasma solani’. It has been recorded in vineyards throughout Europe as well as in different countries in Asia, where it now constitutes a threat to Iranian viticulture. BN is strictly dependent on ‘Ca. P. solani’ strains, wild host plants, and insect vectors. The molecular typing of ‘Ca. P. solani’, based on the nonribosomal gene tuf and the two hypervariable markers vmp1 and stamp, is valuable for the reconstruction and clarification of the pathways of BN spread. In this study, an RFLP analysis was performed on the vmp1 gene, and a single-nucleotide polymorphism analysis confirmed new vmp types in ‘Ca. P. solani’. A stamp gene phylogenetic analysis allowed us to distinguish between the new genotype infections in the grapevines and the ‘weeds’ Convolvulus arvensis and Erigeron bonariensis in Iranian vineyards, highlighting the close genetic relatedness of the strains of ‘Ca. P. solani’ found in Iran and Azerbaijan. The most common genotype in the grapevines was tuf b/V24/stamp III, which was associated with C. arvensis. This information contributes toward the identification of further routes of introduction of ‘Ca. P. solani’ in Iran to sustain the control measures for the management of BN. Full article

(This article belongs to the Special Issue Phytoplasmas: Molecular Characterization and Host-Pathogen Interactions)

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Review

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23 pages, 1169 KiB

Open AccessReview

Phytoplasma Taxonomy: Nomenclature, Classification, and Identification

by Wei Wei and Yan Zhao

Biology 2022, 11(8), 1119; https://doi.org/10.3390/biology11081119 - 26 Jul 2022

Cited by 32 | Viewed by 4771

Abstract

Phytoplasmas are pleomorphic, wall-less intracellular bacteria that can cause devastating diseases in a wide variety of plant species. Rapid diagnosis and precise identification of phytoplasmas responsible for emerging plant diseases are crucial to preventing further spread of the diseases and reducing economic losses. Phytoplasma taxonomy (identification, nomenclature, and classification) has lagged in comparison to culturable bacteria, largely due to lack of axenic phytoplasma culture and consequent inaccessibility of phenotypic characteristics. However, the rapid expansion of molecular techniques and the advent of high throughput genome sequencing have tremendously enhanced the nucleotide sequence-based phytoplasma taxonomy. In this article, the key events and milestones that shaped the current phytoplasma taxonomy are highlighted. In addition, the distinctions and relatedness of two parallel systems of ‘Candidatus phytoplasma’ species/nomenclature system and group/subgroup classification system are clarified. Both systems are indispensable as they serve different purposes. Furthermore, some hot button issues in phytoplasma nomenclature are also discussed, especially those pertinent to the implementation of newly revised guidelines for ‘Candidatus Phytoplasma’ species description. To conclude, the challenges and future perspectives of phytoplasma taxonomy are briefly outlined. Full article

(This article belongs to the Special Issue Phytoplasmas: Molecular Characterization and Host-Pathogen Interactions)

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