The genus '
Phytoplasma' was proposed to accommodate cell wall-less bacteria that are molecularly and biochemically incompletely characterized, and colonize plant phloem and insect vector tissues. ...This provisional classification is highly relevant due to its application in epidemiological and ecological studies, mainly aimed at keeping the severe phytoplasma plant diseases under control worldwide. Given the increasing discovery of molecular diversity within the genus '
. Phytoplasma', the proposed guidelines were revised and clarified to accommodate those '
. Phytoplasma' species strains sharing >98.65 % sequence identity of their full or nearly full 16S rRNA gene sequences, obtained with at least twofold coverage of the sequence, compared with those of the reference strain of such species. Strains sharing <98.65 % sequence identity with the reference strain but >98.65 % with other strain(s) within the same '
. Phytoplasma' species should be considered related strains to that '
. Phytoplasma' species. The guidelines herein, keep the original published reference strains. However, to improve '
. Phytoplasma' species assignment, complementary strains are suggested as an alternative to the reference strains. This will be implemented when only a partial 16S rRNA gene and/or a few other genes have been sequenced, or the strain is no longer available for further molecular characterization. Lists of '
. Phytoplasma' species and alternative reference strains described are reported. For new '
. Phytoplasma' species that will be assigned with identity ≥98.65 % of their 16S rRNA gene sequences, a threshold of 95 % genome-wide average nucleotide identity is suggested. When the whole genome sequences are unavailable, two among conserved housekeeping genes could be used. There are 49 officially published '
Phytoplasma' species, including '
. P. cocostanzaniae' and '
. P. palmae' described in this manuscript.
Among grapevine yellows, Bois noir (BN), associated with '
Phytoplasma solani', represents the biggest threat in the main wine-growing areas worldwide, causing significant losses in berry quality and ...yields. BN epidemiology involves multiple plant hosts and several insect vectors, making considerably complex the development of effective management strategies. Since application of insecticides on the grapevine canopy is not effective to manage vectors, BN management includes an integrated approach based on treatments to the canopy to make the plant more resistant to the pathogen and/or inhibit the vector feeding, and actions on reservoir plants to reduce possibilities that the vector reaches the grapevine and transmit the phytoplasma. Innovative sustainable strategies developed in the last twenty years to improve the BN management are reviewed and discussed.
Grapevine (
) is one of the most widely cultivated plant species of agricultural interest, and is extensively appreciated for its fruits and the wines made from its fruits. Considering the high ...socio-economic impact of the wine sector all over the world, in recent years, there has been an increase in work aiming to investigate the biodiversity of grapevine germplasm available for breeding programs. Various studies have shed light on the genetic diversity characterizing the germplasm from the cradle of
domestication in Georgia (South Caucasus). Georgian germplasm is placed in a distinct cluster from the European one and possesses a rich diversity for many different traits, including eno-carpological and phenological traits; resistance to pathogens, such as oomycetes and phytoplasmas; resistance to abiotic stresses, such as sunburn. The aim of this review is to assess the potential of Georgian cultivars as a source of useful traits for breeding programs. The unique genetic and phenotypic aspects of Georgian germplasm were unraveled, to better understand the diversity and quality of the genetic resources available to viticulturists, as valuable resources for the coming climate change scenario.
Bacteria of the Paenibacillus genus are becoming important in many fields of science, including agriculture, for their positive effects on the health of plants. However, there are little information ...available on this genus compared to other bacteria (such as Bacillus or Pseudomonas), especially when considering genomic information. Sequencing the genomes of plant-beneficial bacteria is a crucial step to identify the genetic elements underlying the adaptation to life inside a plant host and, in particular, which of these features determine the differences between a helpful microorganism and a pathogenic one. In this study, we have characterized the genome of Paenibacillus pasadenensis, strain R16, recently investigated for its antifungal activities and plant-associated features. An hybrid assembly approach was used integrating the very precise reads obtained by Illumina technology and long fragments acquired with Oxford Nanopore Technology (ONT) sequencing. De novo genome assembly based solely on Illumina reads generated a relatively fragmented assembly of 5.72 Mbp in 99 ungapped sequences with an N50 length of 544 Kbp; hybrid assembly, integrating Illumina and ONT reads, improved the assembly quality, generating a genome of 5.75 Mbp, organized in 6 contigs with an N50 length of 3.4 Mbp. Annotation of the latter genome identified 4987 coding sequences, of which 1610 are hypothetical proteins. Enrichment analysis identified pathways of particular interest for the endophyte biology, including the chitin-utilization pathway and the incomplete siderophore pathway which hints at siderophore parasitism. In addition the analysis led to the identification of genes for the production of terpenes, as for example farnesol, that was hypothesized as the main antifungal molecule produced by the strain. The functional analysis on the genome confirmed several plant-associated, plant-growth promotion, and biocontrol traits of strain R16, thus adding insights in the genetic bases of these complex features, and of the Paenibacillus genus in general.
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.
Plants develop in a microbe-rich environment and must interact with a plethora of microorganisms, both pathogenic and beneficial. Indeed, such is the case of
, and its model organisms
and
, a ...bacterial genus that has received particular attention because of its beneficial effect on plants and its pathogenic strains. The present study aims to compare plant-beneficial and pathogenic strains belonging to the
species to get new insights into the distinction between the two types of plant-microbe interactions. In assays carried out under greenhouse conditions,
pv.
strain 260-02 was shown to promote plant-growth and to exert biocontrol of
pv.
strain DC3000, against the
fungus and the
. This
strain also had a distinct volatile emission profile, as well as a different plant-colonization pattern, visualized by confocal microscopy and
labeled strains, compared to strain DC3000. Despite the different behavior, the
strain 260-02 showed great similarity to pathogenic strains at a genomic level. However, genome analyses highlighted a few differences that form the basis for the following hypotheses regarding strain 260-02.
strain 260-02: (i) possesses non-functional virulence genes, like the mangotoxin-producing operon
; (ii) has different regulation pathways, suggested by the difference in the autoinducer system and the lack of a virulence activator gene; (iii) has genes encoding DNA methylases different from those found in other
strains, suggested by the presence of horizontal-gene-transfer-obtained methylases that could affect gene expression.
Citrus Decline Disease was recently reported to affect several citrus species in Iran when grafted on a local rootstock variety, Bakraee. Preliminary studies found “
Phytoplasma aurantifoliae” and “
...Liberibacter asiaticus” as putative etiological agents, but were not ultimately able to determine which one, or if an association of both, were causing the disease. The current study has the aim of characterizing the microbiota of citrus plants that are either asymptomatic, showing early symptoms, or showing late symptoms through amplification of the V1–V3 region of 16S rRNA gene using an Illumina sequencer in order to (i) clarify the etiology of the disease, and (ii) describe the microbiota associated to different symptom stages. Our results suggest that liberibacter may be the main pathogen causing Citrus Decline Disease, but cannot rule out the possibility of phytoplasma being involved as well. The characterization of microbiota shows that the leaves show only two kinds of communities, either symptomatic or asymptomatic, while roots show clear distinction between early and late symptoms. These results could lead to the identification of bacteria that are related to successful plant defense response and, therefore, to immunity to the Citrus Decline Disease.
Mgaloblishvili, a
cultivar, exhibits unique resistance traits against
, the downy mildew agent. This offers the unique opportunity of exploring the molecular responses in compatible and incompatible ...plant-pathogen interaction. In this study, whole transcriptomes of Mgaloblishvili, Pinot noir (a
susceptible cultivar), and Bianca (a resistant hybrid) leaves, inoculated and non-inoculated with the pathogen
were used to identify
effector-encoding genes and plant susceptibility/resistance genes. Multiple effector-encoding genes were identified in
transcriptome, with remarkable expression differences in relation to the inoculated grapevine cultivar. Intriguingly, five apoplastic effectors specifically associated with resistance in
. Gene coexpression network analysis identified specific modules and metabolic changes occurring during infection in the three grapevine cultivars. Analysis of these data allowed, for the first time, the detection in
of a putative
susceptibility gene, encoding a LOB domain-containing protein. Finally, the de novo assembly of Mgaloblishvili, Pinot noir, and Bianca transcriptomes and their comparison highlighted novel candidate genes that might be at the basis of the resistant phenotype. These results open the way to functional analysis studies and to new perspectives in molecular breeding of grapevine for resistance to
.
During field surveys conducted from July to October 2018–2020 in the eastern part of Georgia (Caucasus region), 145 out of 8000 (1.8%) and 147 out of 6600 (2.2%) grapevine plants, respectively, from ...mother stock/collection fields and commercial vineyards, were found exhibiting typical or suspicious grapevine yellows (GY) symptoms. Most of the symptomatic grapevine plants of Georgian cultivars showed mild symptoms with no berry alterations. Leaf samples from symptomatic plants were analyzed by serological (DAS- -ELISA) and molecular (two previously published protocols of TaqMan triplex real-time PCR, here named Set I and Set II) tools for detecting GY-associated phytoplasmas. The presence of GY phytoplasmas was not detected in any examined grapevines by a serological method. GY phytoplasmas were identified in 22.41% and 6.9% symptomatic plants from mother stock and collection vineyards and in 48.3 and 19.0% symptomatic plants from commercial vineyards by Set I and Set II PCRs, respectively. As expected from previous studies reporting the wide presence of bois noir (BN) in Georgian vineyards, ‘Candidatus Phytoplasma solani’(CaPsol) was detected in most phytoplasma-infected plants (47.6%), with the highest infection rate in Chardonnay. Phytoplasmas belonging to taxonomic group 16SrV were detected in 45.6% of the phytoplasma-infected grapevines. To the best of our knowledge, this is the first report of 16SrV phytoplasmas in Georgia and in the Caucasus region. Further molecular typing of 16SrV phytoplasma strains is necessary to determine if such strains are associated with flavescence dorée (FD). The knowledge of typical GY symptoms and the utilization of accurate diagnostic tools are crucial for preventing pathogen spread and producing healthy planting material. Based on the results obtained in this study, the presence of BN and 16SrV phytoplasmas should be monitored in the next years using triplex real-time PCR.
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