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Pulsed-field gel electrophoresis (PFGE) is a powerful technique for genomic studies of unculturable plant-pathogenic phytoplasmas, which enables separation of full-length phytoplasma chromosomes from contaminating host plant nucleic acids. The PFGE method described here involves isolation of phytoplasmal DNA from high-titer phytoplasma-infected herbaceous plants using a phytoplasma enrichment procedure, embedding of phytoplasma chromosomes in agarose blocks, and separation of entire phytoplasma chromosomes from contaminating host plant nucleic acids by electrophoresis. Full-length phytoplasma chromosomes are resolved as single, discrete bands in the gel. The identity of these bands can be confirmed by Southern blot hybridization using a ribosomal DNA fragment as a probe. The method does not utilize gamma-irradiation to linearize phytoplasma chromosomes prior to electrophoresis.

Plants of Convolvulus arvensis exhibiting symptoms of undersized leaves, shoot proliferation and yellowing, collectively defined as bindweed yellows, were sampled in different regions of Europe and assessed for phytoplasma infection by PCR amplification using phytoplasma universal rRNA operon primer pairs. Positive results were obtained for all diseased plants. RFLP analysis of amplicons comprising the16S rRNA gene alone or the16S rRNA gene and 16-23S intergenic spacer region indicated that the detected phytoplasmas were distinguishable from all other previously described rRNA gene sequences. Analysis of 16S rRNA gene sequences derived from seven selected phytoplasma strains (BY-S57/11, BY-S62/11, BY-I1015, BY-I1016, BY-BH1, BY-BH2 and BY-G) showed that they were nearly identical (99.9–100 % gene sequence similarity) but shared less than 97.5 % similarity with comparable sequences of other phytoplasmas. Thus, BY phytoplasmas represent a new taxon whose closest relatives are stolbur phytoplasma strains and ‘ Candidatus Phytoplasma fragariae ’ with which they share 97.2 % and 97.1 % 16S rRNA gene sequence similarity, respectively. Phylogenetic analysis of 16S rRNA gene sequences confirmed that bindweed yellows phytoplasma strains collectively represent a distinct lineage within the phytoplasma clade and share a common ancestor with previously published or proposed ‘Candidatus Phytoplasma’ taxa within a major branch including aster yellows and stolbur phytoplasmas. On the basis of unique 16S rRNA gene sequences and biological properties that include a single host plant species and a geographical distribution limited to parts of Europe, the bindweed yellows (BY) phytoplasmas represent a coherent but discrete taxon, ‘Candidatus Phytoplasma convolvuli’, with strain BY-S57/11 (GenBank accession no. JN833705) as the reference strain.

Mycoplasma-like organisms (MLOs) were detected and characterized by RFLP analysis in declining trees of Alnus glutinosa and A. cordata in Southern Italy for the first time. The infected trees showed symptoms of yellowing, sparse foliage, premature autumn colouration, sprouting, deliquescent branching, phloem necrosis, dieback and witches’ brooms.

In southern Italy, Spartium junceum (Spanish broom) is severely affected by a phytoplasmal disease, Spartium witches’‐broom (SpaWB). The volatile fractions extracted from flowers of healthy and diseased plants, examined by gas chromatography and gas chromatography–mass spectrometry, appeared to be quantitatively and qualitatively different. In both the healthy and the diseased plants, the main components were n‐alkanes, which occurred at a rate of 55.2% and 38.8%, respectively. The level of aliphatic acids was considerably lower in flowers of the diseased plants than in those of the healthy plants (4.5% vs. 18.7%). Sesquiterpenes were detected only in the diseased plants. It is possible that the changes in the composition of secondary metabolites of diseased plants can be related to plant defense responses. Abbreviations: AP, apple proliferation; EY, elm yellows; SpaWB, Spartium witches’‐broom

A phytoplasma has been detected in Oplismenus burmannii (Retz.) P. Beauv. and Digitaria sanguinalis (L.) Scop. plants with symptoms of chlorotic streaks and white leaf disease in India. By sequence and phylogenetic analyses of polymerase chain reaction-amplified rDNA sequences, the detected phytoplasma was identified as ‘Candidatus Phytoplasma cynodontis’, a member of the 16SrXIV group, and the causal agent of Bermuda grass white leaf disease. This is the first report on the occurrence of ‘Ca. Phytoplasma cynodontis’ in O. burmannii and D. sanguinalis grasses.

Chromosome sizes of 71 phytoplasmas belonging to 12 major phylogenetic groups including several of the aster yellows subgroups were estimated from electrophoretic mobilities of full-length chromosomes in pulsed-field gels. Considerable variation in genome size, from 660 to 1,130 kilobases (kb), was observed among aster yellows phytoplasmas. Chromosome size heterogeneity was also observed in the stolbur phytoplasma group (range 860 to 1,350 kb); in this group, isolate STOLF contains the largest chromosome found in a phytoplasma to date. A wide range of chromosome sizes, from 670 to 1,075 kb, was also identified in the X-disease group. The other phytoplasmas examined, which included members of the apple proliferation, Italian alfalfa witches' broom, faba bean phyllody, pigeon pea witches' broom, sugarcane white leaf, Bermuda grass white leaf, ash yellows, clover proliferation, and elm yellows groups, all have chromosomes smaller than 1 megabase, and the size ranges within each of these groups is narrower than in the aster yellows, stolbur, and X-disease groups. The smallest chromosome, approximately 530 kb, was found in two Bermuda grass white leaf phytoplasma isolates. This not only is the smallest mollicute chromosome found to date, but also is the smallest chromosome known for any cell. More than one large DNA band was observed in several phytoplasma preparations. Possible explanations for the occurrence of more than one band may be infection of the host plant by different phytoplasmas, the presence of more than one chromosome in the same organism, or the presence of large extrachromosomal DNA elements.

Vineyards of southern France and northern Italy are affected by the flavescence dorée (FD) phytoplasma, a quarantine pathogen transmitted by the leafhopper of Nearctic origin Scaphoideus titanus . To better trace propagation of FD strains and identify possible passage between the vineyard and wild plant compartments, molecular typing of phytoplasma strains was applied. The sequences of the two genetic loci map and uvrB - degV , along with the sequence of the secY gene, were determined among a collection of FD and FD-related phytoplasmas infecting grapevine, alder, elm, blackberry, and Spanish broom in Europe. Sequence comparisons and phylogenetic analyses consistently indicated the existence of three FD phytoplasma strain clusters. Strain cluster FD1 (comprising isolate FD70) displayed low variability and represented 17% of the disease cases in the French vineyard, with a higher incidence of the cases in southwestern France. Strain cluster FD2 (comprising isolates FD92 and FD-D) displayed no variability and was detected both in France (83% of the cases) and in Italy, whereas the more-variable strain cluster FD3 (comprising isolate FD-C) was detected only in Italy. The clonal property of FD2 and its wide distribution are consistent with diffusion through propagation of infected-plant material. German Palatinate grapevine yellows phytoplasmas (PGY) appeared variable and were often related to some of the alder phytoplasmas (AldY) detected in Italy and France. Finally, phylogenetic analyses concluded that FD, PGY, and AldY were members of the same phylogenetic subclade, which may have originated in Europe.

In southern and central Italy, a witches' broom and decline disease of Sarothamnus scoparius has been observed. In affected plants, phytoplasmas were detected by PCR amplification of ribosomal DNA. Restriction fragment length polymorphism analysis of PCR-amplified DNA revealed that the diseased plants were infected by a phytoplasma that is closely related to the spartium witches' broom phytoplasma, a member of the apple proliferation group.

The trivial name ‘phytoplasma’ has been adopted to collectively name wall-less, non-helical prokaryotes that colonize plant phloem and insects, which were formerly known as mycoplasma-like organisms. Although phytoplasmas have not yet been cultivated in vitro, phylogenetic analyses based on various conserved genes have shown that they represent a distinct, monophyletic clade within the class Mollicutes. It is proposed here to accommodate phytoplasmas within the novel genus ‘Candidatus (Ca.) Phytoplasma’. Given the diversity within ‘Ca. Phytoplasma’, several subtaxa are needed to accommodate organisms that share Ca. Phytoplasma’, a taxon that includes the species ‘Ca. Phytoplasma aurantifolia’ (the prokaryote associated with witches'-broom disease of small-fruited acid lime), ‘Ca. Phytoplasma australiense’ (associated with Australian grapevine yellows), ‘Ca. Phytoplasma fraxini’ (associated with ash yellows), ‘Ca. Phytoplasma japonicum’ (associated with Japanese hydrangea phyllody), ‘Ca. Phytoplasma brasiliense’ (associated with hibiscus witches'-broom in Brazil), ‘Ca. Phytoplasma castaneae’ (associated with chestnut witches'-broom in Korea), ‘Ca. Phytoplasma asteris' (associated with aster yellows), ‘Ca. Phytoplasma mali’ (associated with apple proliferation), ‘Ca. Phytoplasma phoenicium’ (associated with almond lethal disease), ‘Ca. Phytoplasma trifolii’ (associated with clover proliferation), ‘Ca. Phytoplasma cynodontis' (associated with Bermuda grass white leaf), ‘Ca. Phytoplasma ziziphi’ (associated with jujube witches'-broom), ‘Ca. Phytoplasma oryzae’ (associated with rice yellow dwarf) and six species-level taxa for which the Candidatus species designation has not yet been formally proposed (for the phytoplasmas associated with X-disease of peach, grapevine flavescence dorée, Central American coconut lethal yellows, Tanzanian lethal decline of coconut, Nigerian lethal decline of coconut and loofah witches'-broom, respectively). Additional species are needed to accommodate organisms that, despite their 16S rRNA gene sequence being >97·5 % similar to those of other ‘Ca. Phytoplasma’ species, are characterized by distinctive biological, phytopathological and genetic properties. These include ‘Ca. Phytoplasma pyri’ (associated with pear decline), ‘Ca. Phytoplasma prunorum’ (associated with European stone fruit yellows), ‘Ca. Phytoplasma spartii’ (associated with spartium witches'-broom), ‘Ca. Phytoplasma rhamni’ (associated with buckthorn witches'-broom), ‘Ca. Phytoplasma allocasuarinae’ (associated with allocasuarina yellows), ‘Ca. Phytoplasma ulmi’ (associated with elm yellows) and an additional taxon for the stolbur phytoplasma. Conversely, some organisms, despite their 16S rRNA gene sequence being Ca. Phytoplasma’ species, are not presently described as Candidatus species, due to their poor overall characterization.

Spartium witches'-broom (SpaWB), buckthorn witches'-broom (BWB) and allocasuarina yellows (AlloY) are witches'-broom and yellows diseases of Spartium junceum (Spanish broom), Rhamnus catharticus (buckthorn) and Allocasuarina muelleriana (Slaty she-oak), respectively. These diseases are associated with distinct phytoplasmas. The SpaWB, BWB and AlloY phytoplasmas share Candidatus’ species under the names ‘Candidatus Phytoplasma spartii’, ‘Candidatus Phytoplasma rhamni’ and ‘Candidatus Phytoplasma allocasuarinae’, respectively.

Elm yellows group (16SrV) phytoplasmas, which are associated with devastating diseases in elm, grapevine, blackberry, cherry, peach and several other plant species in America, Europe and Asia, represent one of the most diverse phytoplasma clusters. On the basis of phylogenetic analysis of 16S rDNA sequences, elm yellows group phytoplasmas form a discrete subclade within the phytoplasma clade. Three phylogenetic parameters, namely 16S rRNA, ribosomal protein and secY genes, have been evaluated for their usefulness in differentiating elm yellows group phytoplasmas. RFLP analysis of 16S rRNA sequences differentiated the elm yellows group phytoplasmas into five subgroups. Twelve RFLP subgroups were differentiated on the basis of ribosomal protein and 13 were differentiated using secY gene sequences. Phylogenetic analysis of the ribosomal protein genes and secY gene alone or in combination indicated that the subgroups constitute 12 genetically distinct lineages, each of which appears to have evolved under different ecological constraints such as specific vector or plant hosts. On the basis of unique DNA and biological properties, it is proposed that the elm yellows phytoplasma EY1T represents a novel taxon, ‘Candidatus Phytoplasma ulmi’.

Yellows-diseased plants of Crepis setosa (hawksbeard), Knautia arvensis (field scabious), Convolvulus arvensis (field bindweed), Picris echioides (bristly oxtongue), Echium vulgate (blueweed) and Calendula officinalis (pot marigold) collected in central and southern Italy were examined for phytoplasma infection by means of polymerase chain reaction (PCR) technology using universal phytoplasma primers directed to ribosomal sequences. The detected phytoplasmas were characterized and differentiated using restriction fragment length polymorphism analysis of PCR-amplified DNA. The phytoplasma detected in diseased pot marigold plants was identified as a member of the aster yellows group and proved indistinguishable from a strain of the American aster yellows phytoplasma. The phytoplasma identified in diseased field bindweed plants is a putative new type of the stolbur group that differed from the typical stolbur phytoplasma. Phytoplasmas detected in diseased hawksbeard, blueweed and field scabious plants are all putative new members of the sugarcane white leaf group while the phytoplasma detected in diseased bristly oxtongue plants represents a new member of the faba bean phyllody group. For hawksbeard and field scabious this is the first report on the occurrence of phytoplasma diseases, whereas phytoplasmas infecting bristly oxtongue and blueweed have never been characterized before.

Summary In the neighbouring regions Basilicata, Campania, and Calabria of southern Italy, diseased trees of European field elm (Ulmus minor) were examined for phytoplasmal infection using polymerase chain reaction (PCR) technology. All affected trees examined tested positively. Using a primer pair specific for the EY phytoplasma group and restriction fragment length polymorphism (RFLP) analysis of PCR-amplified ribosomal DNA, the organism detected was identified as the elm yellows (EY) phytoplasma. RFLP analysis of PCR-amplified ribosomal DNA was also employed to attempt differentiation within the EY group which includes, in addition to the EY agent, phytoplasmas infecting Rubus, alder, eucalypts, Spanish broom, and grapevine. Following separate digestion with AluI, RsaI, Sau3AI, MseI, HhaI, and KpnI, all PCR-products from EY-group phytoplasmas examined had similar RFLP profiles. When the same ribosomal DNA fragments were digested with TaqI restriction endonuclease, three different restriction profiles were detected among the EY-group phytoplasmas. These profiles represented, respectively, (1) the EY phytoplasma (2) the phytoplasmas causing rubus stunt and being associated with alder yellows, spartium witches broom, and eucalyptus little leaf, and (3) the flavescence doree phytoplasma. RFLP analysis using TaqI endonuclease enabled for the first time the differentiation of the phytoplasmas associated with alder yellows, eucalyptus little leaf, and spartium witches broom from the EY agent.

In plants of Spanish broom (Spartium junceum) affected by an etiologically uncertain witches'-broom disease, plant-pathogenic phytoplasmas were detected by fluorescence and scanning electron microscopy. Restriction fragment length polymorphism (RFLP) analysis of ribosomal DNA, polymerase chain reaction (PCR)-amplified by means of universal phytoplasma primers, revealed two different phytoplasmas present in plants with similar symptoms. The less frequently detected phytoplasma had the same RFLP profile as elm yellows phytoplasmas, whereas the prevalent agent had an RFLP profile similar to that of phytoplasmas in the apple proliferation strain cluster. Sequence analysis of 16S rDNA confirmed that the prevalent Spartium witches'-broom phytoplasma is a member of the apple proliferation strain cluster, but this organism is distinctly different from other cluster members. With universal, group- and pathogen-specific rDNA primers, the causal agents were detected in most symptomatic plants. The plants testing negatively in direct PCR yielded an amplification product when the rDNA fragment obtained with universal primers was re-amplified with group- or pathogen-specific primers. The nested-PCR assay also revealed that most of the plants examined were doubly infected with the two phytoplasmas detected by direct PCR. In the infected plants, one of these organisms was predominant and readily detectable by direct PCR while the other occurred in low numbers and could only be identified by nested PCR.

Plant-pathogenic phytoplasmas are wall-less, unculturable bacteria of the class Mollicutes that are associated with diseases, collectively referred to as yellows diseases, in more than a thousand plant species worldwide. Many of these diseases are of great economic importance. Phytoplasmas reside in the phloem sieve tubes and are transmitted from plant to plant by phloem-feeding homopteran insects, mainly leafhoppers (Cicadellidae) and planthoppers (Fulgoromorpha), and less frequently psyllids (Psyllidae). Most of the host plants of phytoplasmas are angiosperms in which a wide range of specific and non-specific symptoms are induced. Phytoplasmas, which are phylogenetically more closely related to acholeplasmas than to other mollicutes, have a complex life cycle that involves colonization of different environments, the plant phloem and various organs of the insect vectors. The dynamic architecture of phytoplasma genomes may account for variation in their genome size and adaptation to the diverse environments of their plant and insect hosts. Newly acquired knowledge has made it possible to identify a considerable number of phytoplasma genes that are likely to play major roles in phytoplasma-host interactions. Among these, there are genes encoding surface membrane proteins and effector proteins. Also, it has been shown that phytoplasmas dramatically alter their gene expression upon switching between plant and insect hosts.

During the late summer of 2003, a wilt disease of the weed Italian cockleburr (Xanthium italicum Mor.) was observed in the Basilicata Region of southern Italy. Diseased plants were growing near an apricot orchard in which some trees were severely affected by Verticillium wilt. The most characteristic symptoms of the wilt disease affecting Italian cockleburr were yellowing, stunting, and gradual wilting. Also, diagonal and cross sections of stems revealed brown discoloration of their vascular tissues. To elucidate the etiology of the disease, we attempted detection and identification of the causal agents using traditional and polymerase chain reaction (PCR)-based methods. Small pieces of petiole and stem tissues from diseased and asymptomatic plants were surface disinfested in NaOCl solution, rinsed in sterile distilled water, blotted dry, and plated onto water agar (WA) medium. Following incubation at 22°C, the emerging colonies were transferred to potato dextrose agar (PDA). Verticillium dahliae (one isolate) was consistently identified on the basis of its morphological features according to the description of Smith (2). Using PCR assays with the primer pair ITS5/ITS4 (3), which are directed to fungal nuclear ribosomal DNA (rDNA) repeat sequences, an amplification product of approximately 560 bp was obtained by using total DNA extracted from wilt-affected Italian cockleburr plant tissues (five plants examined) as well as fresh mycelium from the V. dahliae-infected Italian cockleburr pure culture-maintained isolate mentioned above. No visible PCR products were obtained with total DNA from asymptomatic Italian cockleburr plants. Sequence analysis of the ITS5/ITS4 amplicons revealed no differences in their nucleotide positions. The obtained sequence of the V. dahliae-infected Italian cockleburr isolate (GenBank Accession No. AJ865691) was then used as query sequences in a BLAST 2.0 search (1). Sequence of the southern Italian isolate proved to be identical to that of the Greek strain “76 Greece” of V. dahliae (GenBank Accession no. AF104926). To prove Koch's postulates, 10 healthy Italian cockleburr seedlings were experimentally inoculated by dipping trimmed roots in a single-conidial suspension (1.5 × 106 CFU/ml) obtained from 10-day-old colonies of the V. dahliae-infected Italian cockleburr pure culture-maintained isolate. After 4 weeks, all inoculated Italian cockleburr plants showed symptoms identical to those of naturally infected field-grown plants. V. dahliae was consistently reisolated from inoculated plants. Additional inoculation experiments revealed that pepper and eggplant were also susceptible to the V. dahliae-infected Italian cockleburr isolate showing typical Verticillium wilt symptoms. To our knowledge, this is the first report of the occurrence of Verticillium wilt of X. italicum. References: (1) S. F. Altschul et al. Nucleic Acids Res. 25:3389, 1997. (2) H. C. Smith. N.Z. J. Agric. Res. 8:450, 1965. (3) T. J. White et al. Pages 315–322 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, 1990.

In the Campania region of southern Italy, peach trees showing vein enlargement and decline symptoms, as well as apricot and Japanese plum trees showing symptoms similar to that of apricot chlorotic leaf roll and plum leptonecrosis, respectively, were examined for phytoplasma infection using PCR technology. From diseased apricot and plum trees, the target DNA could be amplified with both universal phytoplasma primers and primers that are specific for fruit tree phytoplasmas of the apple proliferation group. However, from samples from diseased peach trees, detectable amplification products were only obtained by nested PCR, in which amplification with universal phytoplasma primers was followed by amplification with primers specific for the apple proliferation group. Following digestion of the amplification products with suitable restriction enzymes, all strains from apricot, plum, and peach showed the same restriction profiles that were identical to those of the European stone fruit yellows phytoplasma, a member of the apple proliferation group.