Genetic diversity of Actinidia spp. shapes the oomycete pattern associated with Kiwifruit Vine Decline Syndrome (KVDS)

Kiwifruit Vine Decline Syndrome (KVDS) is an important soil-borne disease for the Italian kiwifruit industry, causing €300,000 in economic losses in 2020 alone. So far, the organisms recognized as involved in the aetiology of KVDS mainly belong to the Oomycota. As no effective management strategies exist, a promising approach to overcoming KVDS is the use of resistant species as rootstocks or for inclusion in breeding programs. Several Actinidia genotypes showing different level of resistance to KVDS were grown in disease-promoting soils. A metabarcoding approach was set up to identify KVDS-associated oomycetes and investigate whether the main species involved may vary according to plant genotype. Our results clearly showed significant differences between the genotypes in terms of oomycetes present in both plant rhizosphere and endosphere, which were strongly correlated with the symptoms displayed. We found out that the resistance of Actinidia macrosperma to KVDS is related to its ability to shape the pathobiome, particularly as far as the endosphere is concerned. In our conditions, Phytophthora sp. was predominantly found in sensitive genotypes, whilst Globisporangium intermedium was mainly detected in asymptomatic plants, suggesting that the latter species could compete with the recruitment of Phytophthora sp. in plants with different levels of resistance, consequently, explaining the onset of symptoms and the resistance condition.

The Virome of ‘Lamon Bean’: Application of MinION Sequencing to Investigate the Virus Population Associated with Symptomatic Beans in the Lamon Area, Italy

‘Lamon bean’ is a protected geographical indication (PGI) for a product of four varieties of bean (Phaseolus vulgaris L.) grown in a specific area of production, which is located in the Belluno district, Veneto region (N.E. of Italy). In the last decade, the ‘Lamon bean’ has been threatened by severe virus epidemics that have compromised its profitability. In this work, the full virome of seven bean samples showing different foliar symptoms was obtained by MinION sequencing. Evidence that emerged from sequencing was validated through RT-PCR and ELISA in a large number of plants, including different ecotypes of Lamon bean and wild herbaceous hosts that may represent a virus reservoir in the field. Results revealed the presence of bean common mosaic virus (BCMV), cucumber mosaic virus (CMV), peanut stunt virus (PSV), and bean yellow mosaic virus (BYMV), which often occurred as mixed infections. Moreover, both CMV and PSV were reported in association with strain-specific satellite RNAs (satRNAs). In conclusion, this work sheds light on the cause of the severe diseases affecting the ‘Lamon bean’ by exploitation of MinION sequencing.

Synergistic interaction between the type III secretion system of the endophytic bacterium Pantoea agglomerans DAPP-PG 734 and the virulence of the causal agent of olive knot Pseudomonas savastanoi pv. savastanoi DAPP-PG 722

The endophytic bacterium Pantoea agglomerans DAPP-PG 734 was previously isolated from olive knots caused by infection with Pseudomonas savastanoi pv. savastanoi DAPP-PG 722. Whole-genome analysis of this P. agglomerans strain revealed the presence of a Hypersensitive response and pathogenicity (Hrp) type III secretion system (T3SS). To assess the role of the P. agglomerans T3SS in the interaction with P. savastanoi pv. savastanoi, we generated independent knockout mutants in three Hrp genes of the P. agglomerans DAPP-PG 734 T3SS (hrpJ, hrpN, and hrpY). In contrast to the wildtype control, all three mutants failed to cause a hypersensitive response when infiltrated in tobacco leaves, suggesting that P. agglomerans T3SS is functional and injects effector proteins in plant cells. In contrast to P. savastanoi pv. savastanoi DAPP-PG 722, the wildtype strain P. agglomerans DAPP-PG 734 and its Hrp T3SS mutants did not cause olive knot disease in 1-year-old olive plants. Coinoculation of P. savastanoi pv. savastanoi with P. agglomerans wildtype strains did not significantly change the knot size, while the DAPP-PG 734 hrpY mutant induced a significant decrease in knot size, which could be complemented by providing hrpY on a plasmid. By epifluorescence microscopy and confocal laser scanning microscopy, we found that the localization patterns in knots were nonoverlapping for P. savastanoi pv. savastanoi and P. agglomerans when coinoculated. Our results suggest that suppression of olive plant defences mediated by the Hrp T3SS of P. agglomerans DAPP-PG 734 positively impacts the virulence of P. savastanoi pv. savastanoi DAPP-PG 722.

Trigger and Suppression of Antiviral Defenses by Grapevine Pinot Gris Virus (GPGV): Novel Insights into Virus-Host Interaction

Grapevine Pinot gris virus (GPGV) is an emerging trichovirus that has been putatively associated with a novel grapevine disease known as grapevine leaf mottling and deformation (GLMD). Yet the role of GPGV in GLMD disease is poorly understood, since it has been detected both in symptomatic and symptomless grapevines. We exploited a recently constructed GPGV infectious clone (pRI::GPGV-vir) to induce an antiviral response in Nicotiana benthamiana plants. In silico prediction of virus-derived small interfering RNAs and gene expression analyses revealed the involvement of DCL4, AGO5, and RDR6 genes during GPGV infection, suggesting the activation of the posttranscriptional gene-silencing (PTGS) pathway as a plant antiviral defense. PTGS suppression assays in transgenic N. benthamiana 16c plants revealed the ability of the GPGV coat protein to suppress RNA silencing. This work provides novel insights on the interaction between GPGV and its host, revealing the ability of the virus to trigger and suppress antiviral RNA silencing.[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.

Polymorphisms at the 3'end of the movement protein (MP) gene of grapevine Pinot gris virus (GPGV) affect virus titre and small interfering RNA accumulation in GLMD disease

Grapevine Leaf Mottling and Deformation (GLMD) is a grapevine disease that has been associated with a trichovirus, the grapevine Pinot gris virus (GPGV). A wide diversity in the severity of GLMD disease symptoms has been recorded worldwide, but the relationship of this diversity to the sequence variation in the GPGV genome is still a matter of debate. Results from comparative analysis of GPGV genomic sequences have suggested an association of polymorphisms at the 3'-end of the movement protein (MP) with GLMD severity. Here, the 3'-terminus of the MP gene of a GPGV infectious clone derived from an isolate from grapevine showing severe symptoms (fvg-12), was substituted with a 356 bp synthetic DNA fragment having a sequence resembling that of another GPGV isolate (fvg-15), recovered from an asymptomatic grapevine. The clone containing this chimeric construct was root-inoculated in virus-free Kober rootstocks along with the clones containing the fvg-12 and fvg-15 full length sequence. Remarkable differences in virus titre, accumulation of GPGV-derived small interfering RNAs (siRNAs), alterations in the gene expression of boron transporters and, to a lesser extent, in symptom expression were recorded among plants infected with either one of the three GPGV derived clones. In particular, the chimeric clone behaviour was indistinguishable from that of the donor of the small 356 bp fragment and significantly different from the other. Thus, this work experimentally confirmed the critical role of the GPGV-MP C-terminus in determining the fate of the infection, as it had been previously hypothesized on the basis of comparative sequence analysis.

Genome Sequence and Antifungal Activity of Two Niche-Sharing Pseudomonas protegens Related Strains Isolated from Hydroponics

This work reports the comparison of the genome sequence and the ability to inhibit fungal growth of two Pseudomonas protegens related strains that were isolated from the same hydroponic culture of lamb's lettuce. The two strains were very similar in their core genome but one strain, Pf4, contained three gene clusters for the production of secondary metabolites, i.e., pyoluteorin (plt), pyrrolnitrin (prn), and rhizoxin (rzx), that were missing in the other strain, Pf11. The difference between the two strains was not due to simple insertion events, but to a relatively complex differentiation focused on the accessory genomes. In dual culture assays, both strains inhibited nearly all tested fungal strains, yet Pf4 exerted a significantly stronger fungal growth inhibition than Pf11. In addition to the differences in the secondary metabolite production associated genes abundance, the genome of Pf4 was more stable, smaller in size and with a lower number of transposons. The preservation of a dynamic equilibrium within natural populations of different strains comprised in the same species but differing in their secondary metabolite repertoire and in their genome stability may be functional to the adaptation to environmental changes.

Agroinoculation of Grapevine Pinot Gris Virus in tobacco and grapevine provides insights on viral pathogenesis

The Grapevine Pinot Gris disease (GPG-d) is a novel disease characterized by symptoms such as leaf mottling and deformation, which has been recently reported in grapevines, and mostly in Pinot gris. Plants show obvious symptoms at the beginning of the growing season, while during summer symptom recovery frequently occurs, manifesting as symptomless leaves. A new Trichovirus, named Grapevine Pinot gris virus (GPGV), which belongs to the family Betaflexiviridae was found in association with infected plants. The detection of the virus in asymptomatic grapevines raised doubts about disease aetiology. Therefore, the primary target of this work was to set up a reliable system for the study of the disease in controlled conditions, avoiding interfering factor(s) that could affect symptom development. To this end, two clones of the virus, pRI::GPGV-vir and pRI::GPGV-lat, were generated from total RNA collected from one symptomatic and one asymptomatic Pinot gris grapevine, respectively. The clones, which encompassed the entire genome of the virus, were used in Agrobacterium-mediated inoculation of Vitis vinifera and Nicotiana benthamiana plants. All inoculated plants developed symptoms regardless of their inoculum source, demonstrating a correlation between the presence of GPGV and symptomatic manifestations. Four months post inoculum, the grapevines inoculated with the pRI::GPGV-lat clone developed asymptomatic leaves that were still positive to GPGV detection. Three to four weeks later (i.e. ca. 5 months post inoculum), the same phenomenon was observed in the grapevines inoculated with pRI::GPGV-vir. This observation perfectly matches symptom progression in infected field-grown grapevines, suggesting a possible role for plant antiviral mechanisms, such as RNA silencing, in the recovery process.

Assembly of Phytoplasma Genome Drafts from Illumina Reads Using Phytoassembly

Genome drafts for the phytoplasmas may be rapidly and efficiently assembled from NGS sequence data alone exploiting the proper bioinformatic tools and starting from properly collected samples. Here, we describe the use of the Phytoassembly pipeline ( https://github.com/cpolano/phytoassembly ), a fully automated tool that accepts as input row Illumina data from two samples (a phytoplasma infected sample and a healthy reference sample) to produce a phytoplasma genome draft, using the healthy plant host genome as a filter and profiting from the difference in reads coverage between the genome of the pathogen and that of the host. For phytoplasma infected samples containing >2% of pathogen DNA and an isogenic healthy reference sequence the resulting assemblies span the almost entire genomes.

An Effective Pipeline Based on Relative Coverage for the Genome Assembly of Phytoplasmas and Other Fastidious Prokaryotes

BACKGROUND

For the plant pathogenic phytoplasmas, as well as for several fastidious prokaryotes, axenic cultivation is extremely difficult or not possible yet; therefore, even with second generation sequencing methods, obtaining the sequence of their genomes is challenging due to host sequence contamination.

OBJECTIVE

With the Phytoassembly pipeline here presented, we aim to provide a method to obtain high quality genome drafts for the phytoplasmas and other uncultivable plant pathogens, by exploiting the coverage differential in the ILLUMINA sequences from the pathogen and the host, and using the sequencing of a healthy, isogenic plant as a filter.

VALIDATION

The pipeline has been benchmarked using simulated and real ILLUMINA runs from phytoplasmas whose genome is known, and it was then used to obtain high quality drafts for three new phytoplasma genomes.

CONCLUSION

For phytoplasma infected samples containing >2-4% of pathogen DNA and an isogenic reference healthy sample, the resulting assemblies can be next to complete. The Phytoassembly source code is available on GitHub at https://github.com/cpolano/phytoassembly.

Genomic Structural Variations Affecting Virulence During Clonal Expansion of Pseudomonas syringae pv. actinidiae Biovar 3 in Europe

Pseudomonas syringae pv. actinidiae (Psa) biovar 3 caused pandemic bacterial canker of Actinidia chinensis and Actinidia deliciosa since 2008. In Europe, the disease spread rapidly in the kiwifruit cultivation areas from a single introduction. In this study, we investigated the genomic diversity of Psa biovar 3 strains during the primary clonal expansion in Europe using single molecule real-time (SMRT), Illumina and Sanger sequencing technologies. We recorded evidences of frequent mobilization and loss of transposon Tn6212, large chromosome inversions, and ectopic integration of IS sequences (remarkably ISPsy31, ISPsy36, and ISPsy37). While no phenotype change associated with Tn6212 mobilization could be detected, strains CRAFRU 12.29 and CRAFRU 12.50 did not elicit the hypersensitivity response (HR) on tobacco and eggplant leaves and were limited in their growth in kiwifruit leaves due to insertion of ISPsy31 and ISPsy36 in the hrpS and hrpR genes, respectively, interrupting the hrp cluster. Both strains had been isolated from symptomatic plants, suggesting coexistence of variant strains with reduced virulence together with virulent strains in mixed populations. The structural differences caused by rearrangements of self-genetic elements within European and New Zealand strains were comparable in number and type to those occurring among the European strains, in contrast with the significant difference in terms of nucleotide polymorphisms. We hypothesize a relaxation, during clonal expansion, of the selection limiting the accumulation of deleterious mutations associated with genome structural variation due to transposition of mobile elements. This consideration may be relevant when evaluating strategies to be adopted for epidemics management.

Polyketide synthases of Diaporthe helianthi and involvement of DhPKS1 in virulence on sunflower

BACKGROUND

The early phases of Diaporthe helianthi pathogenesis on sunflower are characterized by the production of phytotoxins that may play a role in host colonisation. In previous studies, phytotoxins of a polyketidic nature were isolated and purified from culture filtrates of virulent strains of D. helianthi isolated from sunflower. A highly aggressive isolate (7/96) from France contained a gene fragment of a putative nonaketide synthase (lovB) which was conserved in a virulent D. helianthi population.

RESULTS

In order to investigate the role of polyketide synthases in D. helianthi 7/96, a draft genome of this isolate was examined. We were able to find and phylogenetically analyse 40 genes putatively coding for polyketide synthases (PKSs). Analysis of their domains revealed that most PKS genes of D. helianthi are reducing PKSs, whereas only eight lacked reducing domains. Most of the identified PKSs have orthologs shown to be virulence factors or genetic determinants for toxin production in other pathogenic fungi. One of the genes (DhPKS1) corresponded to the previously cloned D. helianthi lovB gene fragment and clustered with a nonribosomal peptide synthetase (NRPS) -PKS hybrid/lovastatin nonaketide like A. nidulans LovB. We used DhPKS1 as a case study and carried out its disruption through Agrobacterium-mediated transformation in the isolate 7/96. D. helianthi DhPKS1 deleted mutants were less virulent to sunflower compared to the wild type, indicating a role for this gene in the pathogenesis of the fungus.

CONCLUSION

The PKS sequences analysed and reported here constitute a new genomic resource that will be useful for further research on the biology, ecology and evolution of D. helianthi and generally of fungal plant pathogens.

Plasmon resonance tuning using DNA origami actuation

A strategy for an innovative, continuous and reversible LSPR tuning using DNA origami actuation to modulate the nanometric separation of two gold nanoparticles has been developed. The actuation mechanism is based on DNA hybridization, in particular three different DNA sequences were shown to induce resonance shift of up to 6 nm.

A DNA origami nanorobot controlled by nucleic acid hybridization

A prototype for a DNA origami nanorobot is designed, produced, and tested. The cylindrical nanorobot (diameter of 14 nm and length of 48 nm) with a switchable flap, is able to respond to an external stimulus and reacts by a physical switch from a disarmed to an armed configuration able to deliver a cellular compatible message. In the tested design the robot weapon is a nucleic acid fully contained in the inner of the tube and linked to a single point of the internal face of the flap. Upon actuation the nanorobot moves the flap extracting the nucleic acid that assembles into a hemin/G-quadruplex horseradish peroxidase mimicking DNAzyme catalyzing a colorimetric reaction or chemiluminescence generation. The actuation switch is triggered by an external nucleic acid (target) that interacts with a complementary nucleic acid that is beard externally by the nanorobot (probe). Hybridization of probe and target produces a localized structural change that results in flap opening. The flap movement is studied on a two-dimensional prototype origami using Förster resonance energy transfer and is shown to be triggered by a variety of targets, including natural RNAs. The nanorobot has potential for in vivo biosensing and intelligent delivery of biological activators.

A Genomic redefinition of Pseudomonas avellanae species

The circumscription of bacterial species is a complex task. So far, DNA-DNA hybridization (DDH), 16S rRNA gene sequencing, and multiocus sequence typing analysis (MLSA) are currently the preferred techniques for their genetic determination. However, the average nucleotide identity (ANI) analysis of conserved and shared genes between two bacterial strains based on the pair-wise genome comparisons, with support of the tetranucleotide frequency correlation coefficients (TETRA) value, has recently been proposed as a reliable substitute for DDH. The species demarcation boundary has been set to a value of 95-96% of the ANI identity, with further confirmation through the assessment of the corresponding TETRA value. In this study, we performed a genome-wide MLSA of 14 phytopathogenic pseudomonads genomes, and assessed the ANI and TETRA values of 27 genomes, representing seven out of the nine genomospecies of Pseudomonas spp. sensu Gardan et alii, and their phylogenetic relationships using maximum likelihood and Bayesian approaches. The results demonstrate the existence of a well demarcated genomic cluster that includes strains classified as P. avellanae, P. syringae pv. theae, P. s. pv. actinidiae and one P. s. pv. morsprunorum strain all belonging to the single species P. avellanae. In addition, when compared with P. avellanae, five strains of P. s. pv. tomato, including the model strain DC3000, and one P. s. pv. lachrymans strain, appear as very closely related to P. avellanae, with ANI values of nearly 96% as confirmed by the TETRA analysis. Conversely, one representative strain, previously classified as P. avellanae and isolated in central Italy, is a genuine member of the P. syringae species complex and can be defined as P. s. pv. avellanae. Currently. The core and pan genomes of P. avellanae species consist of 3,995 and 5,410 putative protein-coding genes, respectively.

Genome wide sequence analysis grants unbiased definition of species boundaries in "Candidatus Phytoplasma"

The phytoplasmas are currently named using the Candidatus category, as the inability to grow them in vitro prevented (i) the performance of tests, such as DNA-DNA hybridization, that are regarded as necessary to establish species boundaries, and (ii) the deposition of type strains in culture collections. The recent accession to complete or nearly complete genome sequence information disclosed the opportunity to apply to the uncultivable phytoplasmas the same taxonomic approaches used for other bacteria. In this work, the genomes of 14 strains, belonging to the 16SrI, 16SrIII, 16SrV and 16SrX groups, including the species "Ca. P. asteris", "Ca. P. mali", "Ca. P. pyri", "Ca. P. pruni", and "Ca. P. australiense" were analyzed along with Acholeplasma laidlawi, to determine their taxonomic relatedness. Average nucleotide index (ANIm), tetranucleotide signature frequency correlation index (Tetra), and multilocus sequence analysis of 107 shared genes using both phylogenetic inference of concatenated (DNA and amino acid) sequences and consensus networks, were carried out. The results were in large agreement with the previously established 16S rDNA based classification schemes. Moreover, the taxonomic relationships within the 16SrI, 16SrIII and 16SrX groups, that represent clusters of strains whose relatedness could not be determined by 16SrDNA analysis, could be comparatively evaluated with non-subjective criteria. "Ca. P. mali" and "Ca. P. pyri" were found to meet the genome characteristics for the retention into two different, yet strictly related species; representatives of subgroups 16SrI-A and 16SrI-B were also found to meet the standards used in other bacteria to distinguish separate species; the genomes of the strains belonging to 16SrIII were found more closely related, suggesting that their subdivision into Candidatus species should be approached with caution.

Pseudomonas syringae pv. actinidiae: a re-emerging, multi-faceted, pandemic pathogen

Pseudomonas syringae pv. actinidiae is the causal agent of bacterial canker of green-fleshed kiwifruit (Actinidia deliciosa) and yellow-fleshed kiwifruit (A. chinensis). A recent, sudden, re-emerging wave of this disease has occurred, almost contemporaneously, in all of the main areas of kiwifruit production in the world, suggesting that it can be considered as a pandemic disease. Recent in-depth genetic studies performed on P. syringae pv. actinidiae strains have revealed that this pathovar is composed of four genetically different populations which, to different extents, can infect crops of the genus Actinidia worldwide. Genome comparisons of these strains have revealed that this pathovar can gain and lose the phaseolotoxin gene cluster, as well as mobile genetic elements, such as plasmids and putative prophages, and that it can modify the repertoire of the effector gene arrays. In addition, the strains currently causing worldwide severe economic losses display an extensive set of genes related to the ecological fitness of the bacterium in planta, such as copper and antibiotic resistance genes, multiple siderophore genes and genes involved in the degradation of lignin derivatives and other phenolics. This pathogen can therefore easily colonize hosts throughout the year.

TAXONOMY

Bacteria; Proteobacteria, gamma subdivision; Order Pseudomonadales; Family Pseudomonadaceae; Genus Pseudomonas; Pseudomonas syringae species complex, genomospecies 8; Pathovar actinidiae.

MICROBIOLOGICAL PROPERTIES

Gram-negative, aerobic, motile, rod-shaped, polar flagella, oxidase-negative, arginine dihydrolase-negative, DNA 58.5-58.8 mol.% GC, elicits the hypersensitive response on tobacco leaves.

HOST RANGE

Primarily studied as the causal agent of bacterial canker of green-fleshed kiwifruit (Actinidia deliciosa), it has also been isolated from yellow-fleshed kiwifruit (A. chinensis). In both species, it causes severe economic losses worldwide. It has also been isolated from wild A. arguta and A. kolomikta.

DISEASE SYMPTOMS

In green-fleshed and yellow-fleshed kiwifruits, the symptoms include brown-black leaf spots often surrounded by a chlorotic margin, blossom necrosis, extensive twig die-back, reddening of the lenticels, extensive cankers along the main trunk and leader, and bleeding cankers on the trunk and the leader with a whitish to orange ooze.

EPIDEMIOLOGY

Pseudomonas syringae pv. actinidiae can effectively colonize its host plants throughout the year. Bacterial exudates can disperse a large amount of inoculum within and between orchards. In the spring, temperatures ranging from 12 to 18 °C, together with humid conditions, can greatly favour the multiplication of the bacterium, allowing it to systemically move from the leaf to the young shoots. During the summer, very high temperatures can reduce the multiplication and dispersal of the bacterium. Some agronomical techniques, as well as frost, wind, rain and hail storms, can contribute to further spreading.

DISEASE CONTROL

An integrated approach that takes into consideration precise scheduled spray treatments with effective and environmentally friendly bactericides and equilibrated plant nutrition, coupled with preventive measures aimed at drastically reducing the bacterial inoculum, currently seems to be the possible best solution for coexistence with the disease. The development of resistant cultivars and pollinators, effective biocontrol agents, including bacteriophages, and compounds that induce the systemic activation of plant defence mechanisms is in progress.

USEFUL WEBSITES

Up-to-date information on bacterial canker research progress and on the spread of the disease in New Zealand can be found at: http://www.kvh.org.nz. Daily information on the spread of the disease and on the research being performed worldwide can be found at: http://www.freshplaza.it.

Genome drafts of four phytoplasma strains of the ribosomal group 16SrIII

By applying a coverage-based read selection and filtration through a healthy plant dataset, and a post-assembly contig selection based on homology and linkage, genome sequence drafts were obtained for four phytoplasma strains belonging to the 16SrIII group (X disease clade), namely Vaccinium Witches' Broom phytoplasma (647 754 nt in 272 contigs), Italian Clover Phyllody phytoplasma strain MA (597 245 nt in 197 contigs), Poinsettia branch-inducing phytoplasma strain JR1 (631 440 nt in 185 contigs) and Milkweed Yellows phytoplasma (583 806 nt in 158 contigs). Despite assignment to different 16SrIII subgroups, the genomes of the four strains were similar, comprising a highly conserved core (92-98 % similar in their nucleotide sequence among each other over alignments about 500 kb in length) and a minor strain-specific component. As far as their protein complement was concerned, they did not differ significantly in their basic metabolism potential from the genomes of other wide-host-range phytoplasmas sequenced previously, but were distinct from strains of other species, as well as among each other, in genes encoding functions conceivably related to interactions with the host, such as membrane trafficking components, proteases, DNA methylases, effectors and several hypothetical proteins of unknown function, some of which are likely secreted through the Sec-dependent secretion system. The four genomes displayed a group of genes encoding hypothetical proteins with high similarity to a central domain of IcmE/DotG, a core component of the type IVB secretion system of Gram-negative Legionella spp. Conversely, genes encoding functional GroES/GroEL chaperones were not detected in any of the four drafts. The results also indicated the significant role of horizontal gene transfer among different 'Candidatus Phytoplasma' species in shaping phytoplasma genomes and promoting their diversity.

The influence of local factors on the prediction of fumonisin contamination in maize

BACKGROUND

Contamination by mycotoxins is a major concern to the maize industry in north-east Italy where maize grain is often spoiled by Fusarium spp. In this work, fumonisins, deoxynivalenol and zearalenone were determined and an artificial neural network (ANN) model suitable for predicting mycotoxin contamination of maize at harvest time was developed.

RESULTS

The occurrence of deoxynivalenol and zearalenone was very limited, while fumonisins concentration ranged from 163 and to 3663 µg kg(-1) in 2007, and from 333 to 11473 µg kg(-1) in 2008. Statistical data analysis of factors affecting fumonisins concentration revealed that irrigation, chemical treatment against the European corn borer and harvest date significantly affected the level of contamination (P < 0.05), although the relevance of the factors was different in 2007 and 2008. The neural network approach showed a significant correlation between ascertained values and predictions based on agronomic data.

CONCLUSION

This is the first time that an artificial neural network has been used to predict fumonisin accumulation in maize: the prediction has been shown to have the potential for the development of a new approach for the rapid cataloging of grain lots.

A revertible, autonomous, self-assembled DNA-origami nanoactuator

A DNA-origami actuator capable of autonomous internal motion in accord to an external chemical signal was designed, built, operated and imaged. The functional DNA nanostructure consists of a disk connected to an external ring in two, diametrically opposite points. A single stranded DNA, named probe, was connected to two edges of the disk perpendicularly to the axis of constrain. In the presence of a hybridizing target molecule, the probe coiled into a double helix that stretched the inner disk forcing the edges to move toward each other. The addition of a third single stranded molecule that displaced the target from the probe restored the initial state of the origami. Operation, dimension and shape were carefully characterized by combining microscopy and fluorescence techniques.

On the alleged origin of geminiviruses from extrachromosomal DNAs of phytoplasmas

Background

Several phytoplasmas, wall-less phloem limited plant pathogenic bacteria, have been shown to contain extrachromosomal DNA (EcDNA) molecules encoding a replication associated protein (Rep) similar to that of geminiviruses, a major group of single stranded (ss) DNA plant viruses. On the basis of that observation and of structural similarities between the capsid proteins of geminiviruses and the Satellite tobacco necrosis virus, it has been recently proposed that geminiviruses evolved from phytoplasmal EcDNAs by acquiring a capsid protein coding gene from a co-invading plant RNA virus.

Results

Here we show that this hypothesis has to be rejected because (i) the EcDNA encoded Rep is not of phytoplasmal origin but has been acquired by phytoplasmas through horizontal transfer from a geminivirus or its ancestor; and (ii) the evolution of geminivirus capsid protein in land plants implies missing links, while the analysis of metagenomic data suggests an alternative scenario implying a more ancient evolution in marine environments.

Conclusion

The hypothesis of geminiviruses evolving in plants from DNA molecules of phytoplasma origin contrasts with other findings. An alternative scenario concerning the origin and spread of Rep coding phytoplasmal EcDNA is presented and its implications on the epidemiology of phytoplasmas are discussed.

Air analysis in the assessment of fumonisin contamination risk in maize

BACKGROUND

In maize-growing areas where fumonisin contamination is endemic, there is an urgent need for novel methods to assess the quality of grain lots before their delivery to common drying and storage collection centres. Aerobiological samples of fungal spores released during harvest were analysed to establish a relationship between fumonisin contamination and the abundance of pathogen propagules collected in the combine harvester using a cyclone and membrane filters. Filter-captured propagules were analysed by direct plating, immunoenzymatic assay of specific Fusarium extracellular polysaccharides and real time polymerase chain reaction of the extracted DNA using fum1, a gene involved in the biosynthesis of fumonisin, as a target.

RESULTS

The results showed that time of harvest and environmental conditions strongly influenced the efficiency and performance of the collection system. The data obtained were informative in comparing individual samples collected under similar conditions. The immunoenzymatic assay provided the most reliable data, which improved the ability of a neural network to predict the fumonisin content of lots, when added to agronomic, environmental and phytosanitary data.

CONCLUSION

This is the first attempt to evaluate the Fusarium propagules dispersed during harvesting as a predictive means to assess maize quality. A method based on cyclone/filter capture and immunological detection has been shown to be feasible and to have the potential for the development of a continuous monitoring system, but the prediction capabilities in the present implementation were limited.

Evolutionary analysis of endopolygalacturonase-encoding genes of Botrytis cinerea

Sequence analysis of five of the six endopolygalacturonase-encoding genes (Bcpg1, Bcpg2, Bcpg3, Bcpg4, Bcpg5) from 32 strains of Botrytis cinerea showed marked gene to gene differences in the amount of among-strains diversity. Bcpg4 was almost invariable in all strains; Bcpg3 and Bcpg5 showed a moderate variability, similar to that of non-pathogenicity-associated genes examined in other studies. Conversely, Bcpg1 and Bcpg2 were highly variable and were shown to be under positive selection based on the McDonald-Kreitman test and likelihood ratio test. The evolution of the five endopolygalacturonase genes is explained by their different ecophysiological role. Diversification and balancing selection, as detected in Bcpg1 and Bcpg2, can be used by the pathogen to escape recognition by the host and delay plant reaction in the early phases of infection. The analysis of the polymorphisms and the location of the sites with high probability of being positively selected highlighted the relevance of variability of the BcPG1 and BcPG2 proteins at their C-terminal end. By contrast, the absence of variability in Bcpg4 suggests that the efficiency of the product of this gene is critical for B. cinerea growth in late phases of infection or during intraspecific competition, thus markedly affecting strain fitness.

Phytoplasmas: Genetics, Diagnosis and Relationships with the Plant and Insect Host

Phytoplasmas cannot be cultivated in vitro, and remain the most poorly understood plant pathogens. Despite this limitation, the investigation of their nature with the aid of modern tools has produced noteworthy results during the last 20 years. Using biochemical and molecular approaches, the phylogeny of the phytoplasmas has been described, their chromosomal and extrachromosomal components are being studied, and information on the localization, movement, and metabolic interference occurring in their insect and plant hosts accumulated. At the same time, the application of the new findings in phylogeny and genetics has aided the development of powerful diagnostic tools that have improved the ability to manage diseases which are induced by phytoplasmas.

Degradation of fumonisin B1 by a bacterial strain isolated from soil

A mixed microbial culture degrading fumonisin B l was obtained from soil samples using an enrichment culture procedure. A bacterial isolate from the enrichment culture (strain NCB 1492) degraded fumonisin B1 after incubation for 3 h, as indicated by TLC and HPLC analysis. On the basis of the sequence analysis of 16S rDNA, strain NCB 1492 was related to the Delftia/Comamonas group. Thin-layer chromatographic analysis indicated the presence of metabolites in the NCB 1492 culture filtrates after degradation of fumonisin B1 supplied as sole carbon and nitrogen source in phosphate buffer. Four metabolites were identified by mass spectrometry analysis.

Ochratoxin A-producing strains of Penicillium spp. isolated from grapes used for the production of “passito” wines

The post-harvest mycobiota of dried grapes, used in Friuli Venezia Giulia (Northern-East Italy) for the production of "passito" dessert wines, was investigated in order to detect potential ochratoxin A (OTA)-producers. Five grape cultivars were analysed and only isolates belonging to the genera Aspergillus and Penicillium were evaluated. No Aspergillus spp. was found while 379 strains of Penicillium spp. were isolated. Four strains produced UV fluorescent metabolites on grape juice agar and synthetic liquid media as observed by thin-layer chromatography (TLC). Three of these resulted OTA producers when analyzed by high pressure liquid chromatography (HPLC), following immunoaffinity column purification. According to the results of morphological examinations and ribosomal DNA sequencing, the OTA producer strains did not belong to the species P. verrucosum or P. nordicum. The corresponding passito wines did not contain OTA.

‘Candidatus Erwinia dacicola’, a coevolved symbiotic bacterium of the olive fly Bactrocera oleae (Gmelin)

The taxonomic identity of the hereditary prokaryotic symbiont of the olive fly Bactrocera oleae (Diptera: Tephritidae) was investigated. In order to avoid superficial microbial contaminants and loosely associated saprophytic biota, flies were surface-sterilized at the larval stage and reared under aseptic conditions until adult emergence. B. oleae flies originating from different geographical locations and collected at different times of the year were tested. Bacterial isolation was undertaken from the cephalic oesophageal bulb, which is known to be a specific site of accumulation for the hosted microsymbionts in the adult insect. Despite evidence of multiplication cycles taking place within the insect, attempts at cultivation of the isolated bacteria ex situ were not productive at any stage, leading to the choice of unculturable status definition. PCR amplification and nucleotide sequencing of the entire 16S rRNA gene consistently yielded a single sequence that displayed marked similarity with enterobacterial lineages, with closest matches (97 %) to Erwinia persicina and Erwinia rhapontici. The novel taxon differs from common intestinal bacterial species of fruit flies and from instances of culturable bacteria previously described in B. oleae raised without sterility precautions, which we also observed as minority occupants or occasional contaminants. The symbiont's identity is also distinct from Pseudomonas savastanoi. In all observations, the numerically dominant inhabitant of the olive fly oesophageal organ was the same unculturable organism, whose presence at later stages was also regularly observed in the midgut. A novel species is proposed, by virtue of its unique properties, under the designation ‘Candidatus Erwinia dacicola’.

Polymorphisms in nuclear rDNA and mtDNA reveal the polyphyletic nature of isolates of Phomopsis pathogenic to sunflower and a tight monophyletic clade of defined geographic origin

The molecular diversity of Diaporthe helianthi (anamorph Phomopsis helianthi), the causal agent of sunflower stem canker, was studied in 16 isolates of different geographic origin using nuclear and mitochondrial markers. PCR products corresponding to the internal transcribed spacers (ITS1 and ITS2) of the nuclear ribosomal RNA gene, and to the mitochondrial atp6 gene were sequenced. The ITS1 and ITS2 sequences were compared with those of Phomopsis spp. and Diaporthe spp. obtained from databases. The diversity in the region surrounding the atp6 gene was also studied by restriction analysis using four enzymes. The analyses revealed a marked diversity within the sunflower-isolated strains, which appear to belong to phylogenetically unrelated groups. Noticeably, all the isolates collected in France and in the former Yugoslavia, where severe epiphytotics of sunflower stem canker are frequently reported, showed high similarity to each other forming a clade which clearly differentiated from all other ones within the genus Phomopsis. Conversely, all the isolates collected in Italy, where, despite favourable environmental conditions, the incidence of the disease is low, were only distantly related to the former group and showed sequence similarity with other previously established phylogenetic clades within the Phomopsis/Diaporthe complex.

Mapping and characterization of polymorphism in mtDNA of Cryphonectria parasitica: evidence of the presence of an optional intron

The mitochondrial DNA (mtDNA) of the filamentous ascomycete Cryphonectria parasitica is large and polymorphic so, to better understand the nature of the polymorphisms within populations, a small collection of Italian strains of the fungus was examined. Known mtDNA polymorphisms were mapped and found to cluster in four regions of the mtDNA molecule, particularly in the RFLP region 2 where five different mtDNA haplotypes out of 13 strains were identified. This region included an area of 8.4kbp which was entirely sequenced in strain Ep155 showing the presence of two introns. An internal 3.2kbp portion was sequenced also in six additional strains. Sequence comparison of the C. parasitica mitochondrial intronic ORFs revealed similarities to known endonucleases such as those of Podospora anserina and Neurospora crassa. DNA sequence analysis showed that three polymorphisms of this mtDNA region within this population of 12 strains were due to the optional presence in the ND5 gene of an intron and of an intervening sequence within the intron. Evidence was also found within this population of mixed mitochondrial types within a single strain.

PCR-mediated whole genome amplification of phytoplasmas

A method was developed for genome analysis of phytoplasmas, bacterial plant pathogens that cannot be cultivated in vitro in cell-free media. The procedure includes a CsCl-bisbenzimide gradient buoyant centrifugation followed by polymerase chain reaction (PCR)-mediated whole genome amplification. The latter step involves digestion of the DNA by a restriction enzyme with an A/T-rich recognition sequence. Due to the different A/T content in the DNA of the pathogen and its plant host, the fragments originating from phytoplasma are shorter and are preferentially amplified in the PCR reaction. Products obtained were cloned and screened by dot-blot hybridization. Results showed that about 90% of recombinant clones appeared to harbor phytoplasma specific DNA inserts. Sequencing of randomly selected clones was carried out and comparison with the NCBI database confirmed the bacterial origin for the sequences, which have been assigned a putative function. The origin of the recombinant clones was further confirmed by the generation of specific amplicons from the phytoplasma-infected plant and not from the healthy control, using PCR primers devised from the sequences of the recombinant clones. This method could be used for genome-wide comparisons between phytoplasmas.

Classification, nomenclature, and plant pathogenic bacteria - a clarification

ABSTRACT In a recent Letter to the Editor of Phytopathology, proposals were made for endorsement and for rejection of selected names of plant pathogenic Pseudomonas spp. and Xanthomonas spp. We believe that support for, and rejection of, several names was based on misconceptions concerning the Approved Lists of Bacterial Names and entails misinterpretations of several Rules of the International Code of Nomenclature of Bacteria. This letter aims to clarify those misconceptions and misinterpretations.

Expression of chloramphenicol acetyltransferase in Bacillus subtilis under the control of a phytoplasma promoter

A cloned putative promoter region upstream of the 16S rRNA gene of the western X-disease phytoplasma was inserted behind the promoterless chloramphenicol acetyltransferase gene of plasmid pPL603. The DNA construct was used to transform Bacillus subtilis cells. The transformants were assayed for chloramphenicol acetyltransferase activity, showing that the phytoplasma promoter is efficiently expressed in a B. subtilis background.

Diversity of phytoplasmas isolated from insects, determined by a DNA heteroduplex mobility assay and a length polymorphism of the 16S-23S rDNA spacer region analysis

Two techniques were developed for the analysis of non-cultivable mollicutes in insects. The first was aimed at detecting organisms belonging to undiscovered groups within the phytoplasma clade. After prescreening by polymerase chain reaction with phytoplasma-specific primers, nucleic acids from 54 positive samples were amplified using phytoplasma-specific fluorescein-labelled primers flanking the 16S-23S rDNA spacer region, which is variable in length among the phytoplasmas. The sizes of all the detected products were only those expected for already-described phytoplasma subclades. It was also shown that a single leafhopper might carry different phytoplasmas, at similar or very different relative concentrations. The second technique, based on the heteroduplex mobility assay, was designed for the detection of organisms phylogenetically similar to phytoplasmas but not recognized by the specific primer pair. As a result, signals generated by ribosomal DNA of organisms which appear to be closely related but not identical to phytoplasmas were detected.

Sequence analysis of domains III and IV of the 23S rRNA gene of verticillate streptomycetes

Domains III and IV of the 23S rRNA gene of 25 strains of verticillate streptomycetes were sequenced. None of the sequences was identical to any other, with regions of variability being restricted to parts of helices 54 and 64. No relationships were detected between the similarities in the sequence and the assignment to phenetic clusters as defined by the numerical taxonomy studies. Limited agreement was also found between similarity of the sequences and DNA-DNA homology values. However, species (> 70% DNA-DNA homology values)-specific diagnostic oligonucleotides generally could be defined, except for Streptomyces baldaccii. Therefore the determination of the 23S rRNA sequence may be of greater value for fingerprinting individual strains than for taxonomic or identification purposes.

Chromosome mapping of the sweet potato little leaf phytoplasma reveals genome heterogeneity within the phytoplasmas

To further understand the genomic diversity and genetic architecture of phytoplasmas, a physical and genetic map of the sweet potato little leaf (SPLL) strain V4 phytoplasma chromosome was determined. PFGE was used to determine the size of the SPLL-V4 genome, which was estimated to be 622 kb. A physical map was prepared by two-dimensional reciprocal digestions using the restriction endonucleases BssHII, Smal, Eagl and I-Ceul. Sixteen cleavage sites were located on the map. Southern hybridizations of digested SPLL-V4 chromosomal DNA were done using random clones and PCR-amplified genes as probes. This confirmed fragment positions and located the two rRNA operons and the linked fus/tuf genes encoding elongation factors G and Tu, respectively, on the physical map. An inversion of one of the rRNA operons was observed from hybridization data. Sequence analysis of one of the random clones identified a gid gene encoding a glucose-inhibited division protein. Digestions of the tomato big bud (TBB) phytoplasma chromosome with the same four enzymes revealed genome heterogeneity when compared to the closely related SPLL-V4, and a preliminary chromosome size for the TBB phytoplasma of 662 kb was estimated. This mapping information has revealed that significant genome diversity exists within the phytoplasmas.

Geminivirus-related extrachromosomal DNAs of the X-clade phytoplasmas share high sequence similarity

Southern blot hybridization analysis revealed that the extrachromosomal DNAs (EC-DNAs) associated with Vaccinium witches' broom (VAC) and walnut witches' broom phytoplasmas and various strains of the Italian clover phyllody phytoplasma (ICPh) were highly homologous among themselves but distinct from EC-DNAs of aster yellows related phytoplasmas occurring in the same insect and plant hosts and collected at the same site as the ICPh strains. The EC-DNAs of various strains of the ICPh differed significantly in number and size, more markedly among samples from different host plant species than among samples from the same host plant species. However, experiments on insect-mediated transmission suggested that the size variation is not associated with plant host specificity. Sequence analysis of cloned fragments revealed the presence of highly conserved ORFs (with substantially invariant putative translation products) but also the presence of regions rich in short direct and inverted repeats, which may be the cause of the size variations. The partial sequence of an EC-DNA associated with VAC encoding a putative replication-associated protein indicated their close phylogenetic relationship with geminiviruses.

The Cryphonectria parasitica plasmid pUG1 contains a large ORF with motifs characteristic of family B DNA polymerases

The isolation and characterization of the circular mitochondrial plasmid pUG1 from the ascomycete Cryphonectria parasitica is described. The entire sequence (4182 bp) was obtained and high similarities to DNA-dependent DNA polymerases were revealed. Strikingly common features with the DNA polymerases encoded by the Neurospora intermedia plasmids Fiji and LaBelle, such as matches to the conserved motifs A and B and the presence of TTD instead of DTD in motif C, were found, suggesting the existence of a distinct group of members of the B DNA family polymerases. These strong similarities between the plasmids might suggest a common origin of the C.parasitica and the Neurospora plasmids.

Physical map of the Western X-disease phytoplasma chromosome

A physical map of the chromosome of the western X-disease phytoplasma was constructed and represents the first physical map of a phytoplasma chromosome. The western X-disease phytoplasma is a nonculturable, plant-pathogenic member of the class Mollicutes and is the causal agent of a severe disease of fruit trees in North America. The map was generated by performing restriction digests of the chromosome and resolving the restriction fragments by pulsed-field gel electrophoresis. Southern blot analysis using cloned phytoplasma probes confirmed the arrangement of contiguous restriction fragments. The locations of 20 restriction sites for the enzymes SalI, XhoI, BssHII, RsrII, SmaI, and NotI were mapped on the chromosome, which is circular and comprises approximately 670 kb. The locations or the two rRNA operons and of four previously cloned fragments of chromosomal DNA were also placed on the map.

Phylogenetic classification of phytopathogenic mollicutes by sequence analysis of 16S ribosomal DNA

The phylogenetic relationships of 17 phytopathogenic mycoplasmalike organisms (MLOs) representing seven major taxonomic groups established on the basis of MLO 16S ribosomal DNA (rDNA) restriction patterns were examined by performing a sequence analysis of the 16S rDNA gene. The sequence data showed that the MLOs which we examined are members of a relatively homogeneous group that evolved monophyletically from a common ancestor. In agreement with results obtained previously with other MLOs, our results also revealed that the organisms are more closely related to Acholeplasma laidlawii and other members of the anaeroplasma clade than to any other mollicutes. A phylogenetic tree based on 16S rDNAs showed that the MLOs which we examined can be divided into the following five primary clusters: (i) the aster yellows strain cluster; (ii) the apple proliferation strain cluster; (iii) the western-X disease strain cluster; (iv) the sugarcane white leaf strain cluster; and (v) the elm yellows strain cluster. The aster yellows, western-X disease, and elm yellows strain clusters were divided into two subgroups each. MLOs whose 16S rDNA sequences have been determined previously by other workers can be placed in one of the five groups. In addition to the overall division based on 16S rDNA sequence homology data, the primary clusters and subgroups could be further defined by a number of positions in the 16S rDNAs that exhibited characteristic compositions, especially in the variable regions of the gene.

Identification of Clavibacter michiganensis subsp. sepedonicus using the polymerase chain reaction

From the sequence of a subcloned DNA fragment of a highly conserved plasmid of Clavibacter michiganensis subsp. sepedonicus a pair of oligonucleotides were devised for use as polymerase chain reaction primers. The primer sequences do not show significant homology with any other sequence deposited in public databases. Polymerase chain reactions carried out using this primer pair and untreated cells of all strains of C. michiganesis sepedonicus tested resulted in the amplification of a DNA fragment of about 670 base pairs. No amplification was observed when bacteria belonging to other species were submitted to polymerase chain reaction under the same conditions. The detection limit of the assay was 4 x 10(3) bacteria.