Centro Of Ricerca Per La Frutticoltura

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Centro Of Ricerca Per La Frutticoltura

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Scortichini M.,Centro Of Ricerca Per La Frutticoltura | Marcelletti S.,Centro Of Ricerca Per La Frutticoltura | Ferrante P.,Centro Of Ricerca Per La Frutticoltura | Firrao G.,University of Udine
PLoS ONE | Year: 2013

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. © 2013 Scortichini et al.


Lodolini E.M.,Polytechnic University of Mozambique | Alfei B.,Agenzia Servizi Settore Agroalimentare delle Marche ASSAM | Santinelli A.,Agenzia Servizi Settore Agroalimentare delle Marche ASSAM | Cioccolanti T.,Associazione Interregionale Olivicola del Medio Adriatico AIOMA Ancona | And 3 more authors.
Scientia Horticulturae | Year: 2016

The objective of the present study was to assess the frost tolerance of 24 olive cultivars after a freezing event that occurred in February 2012 in Marche Region (Central Italy), and their recovery ability during the following growing seasons (2012 and 2013). The studied cultivars were locally, nationally and internationally spread. Trees were three-year-old and in the rest phase at the time of the freezing event. Frost tolerance was determined by two damage visual scoring: defoliation and bark split, both defined three months after the event. During the following growing seasons, the recovery ability of the cultivars was also assessed throughout a third visual index describing the vegetative re-sprouting. Results indicated differences in frost tolerance and recovery ability among the studied cultivars. In particular, ‘Arbequina’ recorded the highest canopy defoliation together with ‘FS17’, ‘Raggia’ and ‘Sargano di San Benedetto’, whereas ‘FS17’, showed the highest level of bark split on primary branches and trunk. This cultivar also registered a strong vegetative re-sprouting, mainly from the basal portion of the trunk. On the contrary, ‘Ascolana dura’ and ‘Orbetana’ resulted the most frost tolerant cultivars and showed the best recovery ability in 2012 and 2013, with a re-sprouting activity from the 1- and 2-year-old shoots. The results suggest low frost tolerance for the tested varieties and supply helpful information for the selection of the most suitable ones for the set of new olive orchards in cold climates. © 2016 Elsevier B.V.


Marcelletti S.,Centro Of Ricerca Per La Frutticoltura | Scortichini M.,Centro Of Ricerca Per La Frutticoltura
PLoS ONE | Year: 2015

The European hazelnut (Corylus avellana) is threatened in Europe by several pseudomonads which cause symptoms ranging from twig dieback to tree death. A comparison of the draft genomes of nine Pseudomonas strains isolated from symptomatic C. avellana trees was performed to identify common and distinctive genomic traits. The thorough assessment of genetic relationships among the strains revealed two clearly distinct clusters: P. avellanae and P. syringae. The latter including the pathovars avellanae, coryli and syringae. Between these two clusters, no recombination event was found. A genomic island of approximately 20 kb, containing the hrp/hrc type III secretion system gene cluster, was found to be present without any genomic difference in all nine pseudomonads. The type III secretion system effector repertoires were remarkably different in the two groups, with P. avellanae showing a higher number of effectors. Homologue genes of the antimetabolite mangotoxin and ice nucleation activity clusters were found solely in all P. syringae pathovar strains, whereas the siderophore yersiniabactin was only present in P. avellanae. All nine strains have genes coding for pectic enzymes and sucrose metabolism. By contrast, they do not have genes coding for indolacetic acid and anti-insect toxin. Collectively, this study reveals that genomically different Pseudomonas can converge on the same host plant by suppressing the host defence mechanisms with the use of different virulence weapons. The integration into their genomes of a horizontally acquired genomic island could play a fundamental role in their evolution, perhaps giving them the ability to exploit new ecological niches. © 2015 Marcelletti, Scortichini. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Andolfi A.,Complesso Universitario Monte SantAngelo | Ferrante P.,Centro Of Ricerca Per La Frutticoltura | Petriccione M.,Consiglio per la Ricerca e la Sperimentazione in Agricultura | Cimmino A.,Complesso Universitario Monte SantAngelo | And 2 more authors.
Journal of Plant Pathology | Year: 2014

Pseudomonas syringae pv. actinidiae, the causal agent of bacterial canker of Actinidia chinensis and A. deliciosa, is currently causing severe economic losses worldwide. A study was conducted to verify if a highly virulent Psa strain, isolated during the current outbreaks of bacterial canker of kiwifruit in Italy, produces phytotoxic metabolites in vitro. Culture filtrate, obtained from 14-day-old cells grown in Pseudomonas minimal medium, induced an evident hypersensitivity-like reaction to both tobacco and kiwifruit leaves. From culture filtrates, extracts were obtained using different solvents and pH values. The extracts and their corresponding aqueous phases, were further tested for phytotoxicity. Basic, hydrophilic, lowmolecular weight and hydrophilic, high-molecular weight compounds belonging to exopolysaccharides were isolated and analyzed. These compunds proved highly phytotoxic to kiwifruit, tobacco leaves and lemon fruits. Gas-chromatography- mass-spectrometry analysis carried out on crude exopolysaccharides showed glucose as the main monosaccharide constituent. These results suggest that phytotoxic metabolites, other than the antimetabolite phaseolotoxin, could be involved in the virulence of the pathogen to kiwifruit species.


Marcelletti S.,Italian Agricultural Research Council | Marcelletti S.,Centro Of Ricerca Per La Frutticoltura | Scortichini M.,Italian Agricultural Research Council
Phytopathology | Year: 2014

A total of 34 phytopathogenic strain genomes belonging to the Pseudomonas syringae species complex and related species, including many pathotype strains, were assessed using average nucleotide identity (ANI) analysis. Their taxonomic relationships were consistently confirmed by the tetranucleotide frequency correlation coefficient (TETRA) values, multilocus sequence typing analysis (MLSA) performed with seven housekeeping genes, using both maximum likelihood and Bayesian methods, and split consensus network analyses. The ANI, MLSA, and split consensus analyses provided consistent and identical results. We confirmed the occurrence of the well-demarcated genomospecies inferred sensu Gardan et al. using DNA-DNA hybridization and ribotyping analyses. However, some P. syringae strains of the pathovars morsprunorum and lachrymans were placed in different genomospecies in our analyses. Genomospecies 1, 2, 4, 6, and 9 resulted well demarcated, whereas strains of genomospecies 3 and 8 had ANI values between 95 and 96% in some cases, confirming that this threshold reveals very closely related species that might represent cases of splitting entities or the convergence of different species to the same ecological niche. This study confirms the robustness of the combination of genomic and phylogenetic approaches in revealing taxonomic relationships among closely related bacterial strains and provides the basis for a further reliable demarcation of the phytopathogenic Pseudomonas species. Within each species, the pathovars might represent distinct ecological units. The possibility of performing extensive and standardized host range and phenotypic tests with many strains of different pathovars can assist phytobacteriologists for better determining the boundaries of these ecological units.


Gambardella M.,University of Santiago de Chile | Contreras E.,University of Santiago de Chile | Alcalde J.,University of Santiago de Chile | Neri D.,Centro Of Ricerca Per La Frutticoltura
Acta Horticulturae | Year: 2016

In raspberry (Rubus idaeus), two groups of cultivars are known: once fruiting, where fruit occurs annually on floricanes, and repeat fruiting (remontant), where a second fruit crop occurs on primocanes in the late summer or fall. Primocane fruiting extends the harvest, resulting in higher yields. The development of primocane fruiting cultivars is a primary objective of current raspberry breeding programs. The phenotypic identification of this trait is not easy because there is a strong interaction genotype/environment, influenced by temperature and photoperiod. In addition, there is a gradual expression of the character. The objective of this research was to generate descriptive data to make the selection of this character in segregating populations more efficient. A description of the degree of primocane fruiting was performed for five raspberry genotypes, ranging from high primocane fruiting to no primocane fruiting. The genotypes studied in order of increasing primocane fruiting were: 'Meeker', 'Tulameen', 'Heritage', 'Autumn Bliss', and UC103 (advanced selection). Plant height was measured, together with number of nodes, number and development of lateral shoots, and number of fruits per lateral shoot. Days from planting to first flower were also measured. With these values, a 1-5 scale was developed that identified the different degrees of primocane fruiting. Additionally, the effects of a chill treatment (2°C for 30 days) applied to plants in the early stages of development in the same genotypes were studied. This treatment was effective only in 'Heritage'. These data have promoted progress in determining the type of inheritance of primocane fruiting in raspberry cultivars.


Tohge T.,Max Planck Institute of Molecular Plant Physiology | Scossa F.,Centro Of Ricerca Per La Frutticoltura | Fernie A.R.,Max Planck Institute of Molecular Plant Physiology
Plant Physiology | Year: 2015

Huge insight into molecular mechanisms and biological network coordination have been achieved following the application of various profiling technologies. Our knowledge of how the different molecular entities of the cell interact with one another suggests that, nevertheless, integration of data from different techniques could drive a more comprehensive understanding of the data emanating from different techniques. Here, we provide an overview of how such data integration is being used to aid the understanding of metabolic pathway structure and regulation. We choose to focus on the pairwise integration of large-scale metabolite data with that of the transcriptomic, proteomics, whole-genome sequence, growth- and yield-associated phenotypes, and archival functional genomic data sets. In doing so, we attempt to provide an update on approaches that integrate data obtained at different levels to reach a better understanding of either single gene function or metabolic pathway structure and regulation within the context of a broader biological process. © 2015 American Society of Plant Biologists. All rights Reserved.


Ferrante P.,Centro Of Ricerca Per La Frutticoltura | Scortichini M.,Centro Of Ricerca Per La Frutticoltura
Plant Pathology | Year: 2014

Frost occurs in all major areas of cultivation, presenting a threat for the production of kiwifruit crops worldwide. A series of experiments were performed on 1-year-old, potted plants or excised twigs of Actinidia chinensis and A. deliciosa to verify whether strict relationships exist between bacterial canker outbreaks from Pseudomonas syringae pv. actinidiae (Psa) attacks and the occurrence of autumn and winter frost events. The association between the occurrence of autumn frost and the sudden outbreak of bacterial canker in A. chinensis in central Italy has been confirmed. Both autumn and winter frosts promote Psa multiplication in the inoculated twigs of both species. The day after the frost, reddish exudates oozing from the inoculation sites were consistently observed in both species, and Psa was re-isolated in some cases. During the thawing of both A. deliciosa and A. chinensis twigs, the 2-cm upward and downward migration of Psa from the inoculation site was observed within 3 min, and the leaves were consistently colonized with the pathogen. A consistent brown discoloration, accompanied with a sour-sap odour, was observed throughout the length of the excised twigs of both Actinidia species after Psa inoculation and winter frost. Psa inoculation induced a remarkably higher necrosis in excised twigs that were not frozen compared with P. s. pv. syringae inoculation. Antifreeze protection using irrigation sprinklers did not influence the short-term period of Psa and P. s. pv. syringae multiplication in both A. deliciosa and A. chinensis twigs. Thus, the damage from frost, freeze thawing and the accumulation of Psa in Actinidia twigs promotes the migration of the pathogen within and between the orchards. Taken together, the results obtained in this study confirmed that A. deliciosa is more frost tolerant than A. chinensis, autumn frosts are more dangerous to these crops than winter frosts, and in the absence of Psa, young kiwifruit plants remain sensitive to frost. © 2013 British Society for Plant Pathology.


Ferrante P.,Centro Of Ricerca Per La Frutticoltura | Takikawa Y.,University of Shizuoka | Scortichini M.,Centro Of Ricerca Per La Frutticoltura
European Journal of Plant Pathology | Year: 2015

A total of 40 Pseudomonas syringae pv. actinidiae (Psa) strains isolated from past and current epidemics of kiwifruit bacterial canker worldwide were compared using repetitive-sequence PCR (rep-PCR) fingerprinting with BOX, ERIC and REP primer sets. The strains were also assessed for the presence of 23 type III secretion system effector genes, tolerance to sodium arsenite, the presence of coronatine and phaseolotoxin and for growth trends in Actinidia deliciosa leaves. Rep-PCR revealed the occurrence of 11 different Psa lineages among the strains and indicated a relevant genetic variability within the strains isolated in Japan during 1984–2011, whereas all strains obtained from the current pandemic showed the same banding pattern. All lineages showed the same growth trend when inoculated into A. deliciosa leaves. The difference between Psa strains from past and current epidemics was confirmed by the detection of different repertoires of type III effector protein genes. Not all Psa strains isolated in Japan during past epidemics of kiwifruit bacterial canker amplify genes of the argK-tox cluster of phaseolotoxin, suggesting their absence or gene mutation. The results of an arsenic tolerance assay indicated that almost all strains isolated in Italy during the current epidemic of kiwifruit bacterial canker were relatively tolerant to 0.15–0.35 mM sodium arsenite, whereas those isolated in Chile and New Zealand were very sensitive. Remarkably, the two strains from China were tolerant or very sensitive. Collectively, these data indicate a composite population structure of this pathogen, which was able to diversify in Japan during 27 years of recurrent infections to A. deliciosa. The current naming of Psa populations based on their numbering and presence/absence of phytotoxins should be reconsidered. © 2015, Euratom: Council for Agricultural Research and analysis of the economy graria; © European Union.


PubMed | Centro Of Ricerca Per La Frutticoltura, Natural History Museum in London, University of Bologna, University of Naples Federico II and 2 more.
Type: Journal Article | Journal: FEMS microbiology ecology | Year: 2016

The interface between biological and geochemical components in the surface crust of a saline soil was investigated using X-ray diffraction, and variable pressure scanning electron microscopy in combination with energy dispersive X-ray spectrometry. Mineral compounds such as halite and gypsum were identified crystallized around filaments of cyanobacteria. A total of 92 genera were identified from the bacterial community based on 16S gene pyrosequencing analysis. The occurrence of the gypsum crystals, their shapes and compartmentalization suggested that they separated NaCl from the immediate microenvironment of the cyanobacteria, and that some cyanobacteria and communities of sulfur bacteria may had a physical control over the distinctive halite and gypsum structures produced. This suggests that cyanobacteria might directly or indirectly promote the formation of a protective envelope made of calcium and sulfur-based compounds.

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