Raied Abou Kubaa

Bio: Raied Abou Kubaa is an academic researcher. The author has contributed to research in topics: Xylella fastidiosa & Biology. The author has an hindex of 7, co-authored 25 publications receiving 151 citations.

The complete nucleotide sequence and genome organization of Fig cryptic virus, a novel bipartite dsRNA virus infecting fig, widely distributed in the Mediterranean basin

Abstract: Two double-stranded RNA (dsRNA) segments of a virus with a bipartite genome identified in fig (Ficus carica L.) and denoted Fig cryptic virus (FCV) were cloned and sequenced. Viral dsRNAs are 1696 bp (RNA-1) and 1415 bp (RNA-2) in size. RNA-1 contains a single ORF (1419 nt) potentially encoding a 54 kDa protein and comprising the conserved amino acid motifs of the RNA-dependent RNA polymerase (RdRp) domain of species of the genus Alphacryptovirus. Its full-length amino acid sequence has the highest identity with Raphanus sativus cryptic virus 2 (RsCV-2) (36%), Beet cryptic virus 3 (BCV-3) (36%) and Fragaria chiloensis cryptic virus (FCCV) (34%). RNA-2 has also a single ORF (1014 nt) coding for a polypeptide with a predicted molecular mass of 38 kDa, identified as the viral coat protein (CP). In a phylogenetic tree constructed with the amino acid sequences of the RdRp domain, FCV clusters in a clade comprising BCV-3 and a number of tentative species of the genus Alphacryptovirus. FCV is not mechanically transmissible. It was detected in fig orchards of six Mediterranean countries (Albania, Algeria, Italy, Lebanon, Syria and Tunisia) where it does not seem to induce a visible disease.

Multilocus sequence typing of Xylella fastidiosa isolated from olive affected by “olive quick decline syndrome” in Italy

Abstract: The recent finding of Xylella fastidiosa ( Xf ) in olive trees in southern Italy, the scanty molecular information on this bacterium and its association with the olive quick decline syndrome (OQDS) prompted the necessity to isolate and acquire more genetic data on the type of strain present in that region. For the first time, the bacterium was isolated from infected olive on culture media. Genetic information were obtained through genomic comparison with other subspecies or strains. The sequences of thirteen genes from its genome, comprising seven housekeeping genes ( leuA, petC, lacF , cysG, holC, nuoL and gltT ) usually used in multilocus sequence typing (MLST) systems, and six genes involved in different biochemical functions ( RNA Pol sigma-70 factor, hypothetical protein HL, 16S rRNA, rfbD, nuoN, and pilU ), were analyzed. The sequences of the biochemical function genes were explored individually to study the genetic structure of this bacterium, while the MLST genes were linked together into one concatameric sequence (4161 bp long) to increase the resolution of the phylogenetic analysis when compared with Xf strains previously reported. Sequence analyses of single genes showed that the Xf olive strain is distinct from the four previously defined taxons ( Xf subsp. fastidiosa , Xf subsp. multiplex , Xf subsp. sandyi and Xf subsp. pauca ) with a dissimilarity rate that reached 4%. In particular, Xf from olive shared the greatest identity with the strain “9a5c” (subsp. pauca ), but was nevertheless distinct from it. Similarly, the MLST based on concatameric sequences confirmed the genetic variance of Xf from olive by generating a novel sequence type profile (ST53). Phylogenetic tree analyses showed that Xf from olive clustered in one clade close to subspecies pauca (strains “9a5c” and “CVC0018”), but was nevertheless distinct from them. These results indicate molecular divergence of this olive bacterium with all other strains yet reported.

Differences in the Endophytic Microbiome of Olive Cultivars Infected by Xylella fastidiosa across Seasons.

Abstract: The dynamics of Xylella fastidiosa infections in the context of the endophytic microbiome was studied in field-grown plants of the susceptible and resistant olive cultivars Kalamata and FS17. Whole metagenome shotgun sequencing (WMSS) coupled with 16S/ITS rRNA gene sequencing was carried out on the same trees at two different stages of the infections: In Spring 2017 when plants were almost symptomless and in Autumn 2018 when the trees of the susceptible cultivar clearly showed desiccations. The progression of the infections detected in both cultivars clearly unraveled that Xylella tends to occupy the whole ecological niche and suppresses the diversity of the endophytic microbiome. However, this trend was mitigated in the resistant cultivar FS17, harboring lower population sizes and therefore lower Xylella average abundance ratio over total bacteria, and a higher α-diversity. Host cultivar had a negligible effect on the community composition and no clear associations of a single taxon or microbial consortia with the resistance cultivar were found with both sequencing approaches, suggesting that the mechanisms of resistance likely reside on factors that are independent of the microbiome structure. Overall, Proteobacteria, Actinobacteria, Firmicutes, and Bacteriodetes dominated the bacterial microbiome while Ascomycota and Basidiomycota those of Fungi.

A new variant of Xylella fastidiosa subspecies multiplex detected in different host plants in the recently emerged outbreak in the region of Tuscany, Italy

Abstract: The vector-borne bacterial pathogen Xylella fastidiosa is widely distributed in the Americas; in the last decade it has emerged as a serious threat for agricultural crops, natural environment and landscape in Europe. Following the first EU outbreak in 2013 in southern Italy, associated with a severe disease in olive trees, annual mandatory surveys are now in place in the Member States, leading to the discovery of bacterial outbreaks in different countries. Among the latest findings, an outbreak has been reported in the Italian region of Tuscany, with infections identified in seven different plant species. In this work, we report the isolation and the genetic characterization of isolates associated with this newly discovered outbreak. Multilocus sequence typing approach revealed the occurrence of isolates harbouring a new sequence type, denoted ST87, genetically related to strains of subsp. multiplex, but different from the genotypes of this subspecies previously characterized in Europe. Five cultured strains were successfully recovered from four of the seven host plants, an important achievement for advancing the studies on genomics and pathogenicity of these isolates and thus assess their potential threat for European agriculture.

Xylella fastidiosa in Olive in Apulia: Where We Stand.

Abstract: A dramatic outbreak of Xylella fastidiosa decimating olive was discovered in 2013 in Apulia, Southern Italy. This pathogen is a quarantine bacterium in the European Union (EU) and created unprecede...

Several subspecies and sequence types are associated with the emergence of Xylella fastidiosa in natural settings in France

Abstract: Xylella fastidiosa is a plant pathogenic bacterium emerging in Europe. In France its emergence has been demonstrated through interceptions of contaminated coffee plants and, in 2015, by a survey of natural settings. The first French focus of contamination was detected in 2015 in Corsica; since then, almost 300 foci have been found and nearly 30 plant species have been declared contaminated, with Polygala myrtifolia remaining the principal host, suffering from severe leaf scorch. This study reports on the diversity of X. fastidiosa identified in France in 2015. Multilocus sequence analysis/typing revealed the presence of mainly X. fastidiosa subsp. multiplex sequence types (STs) ST6 and ST7. A focus of X. fastidiosa subsp. pauca ST53 was identified in mainland France; one sample contaminated by X. fastidiosa subsp. sandyi ST76, one novel recombinant, and coinfections of different isolates in individual samples were also identified, but could not be confirmed by successive samplings, indicating limited or transient contamination. Koch's postulates were fulfilled for two isolates of X. fastidiosa subsp. multiplex on P. myrtifolia, one being ST6 and the other ST7. Comparative genomics of the genome sequences of three French isolates (one ST6 and two ST7) with available sequences revealed that, unlike the American Dixon strain, the French ST6 and ST7 strains are devoid of a plasmid encoding a complete type IV secretion system. Other differences regarding phage sequences were highlighted. Altogether, the results suggest that the emergence of X. fastidiosa in France is linked to several introduction events of diverse strains from different subspecies.

Update of the Scientific Opinion on the risks to plant health posed by Xylella fastidiosa in the EU territory.

Abstract: Additional co-authors: EFSA Panel on Plant Health (PLH), Wopke van der Werf, Antonio Vicent Civera, Jonathan Yuen, Lucia Zappala, Donato Boscia, Gianni Gilioli, Rodrigo Krugner, Alexander Mastin, Anna Simonetto, Joao Roberto Spotti Lopes, Steven White, Jose Cortinas Abrahantes, Alice Delbianco, Andrea Maiorano, Olaf Mosbach‐Schulz, Giuseppe Stancanelli, Michela Guzzo, Stephen Parnell

An Integrated Badnavirus Is Prevalent in Fig Germplasm

Abstract: Fig mosaic occurs worldwide and is the most common and important viral disease of fig. In the quest to identify the causal agent of the disease, several new viruses have been identified, including a new DNA virus, the subject of this communication. Phylogenetic analysis placed the virus, provisionally named Fig badnavirus-1 (FBV-1), in the genus Badnavirus, family Caulimoviridae. The experimental host range of FBV-1 was evaluated and the virus was mechanically transmitted to several herbaceous hosts. FBV-1 was detected in the National Clonal Germplasm Repository fig collection and additional samples from Arkansas, California, Florida, Michigan, Ohio, Oregon, and South Carolina, suggesting its wide distribution in the United States. Further tests revealed the presence of FBV-1 in seedlings and meristem tissue culture plants. Forty-four isolates were used in a study evaluating the population structure of the virus in the United States. Evidence that FBV-1 is integrated in the fig genome is presente...

Intercepted isolates of Xylella fastidiosa in Europe reveal novel genetic diversity.

Abstract: After the first confirmed outbreak of Xylella fastidiosa in the European Union (EU), associated with an olive disease denoted olive quick decline syndrome, mandatory surveys are now carried out in the member States and inspections increased at EU entry points such as ports. Such activities led to the interception of X. fastidiosa-infected coffee plants in consignments originating from Central America. Similarly, the geographic expansion of the olive decline epidemic area of the Apulia region (southern Italy) prompted investigations to identify new host plants. Here we report the interception of three novel bacterial sequence types in Italy, based on multi-locus sequence typing, that cluster with different X. fastidiosa subspecies, illustrating the risk of the introduction of additional pathogen genetic diversity into Europe. In the epidemic area of Apulia, new foci as well as host plant species positive with X. fastidiosa, including cherry, myrtleleaf and rosemary, were found to be all infected with the same sequence type of this bacterium (ST53, or CoDiRO strain). This work highlights the limited knowledge of X. fastidiosa phylogenetic and phenotypic diversity, the risk of novel X. fastidiosa introductions via contaminated plant material, and corroborates other studies indicating that the Apulia epidemic emerged from a single introduction of this pathogen into the region.