Specific and sensitive detection tools for Xanthomonas arboricola pv. corylina, the causal agent of bacterial blight of hazelnut, developed with comparative genomics.

Xanthomonas arboricola pv. corylina (Xac; formerly Xanthomonas campestris pv. corylina) is the causal agent of the bacterial blight of hazelnuts, a devastating disease of trees in plant nurseries and young orchards. Currently, there are no PCR assays to distinguish Xac from all other pathovars of X. arboricola. A comparative genomics approach with publicly available genomes of Xac was used to identify unique sequences, conserved across the genomes of the pathogen. We identified a 2,440 bp genomic region that was unique to Xac and designed identification and detection systems for conventional PCR, qPCR (SYBR® Green and TaqMan™), and loop-mediated isothermal amplification (LAMP). All PCR assays performed on genomic DNA isolated from eight X. arboricola pathovars and closely related bacterial species confirmed the specificity of designed primers. These new multi-platform molecular diagnostic tools may be used by plant clinics and researchers to detect and identify Xac in pure cultures and hazelnut tissues rapidly and accurately.

First Report of Xanthomonas arboricola pv. corylina Causing Bacterial Blight on Hazelnut Tree (Corylus avellana) in Montenegro.

Hazelnut is a minor but rapidly increasing commercially grown species in Montenegro. In June 2021, severe infection, affecting more than 80% of the trees, was observed on 6-year-old hazelnut plants (Corylus avellana) cultivar Hall's Giant, in a 0.3ha plantation near Cetinje, central Montenegro. Numerous, small, 2-3mm in diameter, irregular, brown, necrotic spots, sometimes surrounded by a weak chlorotic halo, were observed on leaves. As the disease progressed, the lesions coalesced and formed large necrotic areas. Necrotic leaves remained attached to the twigs. Longitudinal brown lesions developed on twigs and branches, causing their dieback. Necrotic, unopened buds were noticed as well. No fruits were observed in the orchard. From the diseased leaf, bud and twig bark tissue, yellow, convex, and mucoid bacterial colonies were isolated on yeast extract dextrose CaCO3 medium and 14 isolates were subcultured. The isolates induced hypersensitive reaction in pelargonium leaves (Pelargonium zonale), were Gram-negative, catalase positive, oxidase negative, obligate aerobic, hydrolyzed starch, gelatin and esculin, did not reduce nitrate and did not grow at 37°C and in the presence of 5% NaCl, showing so the same biochemical profile of the reference strain Xanthomonas arboricola pv. corylina (Xac) NCPPB 3037. Using primer pair XarbQ-F/XarbQ-R (Pothier et al., 2011), a 402 bp product was amplified in all 14 isolates and the reference strain, confirming their affiliation to X. arboricola species. Additionally, the isolates were further identified by PCR analysis, using primer pair XapY17-F/XapY17-R (Pagani 2004; Pothier et al., 2011), resulting in a single band of 943 bp characteristic for Xac. The amplification and sequencing of the partial rpoD gene sequence of two selected isolates RKFB 1375 and RKFB 1370, were performed using a set of primers described by Hajri et al., 2012. The obtained DNA sequences showed that the isolates (GenBank Nos. OQ271224 and OQ271225) share 99.47% to 99.92% rpoD sequence identity with Xac strains CP076619.1 and HG992342.1 isolated from hazelnut in France and HG992341.1 in USA. Pathogenicity of all isolates was confirmed by spraying young shoots (20 to 30 cm long, with 5 to 7 leaves) on 2-year-old potted hazelnut plants (cv. Hall's Giant) using a handheld sprayer with the bacterial suspension (108 CFU/mL of sterile tap water), in three replicates. Sterile distilled water (SDW) and NCPPB 3037 Xac strain were used as negative and positive control, respectively. The inoculated shoots were incubated under plastic bags, providing high humidity conditions, in an acclimatized greenhouse at 22-26°C, for 72 h. Lesions surrounded by a halo appeared on leaves of all inoculated shoots within 5 to 6 weeks after inoculation, while leaves sprayed with SDW remained symptomless. Koch's postulates were confirmed by the re-isolation of the pathogen from the necrotic test plant tissue and identity checked by PCR using the primer set of Pothier et al., 2011. Based on pathogenic, biochemical, and molecular characteristics, the isolates from hazelnut plants in Montenegro were identified as X. arboricola pv. corylina. This is the first report of Xac affecting hazelnut in this country. Considering favorable environmental conditions, the pathogen can cause significant economic losses in hazelnut production in Montenegro. Therefore, phytosanitary measures have to be implemented to prevent introduction and spread of the pathogen in other areas.

Complete Genome and Plasmid Sequence Data of Three Strains of Xanthomonas arboricola pv. corylina, the Bacterium Responsible for Bacterial Blight of Hazelnut.

Xanthomonas arboricola pv. corylina is the causal agent of bacterial blight of hazelnut. The bacterium has been listed as an A2 quarantine pathogen in Europe since 1978 and on the regulated non-quarantine pest list since 2019. Three isolates from various geographic regions and isolated at different times were sequenced using a hybrid approach with short- and long-read technologies to generate closed genome and plasmid sequences in order to better understand the biology of this pathogen.

First Report of Xanthomonas arboricola pv. pruni Causing Leaf and Fruit Spot on Apricot (Prunus armeniaca L.) in Montenegro.

In July 2020, symptoms of leaf and fruit spot were observed on two-year old apricot plants (Prunus armeniaca L.), cultivar Rubista in plantation covering approximately 0,5 ha near Podgorica, central Montenegro. The intensity of infection on leaves was more than 70%. Initially, leaf spots were mainly circular, 2 to 5 mm in diameter, water-soaked, surrounded by a weak chlorotic halo, but later became light to dark brown and necrotic. Eventually, the spots merged and necrotic tissue dropped out, leaving a "shot-hole" leaf appearance. On apricot fruits small, dark brown, mainly circular superficial lesions were observed. The lesions merged and formed large necrotic areas reducing the quality of fruits. Symptoms were not observed on woody parts, such as twigs or stem. A total of 10 bacterial strains, forming yellow, convex, and mucoid colonies on yeast extract-dextrose-CaCO3 (YDC) medium, were isolated from symptomatic leaf and fruit tissue. All strains induced hypersensitive reaction in tobacco leaves. They were Gram-negative, strictly aerobic, oxidase negative, catalase positive, hydrolyzed gelatine and esculin but not starch, and did not grow at 37°C, showing similar biochemical properties as a reference strain Xanthomonas arboricola pv. pruni (Xap) (NCPPB 416) used in all tests as a positive control. Strains were further identified by PCR analysis, using primer pair XapY17-F/XapY17-R (Pagani 2004; Pothier et al. 2011), resulting in a single band of 943 bp, characteristic for Xap. Additionally, BOX-PCR with the BOX A1R primer (Schaad et al. 2001) showed 100% homology in genetic profiles of all tested strains and control strain. Amplification and partial sequencing of the gyrB gene of four representative strains was performed using set of primers described by Parkinson et al. (2007). Obtained DNA sequences showed that analysed strains (GenBank nos. MW473770, MW473771, MW473772, and MW473773) share 99.44 to 99.57% of gyrB sequence identity with Xap pathotype strain ICMP51. Pathogenicity of all strains was confirmed by spraying young apricot shoots using a hand-held sprayer, and by infiltration of apricot leaves (cv. Roksana) from the abaxial surface using a syringe without needle, with the bacterial suspension (107 CFU/ml in sterile distilled water), in three replicates. Sterile distilled water and reference Xap strain (NCPPB 416), were used as negative and positive controls, respectively. The inoculated shoots and leaves were maintained at approx. 25°C and high humidity conditions. Tissue necrosis appeared on all inoculated shoots 5 to 11 days and leaves 5 to 9 days after inoculation. Koch's postulates were completed by re-isolation of the pathogen from inoculated tissue and identification by PCR using XapY17-F/XapY17-R primers. Based on pathogenic, biochemical and molecular characteristics, the strains isolated from apricot leaves and fruits in Montenegro were identified as Xap - causal agent of bacterial leaf spot and canker of stone fruits. This quarantine pathogen was previously reported on almond (Panic et al. 1998) and on peach (Popovic et al. 2020) in Montenegro. This is the first report of Xap affecting apricot in this country. Therefore, strict phytosanitary measures have to be implemented to prevent spread of the pathogen in other areas and other susceptible hosts.