Changes in rhizosphere bacterial communities associated with tree decline: grapevine esca syndrome case study.

An investigation was carried out on rhizosphere bacteria to determine if they may be associated with perennial crops affected by nonspecific decline, a phenomenon that is difficult to diagnose and prevent. Esca disease of grapevine was chosen for this case study because of its easy foliar symptom identification. Ribosomal DNA fingerprint analysis by polymerase chain reaction - denaturing gradient gel electrophoresis (PCR-DGGE), quantitative PCR (qPCR), and rDNA amplicon sequencing by next-generation sequencing (NGS) were adopted to investigate the bacterial communities associated with grapevines, which were selected for the presence and absence of external foliar symptoms in 11 vineyards. According to PCR-DGGE and qPCR, bacterial communities differed in site of origin (vineyards), but not between symptomatic and asymptomatic plants, whereas qPCR gave a significantly higher presence of total bacteria and Pseudomonas spp. in asymptomatic plants. NGS confirmed no difference between symptomatic and asymptomatic plants, apart from a few minor genera (<0.5%) such as Salinibacterium, Flavobacterium, Nocardia, and Janthinobacterium, which were, in all cases, higher in asymptomatic plants and whose functional role should be the object of further investigation. The fact that total bacteria and Pseudomonas were more abundant in the rhizosphere of asymptomatic grapevines and that some bacterial genera were associated with the latter, represents a new element when investigating the multiple-origin phenomenon such as esca disease of grapevine.

Volatolomics approach by HS-SPME-GC-MS and multivariate analysis to discriminate olive tree varieties infected by Xylella fastidiosa.

INTRODUCTION: Xylella fastidiosa (Xf) is a pathogenic bacterium that causes diseases in olive trees. Therefore, analytical methods for both the characterisation of the host/pathogen interaction and infection monitoring are needed. Volatile organic compounds (VOCs) are emitted by plants relate to their physiological state, therefore VOCs monitoring can assist in detecting stress or infection states before visible signs are present. OBJECTIVE: In this work, the headspace-solid phase microextraction-gaschromatography-mass spectrometry (HS-SPME-GC-MS) technique was used for the first time to highlight VOCs differences between healthy and Xf-infected olive trees. METHODOLOGY: VOCs from olive tree twig samples were extracted and analysed by HS-SPME-GC-MS, and hence identified by comparing the experimental linear retention indexes with the reference values and by MS data obtained from NIST library. Data were processed by principal component analysis (PCA) and analysis of variance (ANOVA). RESULTS: The HS-SPME step was optimised in terms of adsorbent phase and extraction time. HS-SPME-GC-MS technique was applied to the extraction and analysis of VOCs of healthy and Xf-infected olive trees. More than 100 compounds were identified and the differences between samples were evidenced by the multivariate analysis approach. The results showed the marked presence of methyl esters in Xf-infected samples, suggesting their probable involvement in the mechanism of diffusible signal factor. CONCLUSION: The proposed approach represents an easy and solvent-free method to evaluate the presence of Xf in olive trees, and to evidence volatiles produced by host/pathogen interactions that could be involved in the defensive mechanism of the olive tree and/or in the infective action of Xf.

Diversity Evaluation of Xylella fastidiosa from Infected Olive Trees in Apulia (Southern Italy).

Olive culture is very important in the Mediterranean Basin. A severe outbreak of Olive Quick Decline Syndrome (OQDS) caused by Xylella fastidiosa infection was first noticed in 2013 on olive trees in the southern part of Apulia region (Lecce province, southern Italy). Studies were carried out for detection and diversity evaluation of the Apulian strain of Xylella fastidiosa. The presence of the pathogen in olive samples was detected by PCR amplifying the 16S rDNA, gyrase B subunit (gyrB) and HL hypothetical protein genes and single nucleotide polymorphisms (SNPs) assessment was performed to genotype X. fastidiosa. Twelve SNPs were recorded over gyrB and six SNPs were found for HL gene. Less variations were detected on 16S rDNA gene. Only gyrB and HL provided sufficient information for dividing the Apulian X. fastidiosa olive strains into subspecies. Using HL nucleotide sequences was possible to separate X. fastidiosa into subspecies pauca and fastidiosa. Whereas, nucleotide variation present on gyrB gene allowed separation of X. fastidiosa subsp. pauca from the other subspecies multiplex and fastidiosa. The X. fastidiosa strain from Apulia region was included into the subspecies pauca based on three genes phylogenetic analyses.

Endophytic fungi occurring in fennel, lettuce, chicory, and celery--commercial crops in southern Italy.

The occurrence of endophytic fungi in fennel, lettuce, chicory, and celery crops was investigated in southern Italy. A total of 186 symptomless plants was randomly collected and sampled at the stage of commercial ripeness. Fungal species of Acremonium, Alternaria, Fusarium, and Plectosporium were detected in all four crops; Plectosporium tabacinum was the most common in all crop species and surveyed sites. The effect of eight endophytic isolates (five belonging to Plectosporium tabacinum and three to three species of Acremonium) inoculated on lettuce plants grown in gnotobiosis was assessed by recording plant height, root length and dry weight, collar diameter, root necrosis, and leaf yellowing. P. tabacinum and three species of Acremonium, inoculated on gnotobiotically grown lettuce plants, showed pathogenic activity that varied with the fungal isolate. Lettuce plants inoculated with the isolates Ak of Acremonium kiliense, Ac of Acremonium cucurbitacearum, and P35 of P. tabacinum showed an increased root growth, compared to the non-inoculated control. The high frequency of P. tabacinum isolation recorded in lettuce plants collected in Bari and Metaponto, and in fennel plants from Foggia agricultural districts, suggests a relationship not only between a crop species and P. tabacinum, but also between the occurrence of the endophyte and the crop rotation history of the soil.