Survey of Trunk Pathogens in South African Olive Nurseries

Nanopore-Sequencing Metabarcoding for Identification of Phytopathogenic and Endophytic Fungi in Olive (Olea europaea) Twigs

Metabarcoding approaches for the identification of plant disease pathogens and characterization of plant microbial populations constitute a rapidly evolving research field. Fungal plant diseases are of major phytopathological concern; thus, the development of metabarcoding approaches for the detection of phytopathogenic fungi is becoming increasingly imperative in the context of plant disease prognosis. We developed a multiplex metabarcoding method for the identification of fungal phytopathogens and endophytes in olive young shoots, using the MinION sequencing platform (Oxford Nanopore Technologies). Selected fungal-specific primers were used to amplify three different genomic DNA loci (ITS, beta-tubulin, and 28S LSU) originating from olive twigs. A multiplex metabarcoding approach was initially evaluated using healthy olive twigs, and further assessed with naturally infected olive twig samples. Bioinformatic analysis of basecalled reads was carried out using MinKNOW, BLAST+ and R programming, and results were also evaluated using the BugSeq cloud platform. Data analysis highlighted the approaches based on ITS and their combination with beta-tubulin as the most informative ones according to diversity estimations. Subsequent implementation of the method on symptomatic samples identified major olive pathogens and endophytes including genera such as Cladosporium, Didymosphaeria, Paraconiothyrium, Penicillium, Phoma, Verticillium, and others.

Fungal Pathogens Associated with Aerial Symptoms of Avocado (Persea americana Mill.) in Tenerife (Canary Islands, Spain) Focused on Species of the Family Botryosphaeriaceae

Fungi of the family Botryosphaeriaceae are considered responsible for various symptoms in avocado such as dieback, external necrosis of branches and inflorescences, cankers on branches and trunks, or stem-end rot of fruits. In recent years, these problems are becoming more frequent in avocado orchards in the Canary Islands (Spain). This work includes the characterization of fungal species involved in these diseases, which were isolated from avocado crops in Tenerife Island between 2018 and 2022. A total of 158 vegetal samples were collected, from which 297 fungal isolates were culture-isolated. Fifty-two of them were selected according to their morphological features as representative isolates of Botryosphaeriaceae, and their molecular characterization was carried out, sequencing the ITS1-2 region as well as the β-tubulin and the elongation factor 1-alpha genes. Five species of Botryosphaeriaceae were isolated, including Neofusicoccum australe, N. cryptoaustrale/stellenboschiana, N. luteum, N. parvum, and Lasiodiplodia brasiliensis. This is the first time that L. brasiliensis has been associated with avocado dieback and that N. cryptoaustrale/stellenboschiana has been cited in avocado causing symptoms of dieback and stem-end rot. However, it was not possible to assign our isolates unequivocally to N. cryptoaustrale or N. stellenboschiana even additionally using the rpb2 marker for their molecular characterization. Botryosphaeriaceae family seem to be involved in avocado dieback, in the premature fall of fruits during their development in the field and in post-harvest damage in Tenerife, but further studies are needed to clarify the fungal pathogens associated with symptoms in relation to phenological plant growth stages or less frequently observed.

First Report of Phaeoacremonium iranianum Causing Olive Twig and Branch Dieback

In an olive orchard on the western part of Istria, Croatia, twig and branch dieback was observed on several olive trees. In total, seven samples from symptomatic trees were collected. Samples were analyzed, and four fungal isolates showed morphological similarities to the species Phaeoacremonium. One isolate, chosen as a representative, was taken for molecular identification and pathogenicity tests. Based on the DNA sequence data of the ITS, TUB, and EF1α gene regions, the isolate was identified as P. iranianum. Pathogenicity tests were conducted on detached olive branches and olive trees in the greenhouse. To the best of our knowledge, this is the first report of twig and branch dieback on olive caused by Phaeoacremonium iranianum.

Detection of Pseudophaeomoniella globosa, an Olive Trunk Pathogen, on Olive Pruning Debris

Pseudophaeomoniella globosa has recently been identified as a pathogen contributing to olive trunk diseases in South Africa. Little is known regarding the biology and epidemiology of this pathogen. The aim of this study was to investigate whether olive pruning debris act as an inoculum source of P. globosa in established orchards. A nested species-specific PCR was developed for the detection of this pathogen on 138 samples of pruning debris collected from Paarl (40 wood pieces), Stellenbosch (42 wood pieces), and Worcester (56 pieces) in the Western Cape Province, South Africa. Spore washes were made from the samples (5 to 10 cm in length), after which the nested species-specific primers were used to determine the presence of P. globosa on the wood. P. globosa was detected on 37.5% of the pruning debris collected from Paarl, 61.9% from Stellenbosch, and 39.3% from Worcester. The pruning debris that tested positive for P. globosa were evaluated visually by microscopic observations for P. globosa pycnidia. Dark-brown to black pycnidia were found. Conidia from these pycnidia were measured, cultured, and confirmed as P. globosa by sequencing the internal transcribed spacer region. In this study, the pruning debris in established olive orchards were identified as inoculum sources of P. globosa. This study emphasizes the importance of additional means focused on reducing the inoculum sources of this pathogen in these orchards as an additional management strategy against olive trunk diseases.