DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing Phytophthora Diversity in Anthropized and Natural Ecosystems

Isolation techniques supplemented by sequencing of DNA from axenic cultures have provided a robust methodology for the study of Phytophthora communities in agricultural and natural ecosystems. Recently, metabarcoding approaches have emerged as new paradigms for the detection of Phytophthora species in environmental samples. In this study, Illumina DNA metabarcoding and a conventional leaf baiting isolation technique were compared to unravel the variability of Phytophthora communities in different environments. Overall, 39 rhizosphere soil samples from a natural, a semi-natural and a horticultural small-scale ecosystem, respectively, were processed by both baiting and metabarcoding. Using both detection techniques, 28 out of 39 samples tested positive for Phytophthora. Overall, 1,406,613 Phytophthora internal transcribed spacer 1 (ITS1) sequences and 155 Phytophthora isolates were obtained, which grouped into 21 taxa, five retrieved exclusively by baiting (P. bilorbang; P. cryptogea; P. gonapodyides; P. parvispora and P. pseudocryptogea), 12 exclusively by metabarcoding (P. asparagi; P. occultans; P. psycrophila; P. syringae; P. aleatoria/P. cactorum; P. castanetorum/P. quercina; P. iranica-like; P. unknown sp. 1; P. unknown sp. 2; P. unknown sp. 3; P. unknown sp. 4; P. unknown sp. 5) and four with both techniques (P. citrophthora, P. multivora, P. nicotianae and P. plurivora). Both techniques complemented each other in describing the variability of Phytophthora communities from natural and managed ecosystems and revealing the presence of rare or undescribed Phytophthora taxa

A new approach in the monitoring of the phytosanitary conditions of forests: the case of oak and beech stands in the Sicilian Regional Parks

L'obiettivo del presente studio è stato quello di esaminare lo stato fitosanitario delle quercete e faggete dei tre Parchi Regionali Siciliani (Parco dell'Etna, Parco delle Madonie, Parco dei Nebrodi). Lo studio è stato condotto individuando delle aree di saggio, popolamenti forestali omogenei sotto l'aspetto floristico, ecologico e fitosanitario. Complessivamente sono state delimitate 81 aree di saggio, di cui 54 quercete e 27 faggete. La condizione fitosanitaria di ogni essenza arborea all'interno della rispettiva area di saggio è stata espressa con un indice numerico denominato “classe fitosanitaria” (PC). I popolamenti di quercia hanno mostrato un elevato grado di sofferenza, con alberi sintomatici nell’85% delle aree di saggio. I popolamenti di faggio hanno mostrato una situazione di maggiore stabilità, ad eccezione delle faggete del parco dei Nebrodi che apparivano molto degradate. Sul genere Quercus, sono stati osservati sintomi di infezioni di patogeni fungini comuni nelle foreste delle aree temperate e Mediterranee, quali Biscogniauxia mediterranea, Polyporus sp., Fistulina hepatica, Mycrosphaera alphitoides ed Armillaria sp., mentre su faggio sono state osservate infezioni di Biscogniauxia nummularia, Fomes fomentarius e Neonectria radicicola. Sono state altresì individuate 22 aree che vengono proposte come aree di saggio permanenti dello stato fitosanitario delle foreste nei tre parchi.The objective of this study was to investigate the health conditions of oak and beech stands in the three Regional Parks of Sicily (Etna, Madonie and Nebrodi). A total of 81 sampling areas were investigated, 54 in oak stands and 27 in beech stands. The phytosanitary conditions of each tree within the respective sampling area was expressed with a synthetic index namely phytosanitary class (PC). Oak stands showed severe symptoms of decline, with 85% of the sampling areas including symptomatic trees. In general, beech stands were in better condition, with the exception of Nebrodi Park, where trees showed severe symptoms of decline. On oak trees, infections of fungal pathogens were also observed, including Biscogniauxia mediterranea, Polyporus sp., Fistulina hepatica, Mycrosphaera alphitoides and Armillaria sp. By contrast, on beech trees Biscogniauxia nummularia, Fomes fomentarius and Neonectria radicicola were recognized. Furthermore, twenty-two permanent sampling areas were delimited with the aim of monitoring regularly the health conditions of forests in these three parks

DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing Phytophthora Diversity in Anthropized and Natural Ecosystems

Isolation techniques supplemented by sequencing of DNA from axenic cultures have provided a robust methodology for the study of Phytophthora communities in agricultural and natural ecosystems. Recently, metabarcoding approaches have emerged as new paradigms for the detection of Phytophthora species in environmental samples. In this study, Illumina DNA metabarcoding and a conventional leaf baiting isolation technique were compared to unravel the variability of Phytophthora communities in different environments. Overall, 39 rhizosphere soil samples from a natural, a semi-natural and a horticultural small-scale ecosystem, respectively, were processed by both baiting and metabarcoding. Using both detection techniques, 28 out of 39 samples tested positive for Phytophthora. Overall, 1,406,613 Phytophthora internal transcribed spacer 1 (ITS1) sequences and 155 Phytophthora isolates were obtained, which grouped into 21 taxa, five retrieved exclusively by baiting (P. bilorbang; P. cryptogea; P. gonapodyides; P. parvispora and P. pseudocryptogea), 12 exclusively by metabarcoding (P. asparagi; P. occultans; P. psycrophila; P. syringae; P. aleatoria/P. cactorum; P. castanetorum/P. quercina; P. iranica-like; P. unknown sp. 1; P. unknown sp. 2; P. unknown sp. 3; P. unknown sp. 4; P. unknown sp. 5) and four with both techniques (P. citrophthora, P. multivora, P. nicotianae and P. plurivora). Both techniques complemented each other in describing the variability of Phytophthora communities from natural and managed ecosystems and revealing the presence of rare or undescribed Phytophthora taxa

A Complex Interaction System for Understanding the Ability of Trichoderma to Trigger Defenses in Tomato Plants Challenged by Phytophthora nicotianae

In this study, the early activation of plant-defense-related genes during a three-way plant–antagonist–pathogen interaction in a tomato–Trichoderma–Phytophthora nicotianae model system was evaluated. Thirty-day-old tomato seedlings were treated at the root systems with a suspension of germinated conidia of two selected strains of T. asperellum and T. atroviride and then inoculated with zoospores of P. nicotianae. The defense mechanisms activated by tomato plants upon the simultaneous colonization of the root systems by Trichoderma spp. and P. nicotianae were evaluated 72 h post-inoculation by analyzing the transcriptomic profiles of genes involved in the pathways of salicylic acid (i.e., pathogenesis-related proteins—PR1b1 andPR-P2-encoding genes), jasmonic acid (i.e., lipoxygenases enzymes—TomLoxC- and TomLoxA-encoding genes), and the tomato plant defensin protein (i.e., SlyDF2-encoding gene). The results showed that PR1b1 was more strongly up-regulated in the three-way system including T. asperellum, while the gene PR-P2 was up-regulated in the system including T. atroviride. TomLoxA was significantly up-regulated only in the three-way system including T. asperellum, while TomLoxC was significantly up-regulated in neither of the analyzed three-way systems. Finally, the gene SlyDF2 was significantly up-regulated in tomato seedlings in both three-way systems

Phytophthora Diversity in a Sentinel Arboretum and in a Nature Reserve Area

Most soilborne Phytophthora species are invasive plant pathogens, and nursery plants for transplanting are considered a primary pathway for the introduction of exotic Phytophthora species into plant diversity conservation sites. As a preliminary contribution to the study of Phytophthora populations in plant conservation sites, we compared the diversity of Phytophthora in the protected natural area Complesso Speleologico Villasmundo S. Alfio Nature Reserve (NR) (Siracusa) and the botanical garden (BG) of the University of Catania, eastern Sicily (Italy). Samplings were carried out in spring 2019. Overall, 29 rhizosphere soil samples were collected, 17 from different types of vegetation in NR and 12 from different plant species in BG. Phytophthora species were recovered from soil samples by leaf baiting and isolation on a selective medium. Isolates were identified by combining morphological features with phylogenetic inferences from ITS-rDNA sequence analysis. Overall, 82 Phytophthora isolates, 30 from NR and 52 from BG, were characterized. Five Phytophthora species, P. pseudocryptogea, P. cryptogea, P. bilorbang, P. plurivora and P. gonapodyides, were recovered from NR, while only three species, P. nicotianae, P. multivora and P. parvispora, were found in BG. Factors contributing to shape Phytophthora populations of rhizosphere soil in these two vegetational contexts are discussed

Phytophthora Root and Collar Rot of <i>Paulownia</i>, a New Disease for Europe

Paulownia species are fast growing trees native to China, which are being grown in managed plantings in several European countries for the production of wood and biomasses. In 2018, wilting, stunting, leaf yellowing, and collapse, as a consequence of root and crown rot, were observed in around 40% of trees of a 2-year-old planting of Paulownia elongata × P. fortunei in Calabria (Southern Italy). Two species of Phytophthora were consistently recovered from roots, basal stem bark, and rhizosphere soil of symptomatic trees and were identified as Ph. nicotianae and Ph. palmivora on the basis of both morphological characteristics and phylogenetic analysis of rDNA ITS sequences. Koch’s postulates were fulfilled by reproducing the symptoms on potted paulownia saplings transplanted into infested soil or stem-inoculated by wounding. Both Phytophthora species were pathogenic and caused root rot and stem cankers. Even though P. palmivora was the only species recovered from roots of naturally infected plants, in pathogenicity tests through infested soil P. nicotianae was more virulent. This is the first report of Phytophthora root and crown rot of a Paulownia species in Europe. Strategies to prevent this emerging disease include the use of healthy nursery plants, choice of well-drained soils for new plantations, and proper irrigation management

Inhibitory Activity of Shrimp Waste Extracts on Fungal and Oomycete Plant Pathogens

(1) Background: This study was aimed at determining the in vitro inhibitory effect of new natural substances obtained by minimal processing from shrimp wastes on fungi and oomycetes in the genera Alternaria, Colletotrichum, Fusarium, Penicillium, Plenodomus and Phytophthora; the effectiveness of the substance with the highest in vitro activity in preventing citrus and apple fruit rot incited by P. digitatum and P. expansum, respectively, was also evaluated. (2) Methods: The four tested substances, water-extract, EtOAc-extract, MetOH-extract and nitric-extract, were analyzed by HPLC-ESI-MS-TOF; in vitro preliminary tests were carried out to determine the minimal inhibitory/fungicidal concentrations (MIC and MFC, respectively) of the raw dry powder, EtOAc-extract, MetOH-extract and nitric-extract for each pathogen. (3) Results: in the agar-diffusion-assay, nitric-extract showed an inhibitory effect on all pathogens, at all concentrations tested (100, 75, 50 and 25%); the maximum activity was on Plenodomus tracheiphilus, C. gloeosporioides and Ph. nicotianae; the diameters of inhibition halos were directly proportional to the extract concentration; values of MIC and MFC of this extract for all pathogens ranged from 2 to 3.5%; the highest concentrations (50 to 100%) tested in vivo were effective in preventing citrus and apple fruit molds. (4) Conclusions: This study contributes to the search for natural and ecofriendly substances for the control of pre- and post-harvest plant pathogens