Major and Emerging Fungal Diseases of Citrus in the Mediterranean Region

This chapter deals with major endemic and emerging fungal diseases of citrus as well as with exotic fungal pathogens potentially harmful for citrus industry in the Mediterranean region, with particular emphasis on diseases reported in Italy and Maghreb countries. The aim is to provide an update of both the taxonomy of the causal agents and their ecology based on a molecular approach, as a preliminary step towards developing or upgrading integrated and sustainable disease management strategies. Potential or actual problems related to the intensification of new plantings, introduction of new citrus cultivars and substitution of sour orange with other rootstocks, globalization of commerce and climate changes are discussed. Fungal pathogens causing vascular, foliar, fruit, trunk and root diseases in commercial citrus orchards are reported, including Plenodomus tracheiphilus, Colletotrichum spp., Alternaria spp., Mycosphaerellaceae, Botryosphaeriaceae, Guignardia citricarpa and lignicolous basidiomycetes. Diseases caused by Phytophthora spp. (oomycetes) are also included as these pathogens have many biological, ecological and epidemiological features in common with the true fungi (eumycetes)

Spiroplasma spp.: A Plant, Arthropod, Animal and Human Pathogen

Mollicutes is a class of smallest and free-living bacteria. They have no cell wall and their plasma membrane contains cholesterol; nevertheless, cellular organization does not differ from that of other prokaryotes. They are used as simple model systems for studying general biological problems, such as those concerning membrane structure and functions, symbiosis between arthropods and microrganisms, animal and plant pathogens. Mollicutes includes the family of Spiroplamataceae, which contains Spiroplasma genus, a group of species associated, in different manner, with arthropods (insects, mites, crustaceans). Spiroplasma species can be commensals or parasites and even be involved in more close symbiosis, such as synergism or mutualism. Out of 38 described Spiroplasma species, only three have been associated with plant diseases and three with arthropod diseases. Moreover, some species have been related to animal diseases, such as transmissible spongiform encephalopathy (TSE), and their role in human disease has been assessed. The chapter describes the taxonomic situation of the genus and reports the most important diseases due to the presence of Spiroplasma in different living organisms with special emphasis on citrus in which it causes one of the most economically damaging infectious diseases in a number of citrus growing areas worldwide

First Documentation of Life Cycle Completion of the Alien Rust Pathogen Melampsoridium hiratsukanum in the Eastern Alps Proves Its Successful Establishment in This Mountain Range

Melampsoridium hiratsukanum is an alien rust fungus which has spread pervasively throughout several European countries following introduction into North Europe at the end of the 20th century. The authenticity of several records of the Melampsoridium species infecting alder (Alnus spp.) in the northern hemisphere is questionable, due to the misidentification and confusion that surround many of the older reports. Given this complicated taxonomic history, and since a M. hiratsukanum-like rust is strongly impacting Alnus incana stands in the Alps, probably affecting the bank protection role of this species along rivers, the unambiguous identification of this pathogen was a pressing epidemiological and ecological issue. In this study, field surveys, light (LM) and scanning electron microscopy (SEM), and molecular characterization were put together in an attempt to solve the conundrum. Field monitoring data, LM and SEM analyses of key taxonomic traits (length of ostiolar cells of uredinium, uredinio-spore shape and size, spore echinulation, number and position of germ pores) and ITS-rDNA sequence-based identification, convergently and unambiguously connected the rust that is causing the current epidemic to the non-native M. hiratsukanum. We documented the completion of the M. hiratsukanum life cycle on its two taxonomically unrelated broadleaf/conifer hosts. This is the first report of M. hiratsukanum from naturally infected Larix decidua in Europe

Co-Infections by Fusarium circinatum and Phytophthora spp. on Pinus radiata: Complex Phenotypic and Molecular Interactions

This study investigated the complex phenotypic and genetic response of Monterey pine (Pinus radiata) seedlings to co-infections by F. circinatum, the causal agent of pine pitch canker disease, and the oomycetes Phytophthora xcambivora and P. parvispora. Monterey pine seedlings were wound-inoculated with each single pathogen and with the combinations F. circinatum/P. xcambivora and F. circinatum/P. parvispora. Initially, seedlings inoculated only with F. circinatum showed less severe symptoms than seedlings co-inoculated or inoculated only with P. xcambivora or P. parvispora. However, 30 days post-inoculation (dpi), all inoculated seedlings, including those inoculated only with F. circinatum, showed severe symptoms with no significant differences among treatments. The transcriptomic profiles of three genes encoding pathogenesis-related proteins, i.e., chitinase (PR3), thaumatin-like protein (PR5), phenylalanine ammonia-lyase (PAL), and the pyruvate decarboxylase (PDC)-encoding gene were analyzed at various time intervals after inoculation. In seedlings inoculated with single pathogens, F. circinatum stimulated the up-regulation of all genes, while between the two oomycetes, only P. xcambivora induced significant up-regulations. In seedlings co-inoculated with F. circinatum and P.xcambivora or P. parvispora none of the genes showed a significant over-expression 4 dpi. In contrast, at 11 dpi, significant up-regulation was observed for PR5 in the combination F. circinatum/P.xcambivora and PDC in the combination F. circinatum/P. parvispora, thus suggesting a possible synergism of multiple infections in triggering this plant defense mechanism

Selection processes in simple sequence repeats suggest a correlation with their genomic location: insights from a fungal model system

Background: Adaptive processes shape the evolution of genomes and the diverse functions of different genomic regions are likely to have an impact on the trajectory and outcome of this evolution. The main underlying hypothesis of this study is that the evolution of Simple Sequence Repeats (SSRs) is correlated with the evolution of the genomic region in which they are located, resulting in differences of motif size, number of repeats, and levels of polymorphisms. These differences should be clearly detectable when analyzing the frequency and type of SSRs within the genome of a species, when studying populations within a species, and when comparing closely related sister taxa. By coupling a genome-wide SSR survey in the genome of the plant pathogenic fungus Heterobasidion irregulare with an analysis of intra-and interspecific variability of 39 SSR markers in five populations of the two sibling species H. irregulare and H. annosum, we investigated mechanisms of evolution of SSRs.Results: Results showed a clear dominance of trirepeats and a selection against other repeat number, i.e. di- and tetranucleotides, both in regions inside Open Reading Frames (ORFs) and upstream 5' untranslated region (5'UTR). Locus per locus AMOVA showed SSRs both inside ORFs and upstream 5'UTR were more conserved within species compared to SSRs in other genomic regions, suggesting their evolution is constrained by the functions of the regions they are in. Principal coordinates analysis (PCoA) indicated that even if SSRs inside ORFs were less polymorphic than those in intergenic regions, they were more powerful in differentiating species. These findings indicate SSRs evolution undergoes a directional selection pressure comparable to that of the ORFs they interrupt and to that of regions involved in regulatory functions.Conclusions: Our work linked the variation and the type of SSRs with regions upstream 5'UTR, putatively harbouring regulatory elements, and shows that the evolution of SSRs might be affected by their location in the genome. Additionally, this study provides a first glimpse on a possible molecular basis for fast adaptation to the environment mediated by SSRs

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