Invasion of European pine stands by a North American forest pathogen and its hybridization with a native interfertile taxon

The alien invasive forest pathogen Heterobasidion irregulare is replacing the native Heterobasidion annosum

Invasions by alien pathogens are a major threat to forest conservation. The North American fungal pathogen of conifers Heterobasidion irregulare, inadvertently introduced in Central Italy in the 1940s, has been spreading causing high mortality of Italian stone pine (Pinus pinea). While invading newfound niches, H. irregulare has established itself in the current range of the native congener H. annosum. The aims of this study were to determine whether in time: (I) H. irregulare populations may be increasing in size; (II) H. irregulare may be replacing H. annosum, rather than simply coexisting with it; and, (III) H. annosum may disappear in forests infested by H. irregulare. The presence, abundance and distribution of H. annosum and H. irregulare were assessed through an aerobiological assay replicated ten years apart in a forest in which both species have been coexisting. Replacement index (RI), Markov chains and geometric progressions were used to model the interspecific interaction between the two species and to assess the invasiveness of H. irregulare. Results showed that, in 10 years, the incidence of H. annosum dropped from 39.4 to 6.1%, while that of H. irregulare increased from 57.6 to 81.8%, with the alien pathogen replacing the native species (RI = 84.6%) and spreading at a maximum rate of 139 ha/year. Although our models show that the extinction of H. annosum may be unlikely, the ability of H. irregulare to replace it suggests the alien pathogen may also readily colonize those parts of Europe where H. annosum is more abundant than in Central Italy.

Pyoluteorin Produced by the Biocontrol Agent Pseudomonas protegens Is Involved in the Inhibition of Heterobasidion Species Present in Europe

Pseudomonas protegens (strain DSMZ 13134) is a biocontrol agent with promising antagonistic activity hinging on antibiosis against the fungal forest pathogens Heterobasidion spp. Here, by using High-Performance Liquid Chromatography coupled to Mass Spectrometry (HPLC-MS), we assessed whether monocultures of P. protegens (strain DSMZ 13134) produce the three major determinants of biocontrol activity known for the genus Pseudomonas: 2,4-diacetylphloroglucinol (2,4-DAPG), pyoluteorin (PLT), and pyrrolnitrin (PRN). At the tested culture conditions, we observed the production of PLT at concentrations ranging from 0.01 to 10.21 mg/L and 2,4-DAPG at a concentration not exceeding 0.5 mg/L. Variations of culture conditions involving culture medium, incubation temperature, and incubation period had no consistent influence on PLT production by the bacterium. Assays using culture medium amended with PLT at the same concentration of that present in cell-free filtrate of the bacterium, i.e., 3.77 mg/L, previously documented as effective against Heterobasidion spp., showed a remarkable activity of PLT against genotypes of all the four Heterobasidion species present in Europe, including the non-native invasive H. irregulare. However, such antifungal activity decreased over time, and this may be a constraint for using this molecule as a pesticide against Heterobasidion spp. When the bacterium was co-cultured in liquid medium with genotypes of the different Heterobasidion species, an increased production of PLT was observed at 4 °C, suggesting the bacterium may perform better as a PLT producer in field applications under similar environmental conditions, i.e., at low temperatures. Our results demonstrated the role of PLT in the inhibition of Heterobasidion spp., although all lines of evidence suggest that antibiosis does not rely on a single constitutively produced metabolite, but rather on a plethora of secondary metabolites. Findings presented in this study will help to optimize treatments based on Pseudomonas protegens (strain DSMZ 13134) against Heterobasidion spp.

Comparative Efficacy of State-of-the-Art and New Biological Stump Treatments in Forests Infested by the Native and the Alien Invasive Heterobasidion Species Present in Europe

The Heterobasidion annosum species complex includes major fungal pathogens of conifers worldwide. State-of-the-art preventative stump treatments with urea or with commercial formulations of the fungal biological control agent Phlebiopsis gigantea (i.e., Rotstop^®) may become no longer available or are not approved for use in many areas of Europe infested by the three native Heterobasidion species and by the North American invasive H. irregulare, making the development of new treatments timely. The efficacy of Proradix^® (based on Pseudomonas protegens strain DSMZ 13134), the cell-free filtrate (CFF) of the same bacterium, a strain of P. gigantea (MUT 6212) collected in the invasion area of H. irregulare in Italy, Rotstop^®, and urea was comparatively investigated on a total of 542 stumps of Abies alba, Picea abies, Pinus pinea, and P. sylvestris in forest stands infested by the host-associated Heterobasidion species. Additionally, 139 logs of P. pinea were also treated. Results support the good performances of Rotstop^®, and especially of urea against the native Heterobasidion species on stumps of their preferential hosts and, for the first time, towards the invasive North American H. irregulare on stumps of P. pinea. In some experiments, the effectiveness of Proradix^® and of the strain of P. gigantea was weak, whereas the CFF of P. protegens strain DSMZ 13134 performed as a valid alternative to urea and Rotstop^®. The mechanism of action of this treatment hinges on antibiosis; therefore, further improvements could be possible by identifying the active molecules and/or by optimizing their production. Generally, the performance of the tested treatments is not correlated with the stump size.

Enhanced Outcrossing, Directional Selection and Transgressive Segregation Drive Evolution of Novel Phenotypes in Hybrid Swarms of the Dutch Elm Disease Pathogen Ophiostoma novo-ulmi

In the 1970s, clones of the two subspecies of Ophiostoma novo-ulmi, subsp. americana (SSAM) and subsp. novo-ulmi (SSNU) began to overlap in Europe, resulting in hybrid swarms. By 1983-1986, hybrids with high, SSAM-like growth and pathogenic fitness comprised ~75% of popula-tions at Limburg, Netherlands and Orvieto, Italy. We resampled these populations in 2008 to examine trends in hybrid fitness traits. Since preliminary sampling in 1979-1980, MAT-1 locus frequency had increased from ~0% to ~32% at Orvieto and 5% to ~43% at Limburg, and vegeta-tive incompatibility type frequency had changed from near clonal to extremely diverse at both sites. This represents an enormous increase in outcrossing and recombination potential, due in part to selective acquisition (under virus pressure) of MAT-1 and vic loci from the resident O. ulmi and in part to SSAM × SSNU hybridisation. Overt virus infection in the 2008 samples was low (~4%), diagnostic SSAM and SSNU cu and col1 loci were recombinant, and no isolates exhib-ited a parental SSAM or SSNU colony pattern. At both sites, mean growth rate and mean patho-genicity to 3-5 m clonal elm were high SSAM-like, indicating sustained directional selection for these characters, though at Orvieto growth rate was slower. The once frequent SSNU-specific up-mut colony dimorphism was largely eliminated at both sites. Perithecia formed by Limburg isolates were mainly an extreme, long-necked SSNU-like form, consistent with transgressive segregation resulting from mismatch of SSAM and SSNU developmental loci. Orvieto isolates produced more parental-like perithecia, suggesting the extreme phenotypes may have been se-lected against. The novel phenotypes in the swarms are remodelling O. novo-ulmi in Europe. Locally adapted genotypes may emerge.

Genic introgression from an invasive exotic fungal forest pathogen increases the establishment potential of a sibling native pathogen

Significant hybridization between the invasive North American fungal plant pathogen Heterobasidion irregulare and its Eurasian sister species H. annosum is ongoing in Italy. Whole genomes of nine natural hybrids were sequenced, assembled and compared with those of three genotypes each of the two parental species. Genetic relationships among hybrids and their level of admixture were determined. A multi-approach pipeline was used to assign introgressed genomic blocks to each of the two species. Alleles that introgressed from H. irregulare to H. annosum were associated with pathways putatively related to saprobic processes, while alleles that introgressed from the native to the invasive species were mainly linked to gene regulation. There was no overlap of allele categories introgressed in the two directions. Phenotypic experiments documented a fitness increase in H. annosum genotypes characterized by introgression of alleles from the invasive species, supporting the hypothesis that hybridization results in putatively adaptive introgression. Conversely, introgression from the native into the exotic species appeared to be driven by selection on genes favoring genome stability. Since the introgression of specific alleles from the exotic H. irregulare into the native H. annosum increased the invasiveness of the latter species, we propose that two invasions may be co-occurring: the first one by genotypes of the exotic species, and the second one by alleles belonging to the exotic species. Given that H. irregulare represents a threat to European forests, monitoring programs need to track not only exotic genotypes in native forest stands, but also exotic alleles introgressed in native genotypes.

Evolution and Adaptation of Forest and Crop Pathogens in the Anthropocene

Anthropocene marks the era when human activity is making a significant impact on earth, its ecological and biogeographical systems. The domestication and intensification of agricultural and forest production systems have had a large impact on plant and tree health. Some pathogens benefitted from these human activities and have evolved and adapted in response to the expansion of crop and forest systems, resulting in global outbreaks. Global pathogen genomics data including population genomics and high-quality reference assemblies are crucial for understanding the evolution and adaptation of pathogens. Crops and forest trees have remarkably different characteristics, such as reproductive time and the level of domestication. They also have different production systems for disease management with more intensive management in crops than forest trees. By comparing and contrasting results from pathogen population genomic studies done on widely different agricultural and forest production systems, we can improve our understanding of pathogen evolution and adaptation to different selection pressures. We find that in spite of these differences, similar processes such as hybridization, host jumps, selection, specialization, and clonal expansion are shaping the pathogen populations in both crops and forest trees. We propose some solutions to reduce these impacts and lower the probability of global pathogen outbreaks so that we can envision better management strategies to sustain global food production as well as ecosystem services.

Heterothallism and potential hybridization events inferred for twenty-two yellow morel species

Mating-type genes are central to sexual reproduction in ascomycete fungi and result in the establishment of reproductive barriers. Together with hybridization, they both play important roles in the evolution of fungi. Recently, potential hybridization events and MAT genes were separately found in the Elata Clade of Morchella. Herein, we characterized the MAT1-1-1 and MAT1-2-1 genes of twenty-two species in the Esculenta Clade, another main group in the genus Morchella, and proved heterothallism to be the predominant mating strategy among the twenty-two species tested. Ascospores of these species were multi-nuclear and had many mitochondrial nucleoids. The number of ascospore nuclei might be positively related with the species distribution range. Phylogenetic analyses of MAT1-1-1, MAT1-2-1, intergenic spacer (IGS), and partial histone acetyltransferase ELP3 (F1) were performed and compared with the species phylogeny framework derived from the ribosomal internal transcribed spacer region (ITS) and translation elongation factor 1-alpha (EF1-a) to evaluate their species delimitation ability and investigate potential hybridization events. Conflicting topologies among these genes genealogies and the species phylogeny were revealed and hybridization events were detected between several species. Different evolutionary patterns were suggested for MAT genes between the Esculenta and the Elata Clades. Complex evolutionary trajectories of MAT1-1-1, MAT1-2-1, F1 and IGS in the Esculenta Clade were highlighted. These findings contribute to a better understanding of the importance of hybridization and gene transfer in Morchella and especially for the appearance of reproductive modes during its evolutionary process.

Potential Interactions between Invasive Fusarium circinatum and Other Pine Pathogens in Europe

Pines are major components of native forests and plantations in Europe, where they have both economic significance and an important ecological role. Diseases of pines are mainly caused by fungal and oomycete pathogens, and can significantly reduce the survival, vigor, and yield of both individual trees and entire stands or plantations. Pine pitch canker (PPC), caused by Fusarium circinatum (Nirenberg and O’Donnell), is among the most devastating pine diseases in the world, and is an example of an emergent invasive disease in Europe. The effects of microbial interactions on plant health, as well as the possible roles plant microbiomes may have in disease expression, have been the focus of several recent studies. Here, we describe the possible effects of co-infection with pathogenic fungi and oomycetes with F. circinatum on the health of pine seedlings and mature plants, in an attempt to expand our understanding of the role that biotic interactions may play in the future of PPC disease in European nurseries and forests. The available information on pine pathogens that are able to co-occur with F. circinatum in Europe is here reviewed and interpreted to theoretically predict the effects of such co-occurrences on pine survival, growth, and yield. Beside the awareness that F. circinatum may co-occurr on pines with other pathogens, an additional outcome from this review is an updating of the literature, including the so-called grey literature, to document the geographical distribution of the relevant pathogens and to facilitate differential diagnoses, particularly in nurseries, where some of them may cause symptoms similar to those induced by F. circinatum. An early and accurate diagnosis of F. circinatum, a pathogen that has been recently introduced and that is currently regulated in Europe, is essential to prevent its introduction and spread in plantings and forests.

Reduced Virulence of an Introduced Forest Pathogen over 50 Years

Pathogen incursions are a major impediment for global forest health. How pathogens and forest trees coexist over time, without pathogens simply killing their long-lived hosts, is a critical but unanswered question. The Dothistroma Needle Blight pathogen Dothistroma septosporum was introduced into New Zealand in the 1960s and remains a low-diversity, asexual population, providing a unique opportunity to analyze the evolution of a forest pathogen. Isolates of D. septosporum collected from commercial pine forests over 50 years were compared at whole-genome and phenotype levels. Limited genome diversity and increased diversification among recent isolates support the premise of a single introduction event. Isolates from the 1960s show significantly elevated virulence against Pinus radiata seedlings and produce higher levels of the virulence factor dothistromin compared to isolates collected in the 1990s and 2000s. However, later isolates have no increased tolerance to copper, used in fungicide treatments of infested forests and traditionally assumed to be a strong selection pressure. The isolated New Zealand population of this forest pathogen therefore appears to have become less virulent over time, likely in part to maintain the viability of its long-lived host. This finding has broad implications for forest health and highlights the benefits of long-term pathogen surveys.

Molecular analyses identify hybridization-mediated nuclear evolution in newly discovered fungal hybrids

Hybridization may be a major driver in the evolution of plant pathogens. In a high elevation Alpine larch stand in Montana, a novel hybrid fungal pathogen of trees originating from the mating of Heterobasidion irregulare with H. occidentale has been recently discovered. In this study, sequence analyses of one mitochondrial and four nuclear loci from 11 Heterobasidion genotypes collected in the same Alpine larch stand indicated that hybridization has increased allelic diversity by generating novel polymorphisms unreported in either parental species. Sequence data and ploidy analysis through flow cytometry confirmed that heterokaryotic (n + n) genotypes were not first-generation hybrids, but were the result of multiple backcrosses, indicating hybrids are fertile. Additionally, all admixed genotypes possessed the H. occidentale mitochondrion, indicating that the hybrid progeny may have been backcrossing mostly with H. occidentale. Based on reticulate phylogenetic network analysis by PhyloNet, Bayesian assignment, and ordination tests, alleles can be defined as H. irregulare-like or H. occidentale-like. H. irregulare-like alleles are clearly distinct from all known H. irregulare alleles and are derived from the admixing of both Heterobasidion species. Instead, all but one H. occidentale alleles found in hybrids, although novel, were not clearly distinct from alleles found in the parental H. occidentale population. This discovery demonstrates that Alpine larch can be a universal host favouring the interspecific hybridization between H. irregulare and H. occidentale and the hybridization-mediated evolution of a nucleus, derived from H. irregulare parental species but clearly distinct from it.

Comparative transcriptional and metabolic responses of Pinus pinea to a native and a non-native Heterobasidion species

Heterobasidion irregulare is a causal agent of root and butt-rot disease in conifers, and is native to North America. In 1944 it was introduced in central Italy in a Pinus pinea stand, where it shares the same niche with the native species Heterobasidion annosum. The introduction of a non-native pathogen may have significant negative effects on a naïve host tree and the ecosystem in which it resides, requiring a better understanding of the system. We compared the spatio-temporal phenotypic, transcriptional and metabolic host responses to inoculation with the two Heterobasidion species in a large experiment with P. pinea seedlings. Differences in length of lesions at the inoculation site (IS), expression of host genes involved in lignin pathway and in cell rescue and defence, and analysis of terpenes at both IS and 12 cm above the IS (distal site, DS), were assessed at 3, 14 and 35 days post inoculation (dpi). Results clearly showed that both species elicit similar physiological and biochemical responses in P. pinea seedlings. The analysis of host transcripts and total terpenes showed differences between inoculation sites and between pathogen and mock inoculated plants. Both pathogen and mock inoculations induced antimicrobial peptide and phenylalanine ammonia-lyase overexpression at IS beginning at 3 dpi; while at DS all the analysed genes, except for peroxidase, were overexpressed at 14 dpi. A significantly higher accumulation of terpenoids was observed at 14 dpi at IS, and at 35 dpi at DS. The terpene blend at IS showed significant variation among treatments and sampling times, while no significant differences were ever observed in DS tissues. Based on our results, H. irregulare does not seem to have competitive advantages over the native species H. annosum in terms of pathogenicity towards P. pinea trees; this may explain why the non-native species has not widely spread over the 73 years since its putative year of introduction into central Italy.

Unravelling species boundaries in the Aspergillus viridinutans complex (section Fumigati): opportunistic human and animal pathogens capable of interspecific hybridization

Although Aspergillus fumigatus is the major agent of invasive aspergillosis, an increasing number of infections are caused by its cryptic species, especially A. lentulus and the A. viridinutans species complex (AVSC). Their identification is clinically relevant because of antifungal drug resistance and refractory infections. Species boundaries in the AVSC are unresolved since most species have uniform morphology and produce interspecific hybrids in vitro. Clinical and environmental strains from six continents (n = 110) were characterized by DNA sequencing of four to six loci. Biological compatibilities were tested within and between major phylogenetic clades, and ascospore morphology was characterised. Species delimitation methods based on the multispecies coalescent model (MSC) supported recognition of ten species including one new species. Four species are confirmed opportunistic pathogens; A. udagawae followed by A. felis and A. pseudoviridinutans are known from opportunistic human infections, while A. felis followed by A. udagawae and A. wyomingensis are agents of feline sino-orbital aspergillosis. Recently described human-pathogenic species A. parafelis and A. pseudofelis are synonymized with A. felis and an epitype is designated for A. udagawae. Intraspecific mating assay showed that only a few of the heterothallic species can readily generate sexual morphs in vitro. Interspecific mating assays revealed that five different species combinations were biologically compatible. Hybrid ascospores had atypical surface ornamentation and significantly different dimensions compared to parental species. This suggests that species limits in the AVSC are maintained by both pre- and post-zygotic barriers and these species display a great potential for rapid adaptation and modulation of virulence. This study highlights that a sufficient number of strains representing genetic diversity within a species is essential for meaningful species boundaries delimitation in cryptic species complexes. MSC-based delimitation methods are robust and suitable tools for evaluation of boundaries between these species.

Detection of a Conspecific Mycovirus in Two Closely Related Native and Introduced Fungal Hosts and Evidence for Interspecific Virus Transmission

Hymenoscyphus albidus is a native fungus in Europe where it behaves as a harmless decomposer of leaves of common ash. Its close relative Hymenoscyphus fraxineus was introduced into Europe from Asia and currently threatens ash (Fraxinus sp.) stands all across the continent causing ash dieback. H. fraxineus isolates from Europe were previously shown to harbor a mycovirus named Hymenoscyphus fraxineus Mitovirus 1 (HfMV1). In the present study, we describe a conspecific mycovirus that we detected in H. albidus. HfMV1 was consistently identified in H. albidus isolates (mean prevalence: 49.3%) which were collected in the sampling areas before the arrival of ash dieback. HfMV1 strains in both fungal hosts contain a single ORF of identical length (717 AA) for which a mean pairwise identity of 94.5% was revealed. The occurrence of a conspecific mitovirus in H. albidus and H. fraxineus is most likely the result of parallel virus evolution in the two fungal hosts. HfMV1 sequences from H. albidus showed a higher nucleotide diversity and a higher number of mutations compared to those from H. fraxineus, probably due to a bottleneck caused by the introduction of H. fraxineus in Europe. Our data also points to multiple interspecific virus transfers from H. albidus to H. fraxineus, which could have contributed to the intraspecific virus diversity found in H. fraxineus.

Forest Carbon Sequestration, Pathogens and the Costs of the EU’s 2050 Climate Targets

Carbon sequestration is suggested as a low-cost option for climate change mitigation, the functioning of which can be threatened by pathogen infestation. This study calculates the effects of infectious pathogens on the cost of achieving the EU’s 2050 climate targets by combining the so-called production function method with the replacement cost method. Pathogens are then assumed to affect carbon sink enhancement through the impact on productivity of forest land, and carbon sequestration is valued as the replacement for costly reductions in emissions from fossil fuels for reaching the EU’s 2050 climate targets. To this end, we have constructed a numerical dynamic optimization model with a logistic forest growth function, a simple allometric representation of the spread of pathogens in forests, and reductions in emissions from fossil fuels. The results show that the annual value of forest carbon sequestration ranges between approximately 6.4 and 14.9 billion Euros, depending on the impact and dispersal of pathogens. Relatively large values are obtained for countries with large emissions from fossil fuels, e.g., Germany, France, Spain and Italy, which also face costs of pathogen together with countries with large forest area, such as Romania.

Mitonuclear interactions may contribute to fitness of fungal hybrids

Hybridization between species is being recognized as a major force in the rapid adaptive evolution of fungal plant pathogens. The first stages of interspecific hybridization necessarily involve nuclear-mitochondrial chimeras. In their 2001 publication, Olson and Stenlid reported that mitochondria control the virulence of first generation hybrids between the North American fungal pathogen Heterobasidion irregulare and its congeneric H. occidentale. By assessing saprobic ability and gene expression of H. irregulare × H. annosum sensu stricto hybrids and of their parental genotypes, we demonstrate that mitochondria also influence saprobic growth of hybrids. Moreover, gene expression data suggest that fungal fitness is modulated by an intimate interplay between nuclear genes and mitochondrial type, and is dependent on the specific mitonuclear combination.

Genetic signatures of variation in population size in a native fungal pathogen after the recent massive plantation of its host tree

Historical fluctuations in forests' distribution driven by past climate changes and anthropogenic activities can have large impacts on the demographic history of pathogens that have a long co-evolution history with these host trees. Using a population genetic approach, we investigated that hypothesis by reconstructing the demographic history of Armillaria ostoyae, one of the major pathogens of the maritime pine (Pinus pinaster), in the largest monospecific pine planted forest in Europe (south-western France). Genetic structure analyses and approximate Bayesian computation approaches revealed that a single pathogen population underwent a severe reduction in effective size (12 times lower) 1080-2080 generations ago, followed by an expansion (4 times higher) during the last 4 generations. These results are consistent with the history of the maritime pine forest in the region characterized by a strong recession during the last glaciation (~19 000 years ago) and massive plantations during the second half of the nineteenth century. Results suggest that recent and intensive plantations of a host tree population have offered the opportunity for a rapid spread and adaptation of their pathogens.

A nonnative and a native fungal plant pathogen similarly stimulate ectomycorrhizal development but are perceived differently by a fungal symbiont

The effects of plant symbionts on host defence responses against pathogens have been extensively documented, but little is known about the impact of pathogens on the symbiosis and if such an impact may differ for nonnative and native pathogens. Here, this issue was addressed in a study of the model system comprising Pinus pinea, its ectomycorrhizal symbiont Tuber borchii, and the nonnative and native pathogens Heterobasidion irregulare and Heterobasidion annosum, respectively. In a 6-month inoculation experiment and using both in planta and gene expression analyses, we tested the hypothesis that H. irregulare has greater effects on the symbiosis than H. annosum. Although the two pathogens induced the same morphological reaction in the plant-symbiont complex, with mycorrhizal density increasing exponentially with pathogen colonization of the host, the number of target genes regulated in T. borchii in plants inoculated with the native pathogen (i.e. 67% of tested genes) was more than twice that in plants inoculated with the nonnative pathogen (i.e. 27% of genes). Although the two fungal pathogens did not differentially affect the amount of ectomycorrhizas, the fungal symbiont perceived their presence differently. The results may suggest that the symbiont has the ability to recognize a self/native and a nonself/nonnative pathogen, probably through host plant-mediated signal transduction.

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.

Comparative Genomics of Sibling Fungal Pathogenic Taxa Identifies Adaptive Evolution without Divergence in Pathogenicity Genes or Genomic Structure

It has been estimated that the sister plant pathogenic fungal species Heterobasidion irregulare and Heterobasidion annosum may have been allopatrically isolated for 34-41 Myr. They are now sympatric due to the introduction of the first species from North America into Italy, where they freely hybridize. We used a comparative genomic approach to 1) confirm that the two species are distinct at the genomic level; 2) determine which gene groups have diverged the most and the least between species; 3) show that their overall genomic structures are similar, as predicted by the viability of hybrids, and identify genomic regions that instead are incongruent; and 4) test the previously formulated hypothesis that genes involved in pathogenicity may be less divergent between the two species than genes involved in saprobic decay and sporulation. Results based on the sequencing of three genomes per species identified a high level of interspecific similarity, but clearly confirmed the status of the two as distinct taxa. Genes involved in pathogenicity were more conserved between species than genes involved in saprobic growth and sporulation, corroborating at the genomic level that invasiveness may be determined by the two latter traits, as documented by field and inoculation studies. Additionally, the majority of genes under positive selection and the majority of genes bearing interspecific structural variations were involved either in transcriptional or in mitochondrial functions. This study provides genomic-level evidence that invasiveness of pathogenic microbes can be attained without the high levels of pathogenicity presumed to exist for pathogens challenging naïve hosts.

Taxonomy, biogeography and importance of Heterobasidion viruses

The genus Heterobasidion consists of several species of necrotrophic and saprotrophic fungi, and includes some of the most detrimental organisms in boreal conifer forests. These fungi host a widespread and diverse mycovirus community composed of more than 16 species of Partitiviridae, a species of Narnaviridae and one taxonomically unassigned virus related to the Curvularia thermal tolerance virus. These viruses are able to cross species borders, co-infect single host strains and cause phenotypic changes in their hosts. The abundance of viruses increases over time in Heterobasidion infection centers, and they are targeted by fungal RNA interference. Long-term field studies are essential for obtaining a comprehensive view of virus effects in the nature.

Early physiological responses of Pinus pinea L. seedlings infected by Heterobasidion sp.pl. in an ozone-enriched atmospheric environment

The presence of the American root-rot disease fungus Heterobasidion irregulare Garbel. & Otrosina was detected in Italian coastal pine forests (Pinus pinea L.) in addition to the common native species Heterobasidion annosum (Fries) Brefeld. High levels of tropospheric ozone (O3) as an atmospheric pollutant are usually experienced in Mediterranean pine forests. To explore the effect of interaction between the two Heterobasidion species and ozone pollution on P. pinea, an open-top chamber (OTC) experiment was carried out. Five-year-old P. pinea seedlings were inoculated with the fungal species considered (H. irregulare, H. annosum and mock-inoculation as control), and then exposed in charcoal-filtered open-top chambers (CF-OTC) and non-filtered ozone-enriched chambers (NF+) from July to the first week of August 2010 at the experimental facilities of Curno (North Italy). Fungal inoculation effects in an ozone-enriched environment were assessed as: (i) the length of the inoculation lesion; (ii) chlorophyll a fluorescence (ChlF) responses; and (iii) analysis of resin terpenes. Results showed no differences on lesion length between fungal and ozone treatments, whereas the short-term effects of the two stress factors on ChlF indicate an increased photosynthetic efficiency, thus suggesting the triggering of compensation/repair processes. The total amount of resin terpenes is enhanced by fungal infection of both species, but depressed by ozone to the levels observed in mock-inoculated plants. Variations in terpene profiles were also induced by stem base inoculations and ozone treatment. Ozone might negatively affect terpene defences making plants more susceptible to pathogens and insects.

Speciation in fungal and oomycete plant pathogens

The process of speciation, by definition, involves evolution of one or more reproductive isolating mechanisms that split a single species into two that can no longer interbreed. Determination of which processes are responsible for speciation is important yet challenging. Several studies have proposed that speciation in pathogens is heavily influenced by host-pathogen dynamics and that traits that mediate such interactions (e.g., host mobility, reproductive mode of the pathogen, complexity of the life cycle, and host specificity) must lead to reproductive isolation and ultimately affect speciation rates. In this review, we summarize the main evolutionary processes that lead to speciation of fungal and oomycete plant pathogens and provide an outline of how speciation can be studied rigorously, including novel genetic/genomic developments.

Mating type locus of Chinese black truffles reveals heterothallism and the presence of cryptic species within the T. indicum species complex

Tuber spp. are filamentous ascomycetes which establish symbiosis with the roots of trees and shrub species. By virtue of this symbiosis they produce hypogeous ascocarps, known as truffles. Filamentous ascomycetes can reproduce by homothallism or heterothallism depending on the structure and organization of their mating type locus. The first mating type locus in a truffle species has been recently characterized in Tuber melanosporum and it has been shown that this fungus, endemic in Europe, is heterothallic. The availability of sequence information for T. melanosporum mating type genes is seminal to cloning their orthologs from other Tuber species and assessing their reproductive mode. Here we report on the organization of the mating type region in T. indicum, the black truffle species present in Asia, which is the closest relative to T. melanosporum and is characterized by an high level of morphological and genetic variability. The present study shows that T. indicum is also heterothallic. Examination of Asiatic black truffles belonging to different genetic classes, sorted according to the sequence polymorphism of the internal transcribed spacer rDNA region, has revealed sequence variations and rearrangements in both coding and non-coding regions of the mating type locus, to suggest the existence of cryptic species within the T. indicum complex. The presence of transposable elements within or linked to the mating type region suggests a role of these elements in generating the genotypic diversity present among T. indicum strains. Overall, comparative analyses of the mating type locus have thus allowed us to tackle taxonomical and phylogenetic issues within black truffles and make inferences about the evolution of T. melanosporum-T. indicum lineage. Our results are not only of fundamental but also of applied relevance as T. indicum produces edible fruit bodies that are imported also into Europe and thus may represent a biological threat for T. melanosporum.

Rapid detection of Ceratocystis platani inoculum by quantitative real-time PCR assay

Ceratocystis platani is the causal agent of canker stain of plane trees, a lethal disease able to kill mature trees in one or two successive growing seasons. The pathogen is a quarantine organism and has a negative impact on anthropogenic and natural populations of plane trees. Contaminated sawdust produced during pruning and sanitation fellings can contribute to disease spread. The goal of this study was to design a rapid, real-time quantitative PCR assay to detect a C. platani airborne inoculum. Airborne inoculum traps (AITs) were placed in an urban setting in the city of Florence, Italy, where the disease was present. Primers and TaqMan minor groove binder (MGB) probes were designed to target cerato-platanin (CP) and internal transcribed spacer 2 (ITS2) genes. The detection limits of the assay were 0.05 pg/μl and 2 fg/μl of fungal DNA for CP and ITS, respectively. Pathogen detection directly from AITs demonstrated specificity and high sensitivity for C. platani, detecting DNA concentrations as low as 1.2 × 10(-2) to 1.4 × 10(-2) pg/μl, corresponding to ∼10 conidia per ml. Airborne inoculum traps were able to detect the C. platani inoculum within 200 m of the closest symptomatic infected plane tree. The combination of airborne trapping and real-time quantitative PCR assay provides a rapid and sensitive method for the specific detection of a C. platani inoculum. This technique may be used to identify the period of highest risk of pathogen spread in a site, thus helping disease management.

Population genetic analyses provide insights on the introduction pathway and spread patterns of the North American forest pathogen Heterobasidion irregulare in Italy

A population genetics approach is used to identify the most likely introduction site and introduction pathway for the North American forest pathogen Heterobasidion irregulare using 101 isolates from six sites in Italy and 34 isolates from five sites in North America. Diversity indices based on sequences from ten loci indicate the highest diversity in Italy is found in Castelfusano/Castelporziano and that diversity progressively decreases with increasing distance from that site. AMOVA, Bayesian clustering and principal coordinates analyses based on 12 SSR loci indicate high levels of gene flow among sites, high frequency of admixing, and fail to identify groups of genotypes exclusive to single locations. Cumulatively, these analyses suggest the current infestation is the result of multiple genotypes expanding their range from a single site. Based on two sequenced loci, a single source site in North America could provide enough variability to explain the variability observed in Italy. These results support the notion that H. irregulare was introduced originally in Castelporziano: because Castelporziano has been sealed off from the rest of the world for centuries except for a camp set up by the US military in 1944, we conclude the fungus may have been transported in infected wood used by the military. Finally, spatial autocorrelation analyses using SSR data indicate a significant under-dispersion of alleles up to 0.5-10 km, while a significant overdispersion of alleles was detected at distances over 80 km: these ranges can be used to make predictions on the likely dispersal potential of the invasive pathogen.

History of the invasion of the anther smut pathogen on Silene latifolia in North America

Understanding the routes of pathogen introduction contributes greatly to efforts to protect against future disease emergence. Here, we investigated the history of the invasion in North America by the fungal pathogen Microbotryum lychnidis-dioicae, which causes the anther smut disease on the white campion Silene latifolia. This system is a well-studied model in evolutionary biology and ecology of infectious disease in natural systems. Analyses based on microsatellite markers show that the introduced American M. lychnidis-dioicae probably came from Scotland, from a single population, and thus suffered from a drastic bottleneck compared with genetic diversity in the native European range. The pattern in M. lychnidis-dioicae contrasts with that found by previous studies in its host plant species S. latifolia, also introduced in North America. In the plant, several European lineages have been introduced from across Europe. The smaller number of introductions for M. lychnidis-dioicae probably relates to its life history traits, as it is an obligate, specialized pathogen that is neither transmitted by the seeds nor persistent in the environment. The results show that even a nonagricultural, biotrophic, and insect-vectored pathogen suffering from a very strong bottleneck can successfully establish populations on its introduced host.

Molecular characterization of HetRV8-ir1, a partitivirus of the invasive conifer pathogenic fungus Heterobasidion irregulare

The Heterobasidion annosum (Fr.) Bref. complex includes some of the most destructive conifer pathogenic fungi in the Boreal forest region. H. irregulare, formerly known as the North American pine type of H. annosum, was introduced from North America into Italy during the Second World War and occurs as an invasive pathogen in Pinus pinea stands together with the native European species H. annosum sensu stricto. We describe the complete nucleotide sequence of a new putative partitivirus from an Italian strain of H. irregulare. The bisegmented genome of HetRV8-ir1 encodes an RNA-dependent RNA polymerase of 704 aa and a capsid protein of 638 aa. The polymerase and capsid aa sequences are relatively similar (59-78 %) to those of Fusarium poae virus 1, Pleurotus ostreatus virus 1, and grapevine-associated partitivirus 1. HetRV8-ir1 is the first virus described from H. irregulare, and it is distantly related to previously known partitiviruses of Heterobasidion species.

Biology, epidemiology, and control of Heterobasidion species worldwide

Heterobasidion annosum sensu lato is a species complex comprising five species that are widely distributed in coniferous forests of the Northern Hemisphere and are each characterized by a distinct host preference. More than 1,700 papers have been published on these fungi in the past four decades, making them perhaps the most widely studied forest fungi. Heterobasidion species are at different levels on the saprotroph-necrotroph gradient, and the same individual can switch from one mode to the other. This offers a unique opportunity to study how genomic structure, gene expression, and genetic trade-offs may all interact with environmental factors to determine the life mode of the organism. The abilities of Heterobasidion spp. to infect stumps as saprotrophs and to spread to neighboring trees as pathogens have resulted in significant damages to timber production in managed forests. This review focuses on the current knowledge of the biology, ecology, evolution, and management of these species and is based on classical and modern studies.

The American forest pathogen Heterobasidion irregulare colonizes unexpected habitats after its introduction in Italy

Habitat preference of an invasive fungal tree pathogen is here compared with that of a sympatric and native closely related congener to test the hypothesis that the invasive ability of the exotic organism may be linked to its capacity to colonize substrates unavailable to the indigenous relative. We compared the distribution of infectious airspora of the North American Heterobasidion irregulare introduced into Italy with that of the native H. annosum, both regarded to be able to establish only in the presence of conifers. Geostatistical and statistical analyses were employed to test for association between both species and five Mediterranean vegetation types. Results show that H. annosum is positively associated with pines and negatively associated with deciduous oaks. The probability of finding its spores decreases to almost 0 at distances over 500 m from pines, and this species is virtually absent in pure oak forests. Spores of H. irregulare are present irrespective of vegetation type, and this species can be found not only where pines are present, but also in pure oak forests. This knowledge implies that spread of H. irregulare is not limited by the fragmented distribution of pine woodlands in central Italy and is essential to both predict and hinder its progress in Europe.

Genome wide AFLP markers support cryptic species in Coniophora (Boletales)

Numerous fungal morphospecies include cryptic species that routinely are detected by sequencing a few unlinked DNA loci. However, whether the patterns observed by multi-locus sequencing are compatible with genome wide data, such as amplified fragment length polymorphisms (AFLPs), is not well known for fungi. In this study we compared the ability of three DNA loci and AFLP data to discern between cryptic fungal lineages in the three morphospecies Coniophora olivacea, Coniophora arida, and Coniophora puteana. The sequences and the AFLP data were highly congruent in delimiting the morphotaxa into multiple cryptic species. However, while the DNA sequences indicated introgression or hybridization between some of the cryptic lineages the AFLP data did not. We conclude that as few as three polymorphic DNA loci was sufficient to recognize cryptic lineages within the studied Coniophora taxa. However, based on analyses of a few (three) sequenced loci the hybridization could not easily be distinguished from incomplete lineage sorting. Hence, great caution should be taken when concluding about hybridization based on data from just a few loci.

Emergence of the sudden oak death pathogen Phytophthora ramorum

The recently emerged plant pathogen Phytophthora ramorum is responsible for causing the sudden oak death epidemic. This review documents the emergence of P. ramorum based on evolutionary and population genetic analyses. Currently infection by P. ramorum occurs only in Europe and North America and three clonal lineages are distinguished: EU1, NA1 and NA2. Ancient divergence of these lineages supports a scenario in which P. ramorum originated from reproductively isolated populations and underwent at least four global migration events. This recent work sheds new light on mechanisms of emergence of exotic pathogens and provides crucial insights into migration pathways.

Sequence and simple-sequence repeat analyses of the fungal pathogen Seiridium cardinale indicate California is the most likely source of the cypress canker epidemic for the Mediterranean region

Seiridium cardinale is the pathogenic fungus of unknown origin responsible for a world pandemic known as cypress canker affecting several species of Cupressaceae in both the Northern and Southern Hemisphere. In this study, a comparative genetic analysis of worldwide populations was performed using sequence analysis of a portion of the ?-tubulin locus and seven polymorphic simple-sequence repeat (SSR) loci on 96 isolates. Sequence analysis identified two distinct ?-tubulin alleles, both present in California. Only one of the two alleles was detected in the Mediterranean basin, while two isolates from the Southern Hemisphere were characterized by the presence of the allele absent from the Mediterranean. SSRs identified a total of 46 multilocus genotypes (MGs): genotypic diversity was always higher in the California population, and calculations of the index of association (I(A)) determined the presence of linkage disequilibrium associated with the absence of sexual reproduction only in the Mediterranean population but not in California. In 50 instances, the same MG was found at great geographic distances, implying a role played by humans in spreading the disease. Network analysis performed on SSR data identified three clusters of MGs: California, Morocco, and the rest of the Mediterranean. Both the Morocco and the Mediterranean clusters were linked to the California cluster. Coalescent analysis identified insignificant migration between California and Italy, as expected in the presence of a single introduction event, and very high migration from Italy into Greece, as expected of an outbreak still in exponential growth phase and starting from an Italian source.

The plant pathogen Phytophthora andina emerged via hybridization of an unknown Phytophthora species and the Irish potato famine pathogen, P. infestans

Emerging plant pathogens have largely been a consequence of the movement of pathogens to new geographic regions. Another documented mechanism for the emergence of plant pathogens is hybridization between individuals of different species or subspecies, which may allow rapid evolution and adaptation to new hosts or environments. Hybrid plant pathogens have traditionally been difficult to detect or confirm, but the increasing ease of cloning and sequencing PCR products now makes the identification of species that consistently have genes or alleles with phylogenetically divergent origins relatively straightforward. We investigated the genetic origin of Phytophthora andina, an increasingly common pathogen of Andean crops Solanum betaceum, S. muricatum, S. quitoense, and several wild Solanum spp. It has been hypothesized that P. andina is a hybrid between the potato late blight pathogen P. infestans and another Phytophthora species. We tested this hypothesis by cloning four nuclear loci to obtain haplotypes and using these loci to infer the phylogenetic relationships of P. andina to P. infestans and other related species. Sequencing of cloned PCR products in every case revealed two distinct haplotypes for each locus in P. andina, such that each isolate had one allele derived from a P. infestans parent and a second divergent allele derived from an unknown species that is closely related but distinct from P. infestans, P. mirabilis, and P. ipomoeae. To the best of our knowledge, the unknown parent has not yet been collected. We also observed sequence polymorphism among P. andina isolates at three of the four loci, many of which segregate between previously described P. andina clonal lineages. These results provide strong support that P. andina emerged via hybridization between P. infestans and another unknown Phytophthora species also belonging to Phytophthora clade 1c.