Lecanosticta acicola: A growing threat to expanding global pine forests and plantations

Genomics of the expanding pine pathogen Lecanosticta acicola reveals patterns of ongoing genetic admixture

Lecanosticta acicola is the causal agent for brown spot needle blight that affects pine trees across the northern hemisphere. Based on marker genes and microsatellite data, two distinct lineages have been identified that were introduced into Europe on two separate occasions. Despite their overall distinct geographic distribution, they have been found to coexist in regions of northern Spain and France. Here, we present the first genome-wide study of Lecanosticta acicola, including assembly of the reference genome and a population genomics analysis of 70 natural isolates from northern Spain. We show that most of the isolates belong to the southern lineage but show signs of introgression with northern lineage isolates, indicating mating between the two lineages. We also identify phenotypic differences between the two lineages based on the activity profiles of 20 enzymes, with introgressed strains being more phenotypically similar to members of the southern lineage. In conclusion, we show undergoing genetic admixture between the two main lineages of L. acicola in a region of recent expansion.

IMPORTANCE

Lecanosticta acicola is a fungal pathogen causing severe defoliation, growth reduction, and even death in more than 70 conifer species. Despite the increasing incidence of this species, little is known about its population dynamics. Two divergent lineages have been described that have now been found together in regions of France and Spain, but it is unknown how these mixed populations evolve. Here we present the first reference genome for this important plant pathogenic fungi and use it to study the population genomics of 70 isolates from an affected forest in the north of Spain. We find signs of introgression between the two main lineages, indicating that active mating is occurring in this region which could propitiate the appearance of novel traits in this species. We also study the phenotypic differences across this population based on enzymatic activities on 20 compounds.

Physiological, metabolic and hormonal responses of two Pinus spp. with contrasting susceptibility to brown-spot needle blight disease

Needle blights are serious fungal diseases affecting European natural and planted pine forests. Brown-spot needle blight (BSNB) disease, caused by the fungus Lecanosticta acicola, causes canopy defoliation and severe productivity losses, with consequences depending on host susceptibility. To gain new insights into BSNB plant-pathogen interactions, constitutive and pathogen-induced traits were assessed in two host species with differential disease susceptibility. Six-month-old Pinus radiata D. Don (susceptible) and Pinus pinea L. (more resistant) seedlings were needle inoculated with L. acicola under controlled conditions. Eighty days after inoculation, healthy-looking needles from symptomatic plants were assessed for physiological parameters and sampled for biochemical analysis. Disease progression, plant growth, leaf gas-exchanges and biochemical parameters were complemented with hormonal and untargeted primary metabolism analysis and integrated for a holistic analysis. Constitutive differences between pine species were observed. Pinus pinea presented higher stomatal conductance and transpiration rate and higher amino and organic acids, abscisic acid as well as putrescine content than P. radiata. Symptoms from BSNB disease were observed in 54.54% of P. radiata and 45.45% of P. pinea seedlings, being more pronounced and generalized in P. radiata. For both species, plant height, sub-stomatal CO2 concentration and water-use efficiency were impacted by infection. In P. radiata, total soluble sugars, starch and total flavonoids content increased after infection. No differences in hormone content after infection were observed. However, secondary metabolism was induced in P. pinea visible through total phenolics, flavonoids and putrescine accumulation. Overall, the observed results suggest that P. pinea constitutive and induced traits may function as two layers of a defence strategy which contributed to an increased BSNB resistance in comparison with P. radiata. This is the first integrative study linking plant physiological and molecular traits in Pinus-Lecanosticta acicola pathosystem, contributing to a better understanding of the underlying resistance mechanisms to BSNB disease in pines.

Genetic Diversity of Lecanosticta acicola in Pinus Ecosystems in Northern Spain

Lecanosticta acicola is one of the most damaging species affecting Pinus radiata plantations in Spain. Favourable climatic conditions and unknown endogenous factors of the pathogen and host led to a situation of high incidence and severity of the disease in these ecosystems. With the main aim of understanding the factors intrinsic to this pathogenic species, a study of the population structure in new established plantations with respect to older plantations was implemented. The genetic diversity, population structure and the ability of the pathogen to spread was determined in Northern Spain (Basque Country), where two thirds of the total Pinus radiata plantations of Spain are located. From a total of 153 Lecanosticta acicola isolates analysed, two lineages were present; the southern lineage, which was prevalent, and the northern lineage, which was scarce. A total of 22 multilocus genotypes were detected with a balanced composition of both mating types and evidence for sexual reproduction. In addition to the changing environmental conditions enhancing disease expression, the complexity and diversity of the pathogen will make it difficult to control and to maintain the wood productive system fundamentally based on this forest species.

The increasing threat to European forests from the invasive foliar pine pathogen, Lecanosticta acicola

European forests are threatened by increasing numbers of invasive pests and pathogens. Over the past century, Lecanosticta acicola, a foliar pathogen predominantly of Pinus spp., has expanded its range globally, and is increasing in impact. Lecanosticta acicola causes brown spot needle blight, resulting in premature defoliation, reduced growth, and mortality in some hosts. Originating from southern regions of North American, it devastated forests in the USA's southern states in the early twentieth century, and in 1942 was discovered in Spain. Derived from Euphresco project 'Brownspotrisk,' this study aimed to establish the current distribution of Lecanosticta species, and assess the risks of L. acicola to European forests. Pathogen reports from the literature, and new/ unpublished survey data were combined into an open-access geo-database (http://www.portalofforestpathology.com), and used to visualise the pathogen's range, infer its climatic tolerance, and update its host range. Lecanosticta species have now been recorded in 44 countries, mostly in the northern hemisphere. The type species, L. acicola, has increased its range in recent years, and is present in 24 out of the 26 European countries where data were available. Other species of Lecanosticta are largely restricted to Mexico and Central America, and recently Colombia. The geo-database records demonstrate that L. acicola tolerates a wide range of climates across the northern hemisphere, and indicate its potential to colonise Pinus spp. forests across large swathes of the Europe. Preliminary analyses suggest L. acicola could affect 62% of global Pinus species area by the end of this century, under climate change predictions. Although its host range appears slightly narrower than the similar Dothistroma species, Lecanosticta species were recorded on 70 host taxa, mostly Pinus spp., but including, Cedrus and Picea spp. Twenty-three, including species of critical ecological, environmental and economic significance in Europe, are highly susceptible to L. acicola, suffering heavy defoliation and sometimes mortality. Variation in apparent susceptibility between reports could reflect variation between regions in the hosts' genetic make-up, but could also reflect the significant variation in L. acicola populations and lineages found across Europe. This study served to highlight significant gaps in our understanding of the pathogen's behaviour. Lecanosticta acicola has recently been downgraded from an A1 quarantine pest to a regulated non quarantine pathogen, and is now widely distributed across Europe. With a need to consider disease management, this study also explored global BSNB strategies, and used Case Studies to summarise the tactics employed to date in Europe.

Population structure and diversity of the needle pathogen Dothistroma pini suggests human-mediated movement in Europe

Dothistroma needle blight (DNB) is an important disease of Pinus species that can be caused by one of two distinct but closely related pathogens; Dothistroma septosporum and Dothistroma pini. Dothistroma septosporum has a wide geographic distribution and is relatively well-known. In contrast, D. pini is known only from the United States and Europe, and there is a distinct lack of knowledge regarding its population structure and genetic diversity. The recent development of 16 microsatellite markers for D. pini provided an opportunity to investigate the diversity, structure, and mode of reproduction for populations collected over a period of 12 years, on eight different hosts in Europe. In total, 345 isolates from Belgium, the Czech Republic, France, Hungary, Romania, Western Russia, Serbia, Slovakia, Slovenia, Spain, Switzerland, and Ukraine were screened using microsatellite and species-specific mating type markers. A total of 109 unique multilocus haplotypes were identified and structure analyses suggested that the populations are influenced by location rather than host species. Populations from France and Spain displayed the highest levels of genetic diversity followed by the population in Ukraine. Both mating types were detected in most countries, with the exception of Hungary, Russia and Slovenia. Evidence for sexual recombination was supported only in the population from Spain. The observed population structure and several shared haplotypes between non-bordering countries provides good evidence that the movement of D. pini in Europe has been strongly influenced by human activity in Europe.

Diversity, migration routes, and worldwide population genetic structure of Lecanosticta acicola, the causal agent of brown spot needle blight

Lecanosticta acicola is a pine needle pathogen causing brown spot needle blight that results in premature needle shedding with considerable damage described in North America, Europe, and Asia. Microsatellite and mating type markers were used to study the population genetics, migration history, and reproduction mode of the pathogen, based on a collection of 650 isolates from 27 countries and 26 hosts across the range of L. acicola. The presence of L. acicola in Georgia was confirmed in this study. Migration analyses indicate there have been several introduction events from North America into Europe. However, some of the source populations still appear to remain unknown. The populations in Croatia and western Asia appear to originate from genetically similar populations in North America. Intercontinental movement of the pathogen was reflected in an identical haplotype occurring on two continents, in North America (Canada) and Europe (Germany). Several shared haplotypes between European populations further suggests more local pathogen movement between countries. Moreover, migration analyses indicate that the populations in northern Europe originate from more established populations in central Europe. Overall, the highest genetic diversity was observed in south-eastern USA. In Europe, the highest diversity was observed in France, where the presence of both known pathogen lineages was recorded. Less than half of the observed populations contained mating types in equal proportions. Although there is evidence of some sexual reproduction taking place, the pathogen spreads predominantly asexually and through anthropogenic activity.

Microbial community structure and niche differentiation under different health statuses of Pinus bungeana in the Xiong'an New Area in China

Pinus bungeana is a native but endangered plant species in China, with high ornamental value and adaptability to drought and cold. The relationship between the soil community structure and endophytic microbes in the tissues of P. bungeana under different health statuses is poorly understood. In this study, the endophytic bacterial and fungal communities of P. bungeana under different health statuses were compared and analyzed in the Xiong'an New Area. Using high-throughput deep sequencing [16S and internal transcribed spacer (ITS) rRNA] techniques, the effect of the health status of P. bungeana on the microbial communities in bulk soil, rhizospheric soil, roots, stems, and leaves was determined in this study. We observed that the diversity of the bacterial and fungal communities of the aboveground parts (stems and leaves) of healthy P. bungeana plants was much higher than that of the unhealthy plants. However, the diversity of bacterial and fungal communities in the belowground parts (bulk soil, rhizospheric soil, and roots) showed almost no difference in microbial community richness, indicating that the possible cause of illness was transmitted in a "top-down" manner. Furthermore, there were significant differences in the microbial diversity and community structure in different ecological niches of P. bungeana (P < 0.01). Proteobacteria and Actinobacteria were the dominant bacterial phyla, while Ascomycota, Basidiomycota, and Mortierellomycota were the predominant fungal phyla. Redundancy analysis (RDA) revealed that soil organic matter (SOM), total phosphorous (TP), total potassium (TK), total nitrogen (TN), water content (WC), power of hydrogen (pH), total carbon (TC), and the ratio of carbon to nitrogen (C/N) were significantly correlated with the composition of the microbial communities. Altogether, these results provide a scientific basis for further studies on the mechanism underlying the "aboveground-underground" microbial interactions in plantation forests, which can aid in promoting the healthy and sustainable development of the Millennium Xiulin forest in the Xiong'an New Area.

Lecanosticta pharomachri and Its Newly Discovered Sexual State Causing a Serious Needle Disease of Pinus spp. in Colombia

Brown spot needle blight (BSNB), caused by the fungal pathogen Lecanosticta acicola, is a well-known disease of Pinus spp. in several northern hemisphere countries. In the southern hemisphere, this disease has been reported only in Colombia and, apart from a single report of severe defoliation of Pinus radiata plantations in the early 1980s, has not caused serious damage in this country. An outbreak of a disease resembling BSNB on Mesoamerican Pinus spp. grown in Colombia has raised concern that L. acicola may have reemerged as a pathogen. DNA sequence-based analyses for the internal transcribed spacers, translation elongation factor 1-α and RNA polymerase II second largest subunit regions showed that the outbreaks were caused by L. pharomachri, a species distinct from, but closely related to, L. acicola. The discovery of L. pharomachri in Colombia is the first incidence of the pathogen causing a serious disease problem and the first occurrence on the hosts P. patula and P. maximinoi. A sexual state for L. pharomachri was discovered for the first time, and the description of the species has thus been emended.

Weather Variables Associated with Spore Dispersal of Lecanosticta acicola Causing Pine Needle Blight in Northern Spain

In the last decade, the impact of needle blight fungal pathogens on the health status of forests in northern Spain has marked a turning point in forest production systems based on Pinus radiata species. Dothistroma needle blight caused by Dothistroma septosporum and D. pini, and brown spot needle blight caused by Lecanosticta acicola, coexist in these ecosystems. There is a clear dominance of L. acicola with respect to the other two pathogens and evidence of sexual reproduction in the area. Understanding L. acicola spore dispersal dynamics within climatic determinants is necessary to establish more efficient management strategies to increase the sustainability of forest ecosystems. In this study, spore counts of 15 spore traps placed in Pinus ecosystems were recorded in 2019 and spore abundance dependency on weather data was analysed using generalised additive models. During the collection period, the model that best fit the number of trapped spores included the daily maximum temperature and daily cumulative precipitation, which was associated to higher spore counts. The presence of conidia was detected from January and maximum peaks of spore dispersal were generally observed from September to November.

Fungi of quarantine concern for China I: Dothideomycetes

The current list of Chinese quarantine pests includes 130 fungal species. However, recent changes in the taxonomy of fungi following the one fungus = one name initiative and the implementation of DNA phylogeny in taxonomic revisions, resulted in many changes of these species names, necessitating an update of the current list. In addition, many quarantine fungi lack modern morphological descriptions and authentic DNA sequences, posing significant challenges for the development of diagnostic protocols. The aim of the present study was to review the taxonomy and names of the 33 Chinese quarantine fungi in Dothideomycetes, and provide reliable DNA barcodes to facilitate rapid identification. Of these, 23 names were updated according to the single name nomenclature system, including one new combination, namely Cophinforma tumefaciens comb. nov. (syn. Sphaeropsis tumefaciens). On the basis of phylogenetic analyses and morphological comparisons, a new genus Xenosphaeropsis is introduced to accommodate the monotypic species Xenosphaeropsis pyriputrescens comb. nov. (syn. Sphaeropsis pyriputrescens), the causal agent of a post-harvest disease of pears. Furthermore, four lectotypes (Ascochyta petroselini, Mycosphaerella ligulicola, Physalospora laricina, Sphaeria lingam), three epitypes (Ascochyta petroselini, Phoma lycopersici, Sphaeria lingam), and two neotypes (Ascochyta pinodella, Deuterophoma tracheiphila) are designated to stabilise the use of these names. A further four reference strains are introduced for Cophinforma tumefaciens, Helminthosporium solani, Mycocentrospora acerina, and Septoria linicola. In addition, to assist future studies on these important pathogens, we sequenced and assembled whole genomes for 17 species, including Alternaria triticina, Boeremia foveata, B. lycopersici, Cladosporium cucumerinum, Didymella glomerata, Didymella pinodella, Diplodia mutila, Helminthosporium solani, Mycocentrospora acerina, Neofusicoccum laricinum, Parastagonospora pseudonodorum, Plenodomus libanotidis, Plenodomus lingam, Plenodomus tracheiphilus, Septoria petroselini, Stagonosporopsis chrysanthemi, and Xenosphaeropsis pyriputrescens. Citation: Zhao P, Crous PW, Hou LW, et al. 2021. Fungi of quarantine concern for China I: Dothideomycetes. Persoonia 47: 45-105. https://doi.org/10.3767/persoonia.2021.47.02.

Fungi of quarantine concern for China I: Dothideomycetes

The current list of Chinese quarantine pests includes 130 fungal species. However, recent changes in the taxonomy of fungi following the one fungus = one name initiative and the implementation of DNA phylogeny in taxonomic revisions, resulted in many changes of these species names, necessitating an update of the current list. In addition, many quarantine fungi lack modern morphological descriptions and authentic DNA sequences, posing significant challenges for the development of diagnostic protocols. The aim of the present study was to review the taxonomy and names of the 33 Chinese quarantine fungi in Dothideomycetes, and provide reliable DNA barcodes to facilitate rapid identification. Of these, 23 names were updated according to the single name nomenclature system, including one new combination, namely Cophinforma tumefaciens comb. nov. (syn. Sphaeropsis tumefaciens). On the basis of phylogenetic analyses and morphological comparisons, a new genus Xenosphaeropsis is introduced to accommodate the monotypic species Xenosphaeropsis pyriputrescens comb. nov. (syn. Sphaeropsis pyriputrescens), the causal agent of a post-harvest disease of pears. Furthermore, four lectotypes (Ascochyta petroselini, Mycosphaerella ligulicola, Physalospora laricina, Sphaeria lingam), three epitypes (Ascochyta petroselini, Phoma lycopersici, Sphaeria lingam), and two neotypes (Ascochyta pinodella, Deuterophoma tracheiphila) are designated to stabilise the use of these names. A further four reference strains are introduced for Cophinforma tumefaciens, Helminthosporium solani, Mycocentrospora acerina, and Septoria linicola. In addition, to assist future studies on these important pathogens, we sequenced and assembled whole genomes for 17 species, including Alternaria triticina, Boeremia foveata, B. lycopersici, Cladosporium cucumerinum, Didymella glomerata, Didymella pinodella, Diplodia mutila, Helminthosporium solani, Mycocentrospora acerina, Neofusicoccum laricinum, Parastagonospora pseudonodorum, Plenodomus libanotidis, Plenodomus lingam, Plenodomus tracheiphilus, Septoria petroselini, Stagonosporopsis chrysanthemi, and Xenosphaeropsis pyriputrescens. Citation: Zhao P, Crous PW, Hou LW, et al. 2021. Fungi of quarantine concern for China I: Dothideomycetes. Persoonia 47: 45-105. https://doi.org/10.3767/persoonia.2021.47.02.

Stratification, Scarification and Application of Phytohormones Promote Dormancy Breaking and Germination of Pelleted Scots Pine (Pinus sylvestris L.) Seeds

Seed quality is an important issue in forestry as it is an essential parameter in the production of high quality planting material. Many factors may hinder the harvesting of high quality seeds, including an insufficient number of sunny days, external conditions in temperate climate zones, and fungal pathogens affecting development of seedlings. We undertook to develop a procedure maximizing seed protection and promoting the optimum physiological development of seedlings by examination of the impact of seed pelleting (a general seed protection method) on germination rates and seedling development of Scots pine (Pinus sylvestris L.). Germination of pelleted seeds was examined in relation to substrate (water vs. soil) and LED light spectrum (white vs. red-blue). Several dormancy breaking treatments were applied: stratification/scarification, and growth regulator treatments including gibberellic acid (GA3), indole-3-acetic acid (IAA) and 1-naphthaleneacetic acid (NAA), to stimulate seed germination. Experiments included independent tests for each treatment (stratification/scarification and plant growth regulators), and combinations of both stratification/scarification and phytohormone treatments. The impacts of these treatments and various controlled germination conditions on the fluorescence of chlorophyll were analyzed using the maximum efficiency of photosystem II photochemistry parameter (Fv/Fm). In addition, chlorophyll a and b content in Scots pine seedlings germinated from pelleted seeds, were quantified using high-performance liquid chromatography (HPLC). The combined stratification/scarification and growth regulator treatment was the most effective germination promoting method for pelleted Scots pine seeds. Scots pine seeds are highly likely to be photoblastic. The best germination rate, while maintaining optimal physiological parameters, was achieved in acidic soil (pH 5.0) with white LED light.

Rapid Detection of Pine Pathogens Lecanosticta acicola, Dothistroma pini and D. septosporum on Needles by Probe-Based LAMP Assays

Needle blights are serious needle fungal diseases affecting pines both in natural and productive forests. Among needle blight agents, the ascomycetes Lecanosticta acicola, Dothistroma pini and D. septosporum are of particular concern. These pathogens need specific, fast and accurate diagnostics since they are regulated species in many countries and may require differential management measures. Due to the similarities in fungal morphology and the symptoms they elicit, these species are hard to distinguish using morphological characteristics. The symptoms can also be confused with those caused by insects or abiotic agents. DNA-based detection is therefore recommended. However, the specific PCR assays that have been produced to date for the differential diagnosis of these pathogens can be applied only in a well-furnished laboratory and the procedure takes a relatively long execution time. Surveillance and forest protection would benefit from a faster diagnostic method, such as a loop-mediated isothermal amplification (LAMP) assay, which requires less sophisticated equipment and can also be deployed directly on-site using portable devices. LAMP assays for the rapid and early detection of L. acicola, D. pini and D. septosporum were developed in this work. Species-specific LAMP primers and fluorescent assimilating probes were designed for each assay, targeting the beta tubulin (β-tub2) gene for the two Dothistroma species and the elongation factor (EF-1α) region for L. acicola. Each reaction detected its respective pathogen rapidly and with high specificity and sensitivity in DNA extracts from both pure fungal cultures and directly from infected pine needles. These qualities and the compatibility with inexpensive portable instrumentation position these LAMP assays as an effective method for routine phytosanitary control of plant material in real time, and they could profitably assist the management of L. acicola, D. pini and D. septosporum.