Infestation by Ips amitinus (Eichhoff, 1872), Its Associated Fungi, and Butt Rots in Stands of Pinus sibirica in South-Western Siberia

: In 2019, the bark beetle Ips amitinus (native to central Europe) was identified in southwestern Siberia at a distance exceeding 2500 km east of its previously known easternmost location in the European part of Russia. In Siberia, its invasive populations are characterised by high abundance and harmfulness. Here, I. amitinus accomplishes primary attacks on standing vital trees of Pinus sibirica with a lethal outcome. This invasion has already resulted in massive dieback in stands of pine over a large geographic territory. By, 2021, the invaded area was estimated to cover at least 31,200 km2 . The objectives of this study were to investigate fungi associated with/vectored by I. amitinus in its invasive area in south-western Siberia and wood decay fungi that cause root and butt rots to P. sibirica. This led to the following conclusions: (i) DNA analysis of sixty adult beetles of Ips amitinus collected from P. sibirica in south-west Siberia revealed the presence of 143 fungal taxa; (ii) species richness was significantly higher in beetles collected from dead branches than from (more recently infested) dying branches; (iii) fungal communities were >90% dominated by yeasts, among which the most common were Nakazawaea holstii, Kuraishia molischiana, and N. ambrosiae; (iv) entomopathogenic Beauveria bassiana s.l. was the most common fungus isolated from dead/mycosed beetles of I. amitinus, followed by Lophium arboricola and four Ophiostoma spp.; and (v) Heterobasidion parviporum was the most common decay fungus detected, which was causing heart rot in stems of P. sibirica

Fusarium: more than a node or a foot-shaped basal cell

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org)

Occurrence and pathogenicity of Corinectria spp. - an emerging canker disease of Abies sibirica in Central Siberia

During recent years, a new disease of Siberian fir (A. sibirica) emerged in Central Siberia, exhibiting symptoms of stem/branch deformation, cambium necrosis, and dieback of branches and twigs, the causal agent remaining unknown. The aim was to identify agent of the disease and to investigate its pathogenicity to A. sibirica and Norway spruce (Picea abies). Symptomatic tissues of fir were subjected to pure culture isolation of anticipated pathogen(s). Obtained isolates were subjected to molecular identification, phylogenetic analyses, and pathogenicity tests with A. sibirica saplings, and seeds and seedlings of A. sibirica and P. abies. The study demonstrated that, (i) most commonly isolated fungus from canker wounds of A. sibirica exhibited Acremonium-like anamorphs; (ii) phylogeny demonstrated that investigated fungi belong to genus Corinectria, but are genetically well separated from other worldwide known Corinectria spp.; (iii) one species of isolated fungi has the capacity to cause the disease and kill A. sibirica saplings and seedlings, but also seedlings of P. abies. Guidelines for future research were defined in order to generate needed information on species description, its origin and ecology, and estimation of potential risks upon the eventual invasion of the pathogen to new geographic areas, in particular of Europe

Armillaria root rot fungi host single-stranded RNA viruses

Species of Armillaria are distributed globally and include some of the most important pathogens of forest and ornamental trees. Some of them form large long-living clones that are considered as one of the largest organisms on earth and are capable of long-range spore-mediated transfer as well as vegetative spread by drought-resistant hyphal cords called rhizomorphs. However, the virus community infecting these species has remained unknown. In this study we used dsRNA screening and high-throughput sequencing to search for possible virus infections in a collection of Armillaria isolates representing three diferent species: Armillaria mellea from South Africa, A. borealis from Finland and Russia (Siberia) and A. cepistipes from Finland. Our analysis revealed the presence of both negativesense RNA viruses and positive-sense RNA viruses, while no dsRNA viruses were detected. The viruses included putative new members of virus families Mymonaviridae, Botourmiaviridae and Virgaviridae and members of a recently discovered virus group tentatively named “ambiviruses” with ambisense bicistronic genomic organization. We demonstrated that Armillaria isolates can be cured of viruses by thermal treatment, which enables the examination of virus efects on host growth and phenotype using isogenic virus-infected and virus-free strains.http://www.nature.com/srep/index.htmlpm2022BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

De novo sequencing, assembly and functional annotation of Armillaria borealis genome

Статья из журнала.BACKGROUND: Massive forest decline has been observed almost everywhere as a result of negative anthropogenic and climatic effects, which can interact with pests, fungi and other phytopathogens and aggravate their effects. Climatic changes can weaken trees and make fungi, such as Armillaria more destructive. Armillaria borealis (Marxm. & Korhonen) is a fungus from the Physalacriaceae family (Basidiomycota) widely distributed in Eurasia, including Siberia and the Far East. Species from this genus cause the root white rot disease that weakens and often kills woody plants. However, little is known about ecological behavior and genetics of A. borealis. According to field research data, A. borealis is less pathogenic than A. ostoyae, and its aggressive behavior is quite rare. Mainly A. borealis behaves as a secondary pathogen killing trees already weakened by other factors. However, changing environment might cause unpredictable effects in fungus behavior. RESULTS: The de novo genome assembly and annotation were performed for the A. borealis species for the first time and presented in this study. The A. borealis genome assembly contained ~ 68 Mbp and was comparable with ~ 60 and ~ 79.5 Mbp for the A. ostoyae and A. mellea genomes, respectively. The N50 for contigs equaled 50,544 bp. Functional annotation analysis revealed 21,969 protein coding genes and provided data for further comparative analysis. Repetitive sequences were also identified. The main focus for further study and comparative analysis will be on the enzymes and regulatory factors associated with pathogenicity. CONCLUSIONS: Pathogenic fungi such as Armillaria are currently one of the main problems in forest conservation. A comprehensive study of these species and their pathogenicity is of great importance and needs good genomic resources. The assembled genome of A. borealis presented in this study is of sufficiently good quality for further detailed comparative study on the composition of enzymes in other Armillaria species. There is also a fundamental problem with the identification and classification of species of the Armillaria genus, where the study of repetitive sequences in the genomes of basidiomycetes and their comparative analysis will help us identify more accurately taxonomy of these species and reveal their evolutionary relationships

Hydrodynamically Activated Sawdust of Common Pine Pinus sylvestris L.-substrate for Cultivation of the Strain Gl4–16A Ganoderma lucidum

Приведены результаты исследования по использованию опилок сосны обыкновенной Pinus sylvestris L. c предварительной активацией их в кавитационном гидроударном диспергаторе в течение 25 мин в качестве субстрата для культивирования штамма Gl4–16A Ganoderma lucidum. Установлено, что более эффективно штамм Gl4–16A Ganoderma lucidum колонизирует субстрат с введением в его состав солей (NH4)2SO4 и Na2HPO4. При этом средняя скорость роста базидиомицета на субстрате без введения солей составила 1,39±0,53 мм/сут, а на субстрате с солями азота – 3,22±0,48 мм/сут, и полное обрастание субстрата происходило на 13-е сутки. Установлено, что в процессе культивирования штамма Gl4–16A Ganoderma lucidum на субстрате с солями азота в нем увеличивается содержание экстрактивных веществ с 4,37 до 6,32 %, где более 65 % приходится на долю веществ, экстрагируемых водой. Наблюдается снижение содержания трудногидролизуемых полисахаридов на 13,3, и увеличение негидролизуемой части на 2,4 %, что в расчете на органическую массу составляет 6,8 %. Содержание легкогидролизуемых полисахаридов (ЛГП) снижается на 2,4 %. Однако в расчете на органическую массу это изменение не существенно и доля ЛГП как до, так и после биоконверсии составляет около 15,7 %. Полученные данные могут расширить область использования древесных опилок, что является перспективным направлением как в химической, так и в фармацевтической промышленностиThe results of a study on the use of sawdust of common pine Pinus sylvestris L. with their preliminary activation in a cavitation water-impact dispersant for 25 minutes as a substrate for cultivating the Gl4–16A strain of Ganoderma lucidum are presented. It was found that the Gl4–16A strain of Ganoderma lucidum colonizes the substrate more efficiently with the introduction of (NH4)2SO4 and Na2HPO4 salts into its composition. At the same time, the average growth rate of basidiomycete on the substrate without the introduction of salts was 1.39±0.53 mm/day, and on the substrate with nitrogen salts – 3.22±0.48 mm/day, and complete fouling of the substrate occurred on day 13. It was found that during the cultivation of the Gl4–16A strain of Ganoderma lucidum on a substrate with nitrogen salts, the content of extractive substances in it increases from 4.37 % to 6.32 %, where more than 65 % is accounted for by substances extracted with water. There is a decrease in the content of difficult-to-hydrolyze polysaccharides by 13.3 %, and an increase in the non-hydrolyzable part by 2.4 %, which is 6.8 % per organic mass. The content of easily hydrolyzable polysaccharides (LGA) decreases by 2.4 %, but this change is not significant in terms of organic mass and the share of LGA both before and after bioconversion is about 15.7 %. The obtained data can expand the field of use of sawdust, which is a promising direction, both in the chemical and pharmaceutical industrie

Fusarium: more than a node or a foot-shaped basal cell

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid generaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigaciones en Productos Naturales (CIPRONA