Genome Analyses Reveal the Secondary Metabolites that Potentially Influence the Geographical Distribution of Fusarium pseudograminearum Populations.

Fusarium crown rot (FCR), caused by Fusarium pseudograminearum, significantly impacts wheat yield and quality in China's Huanghuai region. The rapid F. pseudograminearum epidemic and FCR outbreak within a decade remain unexplained. In this study, two high-quality, chromosome-level genomes of F. pseudograminearum strains producing 3-acetyl-deoxynivalenol (3AcDON) and 15-acetyl-deoxynivalenol (15AcDON) toxins were assembled. Additionally, 38 related strains were resequenced. Genomic differences such as single nucleotide polymorphisms (SNPs), insertions/deletions (indels), and structural variations (SVs) among F. pseudograminearum strains were analyzed. The whole-genome SNP locus-based population classification mirrored the toxin chemotype (3AcDON and 15AcDON)-based classification, indicating the presence of genes associated with the trichothecene toxin gene cluster. Further analysis of differential SNP, indel, and SV loci between the 3AcDON and 15AcDON populations revealed a predominant connection to secondary metabolite synthesis genes. Notably, the majority of the secondary metabolite biosynthesis gene cluster loci were located in SNP-dense genomic regions, suggesting high mutability and a possible contribution to F. pseudograminearum population structure and environmental adaptability. This study provides insightful perspectives on the distribution and evolution of F. pseudograminearum and for forecasting the spread of wheat FCR, thereby aiding in the development of preventive measures and control strategies.

Insights into the Ecological Diversification of the Hymenochaetales based on Comparative Genomics and Phylogenomics With an Emphasis on Coltricia.

To elucidate the genomic traits of ecological diversification in the Hymenochaetales, we sequenced 15 new genomes, with attention to ectomycorrhizal (EcM) Coltricia species. Together with published data, 32 genomes, including 31 Hymenochaetales and one outgroup, were comparatively analyzed in total. Compared with those of parasitic and saprophytic members, EcM species have significantly reduced number of plant cell wall degrading enzyme genes, and expanded transposable elements, genome sizes, small secreted proteins, and secreted proteases. EcM species still retain some of secreted carbohydrate-active enzymes (CAZymes) and have lost the key secreted CAZymes to degrade lignin and cellulose, while possess a strong capacity to degrade a microbial cell wall containing chitin and peptidoglycan. There were no significant differences in secreted CAZymes between fungi growing on gymnosperms and angiosperms, suggesting that the secreted CAZymes in the Hymenochaetales evolved before differentiation of host trees into gymnosperms and angiosperms. Nevertheless, parasitic and saprophytic species of the Hymenochaetales are very similar in many genome features, which reflect their close phylogenetic relationships both being white rot fungi. Phylogenomic and molecular clock analyses showed that the EcM genus Coltricia formed a clade located at the base of the Hymenochaetaceae and divergence time later than saprophytic species. And Coltricia remains one to two genes of AA2 family. These indicate that the ancestors of Coltricia appear to have originated from saprophytic ancestor with the ability to cause a white rot. This study provides new genomic data for EcM species and insights into the ecological diversification within the Hymenochaetales based on comparative genomics and phylogenomics analyses.

Intracavity enhancement of GFP fluorescence induced by femtosecond laser pulses.

The phenomenon of fluorescence is widely used in molecular biology for studying the interaction of light with biological objects. In this article, we present an experimental investigation of the enhancement of laser-induced fluorescence of Clytia gregaria green fluorescent protein. The laser-induced fluorescence method applied in our work combines the advantages of femtosecond laser pulses and a photonic crystal cavity, with the time dependence of the fluorescence signal studied. It is shown that a green fluorescent protein solution placed in a microcavity and excited by femtosecond laser pulses leads to an increase in fluorescence on the microcavity modes, which can be estimated by two orders of magnitude. The dependences of fluorescence signal saturation on the average integrated optical pump power are demonstrated and analyzed. The results obtained are of interest for the development of potential applications of biophotonics and extension of convenient methods of laser-induced fluorescence.

Diversity of Dictyostelid Cellular Slime Molds, Including Two Species New to Science, in Forest Soils of Changbai Mountain, China.

Dictyostelid cellular slime molds (dictyostelids) are protists that are common inhabitants of most soils, where they feed upon bacteria. Changbai Mountain is the highest mountain in northeast China. Soil samples collected on Changbai Mountain yielded 11 isolates representing six species of dictyostelid samples. Two of these species (Dictyostelium robusticaule and Heterostelium recretum) were found to be new to science, based on morphology, SSU rDNA sequences, and an ATPase subunit 1 gene (atp1) phylogeny. The present study also demonstrated that the increased accuracy and lower costs associated with the use of atp1 sequences make them a complement of SSU rDNA sequences for identifying dictyostelids. Changbai Mountain is characterized by a higher diversity of dictyostelids than indicated by the few previous reports. Moreover, the data for Changbai Mountain, compared with comparable data for Taiwan, suggest that differences in diversity at the family level are possibly related to latitude. Mixed broadleaf-conifer forests produced more isolates and species than broadleaf forests at the same elevation and also had the highest species richness, which indicates an effect of vegetation on dictyostelids. However, the pattern of slightly decreasing diversity with increasing elevation in dictyostelids was also apparent. IMPORTANCE Dictyostelium robusticaule and Heterostelium recretum are two new species of dictyostelids reported in this study. The potential use of atp1 sequences is a complement of SSU rDNA sequences for the identifying dictyostelids. A pattern of slightly decreasing diversity with increasing elevation in dictyostelids was observed, with the conditions that exist at lower elevations apparently more suitable for dictyostelids, whereas differences of diversity observed at the family level are possibly related to latitude.

Static Culture Combined with Aeration in Biosynthesis of Bacterial Cellulose.

One of the ways to enhance the yield of bacterial cellulose (BC) is by using dynamic aeration and different-type bioreactors because the microbial producers are strict aerobes. But in this case, the BC quality tends to worsen. Here we have combined static culture with aeration in the biosynthesis of BC by symbiotic Medusomyces gisevii Sa-12 for the first time. A new aeration method by feeding the air onto the growth medium surface is proposed herein. The culture was performed in a Binder-400 climate chamber. The study found that the air feed at a rate of 6.3 L/min allows a 25% increase in the BC yield. Moreover, this aeration mode resulted in BC samples of stable quality. The thermogravimetric and X-ray structural characteristics were retained: the crystallinity index in reflection and transmission geometries were 89% and 92%, respectively, and the allomorph Iα content was 94%. Slight decreases in the degree of polymerization (by 12.0% compared to the control-no aeration) and elastic modulus (by 12.6%) are not critical. Thus, the simple aeration by feeding the air onto the culture medium surface has turned out to be an excellent alternative to dynamic aeration. Usually, when the cultivation conditions, including the aeration ones, are changed, characteristics of the resultant BC are altered either, due to the sensitivity of individual microbial strains. In our case, the stable parameters of BC samples under variable aeration conditions are explained by the concomitant factors: the new efficient aeration method and the highly adaptive microbial producer-symbiotic Medusomyces gisevii Sa-12.

Biosynthesis of Bacterial Cellulose by Extended Cultivation with Multiple Removal of BC Pellicles.

Extended cultivation with multiple removal of BC pellicles is proposed herein as a new biosynthetic process for bacterial cellulose (BC). This method enhances the BC surface area by 5-11 times per unit volume of the growth medium, improving the economic efficiency of biosynthesis. The resultant BC gel-films were thin, transparent, and congruent. The degree of polymerization (DP) and elastic modulus (EM) depended on the number of BC pellicle removals, vessel shape, and volume. The quality of BC from removals II-III to VII was better than from removal I. The process scale-up of 1:40 by volume increased DP by 1.5 times and EM by 5 times. A fact was established that the symbiotic Medusomyces gisevii Sa-12 was adaptable to exhausted growth medium: the medium was able to biosynthesize BC for 60 days, while glucose ran low at 24 days. On extended cultivation, DP and EM were found to decline by 39-64% and 57-65%, respectively. The BC gel-films obtained upon removals I-VI were successfully trialed in experimental tension-free hernioplasty.

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 different 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 negative-sense 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 effects on host growth and phenotype using isogenic virus-infected and virus-free strains.

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

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.

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.

Bacterial Nanocellulose Nitrates.

Bacterial nanocellulose (BNC) whose biosynthesis fully conforms to green chemistry principles arouses much interest of specialists in technical chemistry and materials science because of its specific properties, such as nanostructure, purity, thermal stability, reactivity, high crystallinity, etc. The functionalization of the BNC surface remains a priority research area of polymers. The present study was aimed at scaled production of an enlarged BNC sample and at synthesizing cellulose nitrate (CN) therefrom. Cyclic biosynthesis of BNC was run in a semisynthetic glucose medium of 10-72 L in volume by using the Medusomyces gisevii Sa-12 symbiont. The most representative BNC sample weighing 6800 g and having an α-cellulose content of 99% and a polymerization degree of 4000 was nitrated. The nitration of freeze-dried BNC was performed with sulfuric-nitric mixed acid. BNC was examined by scanning electron microscopy (SEM) and infrared spectroscopy (IR), and CN was explored to a fuller extent by SEM, IR, thermogravimetric analysis/differential scanning analysis (TGA/DTA) and 13C nuclear magnetic resonance (NMR) spectroscopy. The three-cycle biosynthesis of BNC with an increasing volume of the nutrient medium from 10 to 72 L was successfully scaled up in nonsterile conditions to afford 9432 g of BNC gel-films. CNs with a nitrogen content of 10.96% and a viscosity of 916 cP were synthesized. It was found by the SEM technique that the CN preserved the 3D reticulate structure of initial BNC fibers a marginal thickening of the nanofibers themselves. Different analytical techniques reliably proved the resultant nitration product to be CN. When dissolved in acetone, the CN was found to form a clear high-viscosity organogel whose further studies will broaden application fields of the modified BNC.

Mobile genetic elements explain size variation in the mitochondrial genomes of four closely-related Armillaria species.

BACKGROUND: Species in the genus Armillaria (fungi, basidiomycota) are well-known as saprophytes and pathogens on plants. Many of them cause white-rot root disease in diverse woody plants worldwide. Mitochondrial genomes (mitogenomes) are widely used in evolutionary and population studies, but despite the importance and wide distribution of Armillaria, the complete mitogenomes have not previously been reported for this genus. Meanwhile, the well-supported phylogeny of Armillaria species provides an excellent framework in which to study variation in mitogenomes and how they have evolved over time. RESULTS: Here we completely sequenced, assembled, and annotated the circular mitogenomes of four species: A. borealis, A. gallica, A. sinapina, and A. solidipes (116,443, 98,896, 103,563, and 122,167 bp, respectively). The variation in mitogenome size can be explained by variable numbers of mobile genetic elements, introns, and plasmid-related sequences. Most Armillaria introns contained open reading frames (ORFs) that are related to homing endonucleases of the LAGLIDADG and GIY-YIG families. Insertions of mobile elements were also evident as fragments of plasmid-related sequences in Armillaria mitogenomes. We also found several truncated gene duplications in all four mitogenomes. CONCLUSIONS: Our study showed that fungal mitogenomes have a high degree of variation in size, gene content, and genomic organization even among closely related species of Armillara. We suggest that mobile genetic elements invading introns and intergenic sequences in the Armillaria mitogenomes have played a significant role in shaping their genome structure. The mitogenome changes we describe here are consistent with widely accepted phylogenetic relationships among the four species.

Application of Toxigenic Alternaria oxytropis to Soybeans and its Effect on Swainsonine Detection in Different Environments.

Alternaria oxytropis is an endophytic fungus of locoweeds that synthesizes swainsonine toxin. In this work, we evaluated the effect of A. oxytropis on soybean seedlings and quantified swainsonine in different culture conditions. Soybean (Glycine max) seeds were co-cultured with A. oxytropis (at different concentrations of mycelial suspensions) in agar media and soil culture, and swainsonine was assayed using LC-MS/MS. The results showed evidence that A. oxytropis infected soybean seedlings produced detectable swainsonine in agar culture while the toxin was undetectable or below the detection limit (0.006% of swainsonine dry weight) in soil media even at higher concentrations of the fungus. These results suggest that swainsonine detection is highly dependent on culture conditions and that soybeans co-cultured with A. oxytropis in soil could potentially be used to limit toxin production.

Enzymatic Hydrolysis of Hydrotropic Pulps at Different Substrate Loadings.

Enzymatic hydrolysis of cellulosic raw materials to produce nutrient broths for microbiological synthesis of ethanol and other valuable products is an important field of modern biotechnology. Biotechnological processing implies the selection of an effective pretreatment technique for raw materials. In this study, the hydrotropic treatment increased the reactivity of the obtained substrates toward enzymatic hydrolysis by 7.1 times for Miscanthus and by 7.3 times for oat hulls. The hydrotropic pulp from oat hulls was more reactive toward enzymatic hydrolysis compared to that from Miscanthus, despite that the substrates had similar compositions. As the initial substrate loadings were raised during enzymatic hydrolysis of the hydrotropic Miscanthus and oat hull pulps, the concentration of reducing sugars increased by 34 g/dm(3) and the yield of reducing sugars decreased by 31 %. The findings allow us to predict the efficiency of enzymatic hydrolysis of hydrotropic pulps from Miscanthus and oat hulls when scaling up the process by volume.