Search Results (1,115)

Phyllanthus emblica is valued for its nutritional and medicinal properties, yet the genomic divergence between localized and widespread cultivars remains poorly understood. We investigated the genomes of two individuals from the endemic cultivar ‘Hongguang’ (HG), propagated via regional grafting, and the commercially widespread ‘Dongkeng’ (DK), known for its superior protein content. Using whole-genome sequencing, we reconstructed phylogenies from two nuclear markers, profiled genome-wide variations, assembled chloroplast genomes, and verified relative plastid copy numbers via real-time quantitative PCRs (qPCRs). Nuclear internal transcribed spacer (ITS) and phytochrome C (PHYC) phylogenies confirmed both samples belonged to the P. emblica lineage, while revealing a distinct genetic identity for the HG individual. Genome-wide variant profiling of the two individuals identified KEGG enrichment in plant hormone signaling pathways; DK variants mapped to the canonical auxin axis, while HG variants were annotated to reversible protein phosphorylation. Comparative chloroplast genomics demonstrated shared maternal inheritance and shared mutations in key photosynthetic genes (psaB, petA, and the ndh cluster) between the two genomes, though qPCR validation revealed a higher relative chloroplast DNA copy number in the DK sample. Despite the two-individual limitation, these findings revealed preliminary genomic variations, offering candidate molecular markers for future population studies and marker-assisted breeding. Full article

Background: Rare fungal infections may represent under-recognized causes of healthcare-associated sepsis, particularly when caused by emerging or difficult-to-identify pathogens. We aimed to characterize Candida viswanathii isolates recovered in the setting of panel-negative candidemia and to assess the contribution of an integrated diagnostic workflow. Methods: We investigated seven C. viswanathii isolates overall, including three recovered at our institution from blood, urine, and bronchoalveolar lavage of a NICU patient, as well as four bloodstream isolates from a second pediatric center included for comparison. Isolates were analyzed by culture and microscopy, three MALDI-TOF MS platforms, internal transcribed spacer sequencing, Fourier transform infrared (FTIR) spectroscopy and antifungal susceptibility testing. Results: C. viswanathii was repeatedly recovered from blood, urine and bronchoalveolar lavage, while the FilmArray BCID2 panel remained negative. All MALDI-TOF MS systems with updated databases correctly identified the yeast at the species level; identification was confirmed by sequencing. Fourier transform infrared analysis showed clustering of clinical isolates and clearly separated C. viswanathii from related Candida species. All isolates exhibited low MICs to echinocandins and amphotericin B as well as moderately elevated fluconazole MICs (2–4 mg/L). Conclusion: This study supports the use of explicit diagnostic algorithms for rare fungal pathogens in yeast-positive, syndromic panel-negative blood cultures. In this setting, updated MALDI-TOF MS libraries and FTIR spectroscopy may provide useful adjunctive support for the recognition and phenotypic discrimination of atypical yeasts within an integrated laboratory workflow. Full article

Biochar can improve soil physicochemical properties and microbial habitats; however, its application rate-dependent effects in maize fields of the black soil region remain insufficiently understood under field conditions. A three-year field experiment was conducted in Jiamusi, Heilongjiang Province, China, from 2023 to 2025, with four biochar application rates: 0 (W0), 10 (W1), 20 (W2), and 40 t ha⁻¹ (W3). Soil physicochemical properties, bacterial communities based on 16S rRNA gene sequencing, and fungal communities based on internal transcribed spacer (ITS) sequencing were analyzed to assess changes in soil fertility and microbial community composition and their relationships with environmental factors. Biochar application significantly increased soil organic matter, alkali-hydrolyzable nitrogen, available potassium, and pH. Although W3 produced the greatest nutrient enhancement, W2 exhibited a more balanced overall response across the measured soil fertility and microbial community indicators. Sequencing depth was adequate for all samples, and bacterial alpha diversity was comparatively well maintained under W2 and W3. Fungal alpha diversity exhibited pronounced interannual variation and increased under W3 in 2025. Year accounted for a greater proportion of variation in microbial community structure than did biochar treatment; however, both treatment and the year × treatment interaction also had significant effects. Among the measured soil fertility and microbial community indicators, W2 produced a comparatively balanced overall response, whereas W3 exerted stronger selective effects on microbial communities. Because crop yield, economic feasibility, labile carbon fractions, and long-term ecological outcomes were not assessed, an agronomically optimal biochar application rate cannot yet be determined. Full article

Macrofungal resources are abundant in Northeast China, but those from Shenyang and its surrounding areas remain insufficiently investigated. In this study, morphological and phylogenetic analyses were carried out on specimens collected from the vicinity of Shenyang, Liaoning Province. Phylogenetic trees were inferred using maximum likelihood and Bayesian inference methods based on sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region and the nuclear ribosomal large subunit (LSU). Three new species, Descolea laevis (Bolbitiaceae), Leucocoprinus shenyangensis (Agaricaceae), and Tephrocybe umbonata (Lyophyllaceae), are described herein. Descolea laevis is characterized by pale yellow to light yellow basidiomata, a nearly smooth pileus surface, clavate to narrowly clavate cheilocystidia, fusiform to clavate pleurocystidia, and amygdaliform to limoniform, verrucose basidiospores. Leucocoprinus shenyangensis is distinguished by white to yellowish-white basidiomata, a pileus covered with light grey squamules, narrowly clavate to subcylindrical cheilocystidia, a hymenidermal pileipellis, and amygdaliform to limoniform basidiospores. Tephrocybe umbonata is characterized by orange-white to greyish-orange basidiomata, a pileus with a blunt umbo, a smooth or slightly finely fibrillose pileus surface, lageniform pleurocystidia with slightly acute apices, and amygdaliform to limoniform basidiospores. Detailed morphological descriptions, illustrations of microscopic structures, and phylogenetic evidence for the three new species are provided. The diagnostic characteristics separating the new taxa from their closely related species are also discussed. Full article

China harbors a diverse array of macrofungi, yet its fungal diversity remains inadequately documented, particularly in under-explored regions such as the temperate forests of the northeast and the subtropical highlands of the southwest. In this study, four agaric species are reported as new records for China based on morphological observations and multilocus phylogenetic analyses. Phylogenetic analyses of the internal transcribed spacer (ITS) and nuclear large subunit (nrLSU) ribosomal RNA gene regions confirmed their generic and species-level placements. Cortinarius infidus was collected from mixed coniferous and broadleaf forests in Liaoning Province, Pseudolaccaria fellea from Pine-dominated forests in Liaoning Province, Volvariella clavocystidiata from pine-dominated coniferous forests in Liaoning Province, and Gerhardtia borealis from mixed coniferous–broadleaf forests in Guizhou Province. Comprehensive macro and micromorphological descriptions, color photographs, line drawings, scanning electron micrographs, and comparisons with closely related taxa and original literature are provided to confirm these identifications. These findings contribute to a better understanding of the distribution patterns of these genera and expand the known fungal diversity of China. Full article

The Yellow River Delta is a representative coastal saline–alkaline ecosystem in China, where high salinity and complex soil properties create a distinct habitat that significantly shapes microbial community structure and function. In this study, we analyzed 34 saline–alkaline soil samples from four regions within the delta. We characterized soil physicochemical properties (salt content, electrical conductivity, and pH) and systematically assessed fungal diversity, potential ecological functions, and their relationships with environmental variables using both internal transcribed spacer high-throughput sequencing and culture-based isolation. Sequencing generated 1,137,196 sequences that clustered into 13,574 operational taxonomic units (OTUs), with Good’s coverage values ranging from 0.96 to 1.00, indicating sufficient sequencing depth. The soils were generally alkaline and exhibited pronounced spatial heterogeneity in salinity and electrical conductivity. Sequencing analyses revealed Ascomycota and Basidiomycota as the dominant fungal phyla. Alpha diversity tended to decline with increasing salt content and electrical conductivity; however, substantial within-group variability indicated strong microenvironmental influences. Beta diversity analyses revealed distinct clustering patterns in community structure among regions based on PCoA ordinations. Redundancy analysis revealed that soil pH had the only significant unique contribution to fungal community variation. However, all three measured edaphic factors together explained only 17% of the total community variation. Functional inference using the FUNGuild database identified diverse fungal trophic modes and several plant-associated taxa in several samples. Culture-based approaches yielded 347 isolates representing 52 genera. Among the isolates, the vast majority (>95%) belonged to Ascomycota, with Basidiomycota represented by only a few isolates, which is consistent with the dominance of Ascomycota observed in the high-throughput sequencing data. Comparisons between sequencing and cultivation results demonstrated complementary diversity profiles and highlighted a substantial reservoir of nonculturable fungi in these soils. Overall, this study clarifies spatial patterns and key environmental drivers of fungal diversity in the Yellow River Delta and establishes a foundational culture collection for future ecological restoration efforts. Full article

Based on morphological and molecular phylogenetic analyses, we describe a new species, Hygrocybe flavomarginata, from the Tibetan Plateau, China. The internal transcribed spacer (ITS) and nuclear large subunit ribosomal DNA (nrLSU) sequences of the new species were divergent from those of related species in Hygrocybe (subgenus Pseudohygrocybe, section Coccineae, subsection Squamulosae). The divergence of H. flavomarginata from related Hygrocybe species was supported by high bootstrap support in the ML phylogenetic analysis of combined ITS and nrLSU sequences. H. flavomarginata is characterized by a small, hygrophanous pileus that is plane to slightly indented, orange with an orange-yellow margin, and a fibrillose-squamulose center. The lamellae are pale waxy yellow with orange-yellow edges, differing from those of related species by being convex rather than arcuate, and by extending beyond the pileus margin. Clamp connections are restricted to the pileus context and absent from both the lamellar trama and the stipitipellis. Full article

Background: Benzimidazole (BZ) resistance in the gastrointestinal nematode Haemonchus contortus is a major constraint to sheep production worldwide. However, data on the prevalence and molecular mechanisms of resistance in Yili Prefecture, Xinjiang—a key livestock region in Northwestern China—remain limited. This study aimed to determine the frequency of BZ resistance-associated single nucleotide polymorphisms (SNPs) in H. contortus populations from Zhaosu and Tekesi counties. Methods: Adult male worms (n = 150) were collected from naturally infected sheep at local abattoirs. Species identity was confirmed morphologically by sequencing the internal transcribed spacer 2 (ITS-2) region. A 385 bp fragment of the isotype-1 β-tubulin gene was amplified and sequenced to detect SNPs at codons 167 (F167Y), 198 (E198A), and 200 (F200Y). Results: The F167Y mutation was absent in all individuals. In contrast, the E198A mutation occurred at exceptionally high frequencies, with resistant allele frequencies (RAF) of 64.7% in Zhaosu and 52.7% in Tekesi. The F200Y mutation showed clear geographical variation: it remained low in Zhaosu (RAF = 9.3%) but was substantially higher in Tekesi (RAF = 33.3%). Haplotype analysis revealed that resistance in Zhaosu was driven primarily by the E198A mutation, whereas the Tekesi population exhibited complex patterns of co-selection of both E198A and F200Y, with a high proportion of double-heterozygous individuals (29.3%). Conclusions: This study provides comprehensive molecular evidence of severe BZ resistance in H. contortus populations from Zhaosu and Tekesi counties, Yili Prefecture. The marked predominance of the E198A mutation, together with the emergence of multi-locus resistance in Tekesi, indicates a rapid escalation of resistance beyond historical levels. These findings suggest that benzimidazoles are likely ineffective in this region and highlight the urgent need to revise local parasite control strategies. Full article

Desertification strongly alters soil microbial communities in dryland ecosystems, yet the reassembly of fungal functional groups and their interactions under increasing aridity remain unclear. This study aimed to determine how desertification reshapes arbuscular mycorrhizal fungi (AMF) and endophytic fungal groups in the rhizosphere of Stipa breviflora and Artemisia frigida, as well as how these shifts are associated with fungal network fragmentation. Rhizosphere soil internal transcribed spacer (ITS) sequencing and AMF-specific amplicon sequencing, combined with root colonization assessment, functional annotation, co-occurrence network analysis, and partial least squares path modeling (PLS-PM), were used to assess shifts in fungal communities along the desertification gradient. Desertification significantly reduced soil multifunctionality and fungal diversity, accompanied by a shift in community composition from environmentally sensitive taxa to stress-tolerant groups. Along the desertification gradient, AMF diversity and colonization decreased, whereas FUNGuild-inferred endophytic fungal abundance and microscopically observed dark septate endophytes (DSEs) colonization increased. FUNGuild-inferred endophytic fungal abundance was negatively correlated with AMF diversity. Co-occurrence networks showed reduced connectivity and increased fragmentation under desertification, especially at the desert steppe and steppe desert stages. PLS-PM analysis revealed that desertification directly increased fungal network fragmentation and indirectly promoted fragmentation through increased FUNGuild-inferred endophytic fungi and reduced AMF diversity, whereas soil multifunctionality mainly reflected environmental deterioration along the gradient. These findings demonstrate the functional reassembly of rhizosphere fungi under desertification and suggest that compensatory shifts among fungal guilds may contribute to ecosystem stability in dryland grasslands. Full article

In resource-poor sandy habitats, alien plant co-invasion often triggers intense belowground competition mediated by rhizosphere microorganisms. However, the mechanisms by which these plants overcome nutrient limitations remain unclear. Here, we conducted an eight-month in situ monitoring of single- and co-invasion plots of Solanum rostratum and Cenchrus pauciflorus Benth. in the Horqin Sandy Land. By integrating soil enzyme assays with 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing, we characterized their rhizosphere microbial community assembly. Co-invasion exposed both species to convergent biotic stress, characterized by the significant enrichment of the pathogenic fungi Didymella and Pseudogymnoascus (linear discriminant analysis (LDA) > 4.0). To mitigate these pressures, the dominant competitor, S. rostratum, specifically recruited a cross-kingdom phosphate-solubilizing consortium comprising Bacillus and Penicillium (LDA > 4.0). This targeted recruitment significantly enhanced rhizosphere activities, increasing phosphatase and sucrase to 86.10 U/g and 2.17 U/g, respectively, thereby maintaining available phosphorus at a high level (35.55 mg/kg). Conversely, the subordinate competitor, C. pauciflorus, lost key native stress-resistant bacteria such as Rubrobacter (relative abundance dropping from 5.39% to 3.27%) and failed to recruit effective microbes, leading to the rapid depletion of available phosphorus (dropping to 21.38 mg/kg). Ultimately, under dual nutrient and pathogenic stress, the precise recruitment and functional integration of cross-kingdom phosphate-solubilizing microbes are strongly linked to the divergent belowground competitive outcomes between these co-invading plants. Full article

We document and illustrate Primula xideensis, a new species collected from Xide County, Sichuan Province, China. Morphologically, it resembles P. stenocalyx, P. farinosa s.l., and P. pulchella, but differs by its roots densely covered with multicellular hairs; elliptic to obovate leaves with non-revolute, irregularly and deeply dentate margins, both surfaces efarinose, shortly hairy, and scabrous; tubular calyx parted to the middle; corolla mouth densely white-farinose; stamens positioned at mid-corolla tube in pin flowers and near the throat in thrum flowers; styles reciprocally placed; and an oblong capsule shorter than the persistent calyx. To clarify its phylogenetic placement, we constructed phylogenetic trees using two datasets: 63 complete chloroplast genome sequences and 75 nuclear ribosomal DNA internal transcribed spacer (nrITS) sequences. Both trees showed similar topologies, consistently placing the new species within a monophyletic group of Sect. Aleuritia, supporting its assignment to this section. For a deeper comparison between the new species and other members of Sect. Aleuritia, we incorporated chloroplast genomes of seven additional species from this section. The results revealed highly conserved chloroplast genomes among all eight species, with only minor differences between the new species and the others. Primula xideensis is currently known only from its type locality. Based on IUCN Red List criteria, its conservation status is assessed as Data Deficient (DD). Full article

Hypogeous ascomycetous fungi (truffles) are challenging to study because they produce underground sporocarps that may not be encountered during traditional fungal surveys. Genea is one such genus that has garnered considerable attention over the past decades due to its role as an ectomycorrhizal partner and contribution to nutrient cycling and ecosystem stability. Yet, very limited information is available about its taxonomy, phylogeny and ecology worldwide. The current study aims to expand the known distribution of Genea species in Central Europe by integrating morphological, molecular and ecological analyses of new collections as well as the assessment of herbarium materials. Light microscopy and SEM were used to determine morphological characteristics along with FT-IR (Fourier transform infrared) spectroscopy measurements, which proved to be a powerful tool for species differentiation. Molecular phylogenetic analyses were conducted using the internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) and D1/D2 domain of the large subunit (28S) of nuclear ribosomal DNA sequences to confirm species identity. In this study, a new species, Genea szemereiensis, along with the first report of Genea pinicola from Hungary, was made. In addition, the ecological parameters of the species, including habitat, altitude, soil nutrients and pH, were revised, which has not been reported previously in detail for this genus. Full article

Tamarindus indica L., a key economic tree species in tropical regions, suffers severely from postharvest decay. From 2023 to 2025, disease fruits exhibiting pericarp softening, pulp browning, and sticky exudates were collected in Yunnan, China. Pathogenicity tests following Koch’s postulates, combined with morphological characterization and phylogenetic analyses of the internal transcribed spacer (ITS), translation elongation factor 1-alpha (TEF 1α), and beta-tubulin (TUB) gene regions, identified the causal pathogen as Botryosphaeria fabicerciana (isolates ZWML-06, ZWML-44, ZWML-17). This is the first report of this postharvest disease on tamarind in Yunnan, filling an etiological gap. Additionally, an endophytic bacterium, designated BV-1, was isolated from asymptomatic pulp tissues. Whole-genome sequencing and phylogenetic analysis identified it as Bacillus velezensis. Strain BV-1 exhibited strong in vitro antagonistic activity against the pathogen, indicating promising biocontrol potential. Functional annotation revealed that BV-1 possesses a complex genetic system with developed transporter systems; its core metabolic network is dominated by nitrogen metabolism and redox processes, suggesting a potential “multi-target” antimicrobial mechanism. This study provides a theoretical basis and novel resources for the green control of postharvest diseases in tamarind. Full article

Trichoderma asperellum and T. asperelloides are two cryptic species that have potential for use as biocontrol and biofertilizer (B&B) agents. Comparison of the reference genomes of the two species revealed that each species had seven chromosomes, but Trichoderma asperellum has about 1000 more genes than T. asperelloides. The number of genes coding for chitinases, cellulases, xylanases, secreted proteases, and genes involved in soil and plant health was slightly greater in T. asperellum than in T. asperelloides. Moreover, T. asperellum had five more genes than T. asperelloides involved in the synthesis of secondary metabolites like peptaibols and siderophores. The B&B genes were distributed on all the chromosomes. No duplicate genes were found for any of the enzymes searched. The investigation also revealed that T. asperellum had 15 copies of the internal transcribed spacer (ITS) region of ribosomal DNA compared to only seven copies in T. asperelloides. Further transcriptomic, proteomic, and efficacy studies are needed to determine the impact of the missing genes in T. asperelloides on its B&B activities compared to those of T. asperellum. The search for B&B genes in T. asperelloides was hindered by the lack of annotation for the genome. Thus, comparison only involves B&B genes searched in T. asperellum and whether homologs to the genes were available or missing in T. asperelloides. A comparison between additional strains of the two species is essential to show whether the data in this study apply to all intraspecies strains of the two species. Full article

White pine blister rust disease (WPBR), caused by Cronartium ribicola, ranks among the most destructive pathogens of five-needle pines. We developed a hydroxynaphthol blue (HNB)-based Loop-mediated isothermal amplification (LAMP) assay enabling rapid, visual detection of C. ribicola directly following DNA extraction. LAMP primers targeting the internal transcribed spacer (ITS) region were designed and validated through in silico comparison with related Cronartium species and in vitro testing against sympatric forest fungi. The optimized 25 μL reaction contained 8.0 mM Mg²⁺, 1.0 mM dNTPs, and an inner-to-outer primer ratio of 8:1, with amplification conducted at 62 °C for 40 min. Positive amplification produced a distinctive color transition from purple to sky blue, enabling visual interpretation without instrumentation. Under the tested conditions, the assay achieved a detection limit of 460 ± 3.2 fg/μL genomic DNA—a 10-fold improvement over conventional PCR in concentration-based sensitivity. Assay applicability was evaluated using 211 field-collected Pinus armandii samples sourced from China. Detection efficiency varied significantly across tissue types. Symptomatic bark exhibited a substantially higher positive detection rate (68.97%, 95% CI: 49.2–84.7%) compared to needles from symptomatic trees (18.75%, 95% CI: 4.1–45.7%). Among asymptomatic samples, 3.75% of bark samples tested positive for C. ribicola DNA, whereas all needle samples were negative. Geographically, positive detections clustered at several discrete sampling sites in southwestern China, predominantly at elevated elevations. The established LAMP-HNB assay provides a rapid, visually interpretable diagnostic tool for early detection and quarantine monitoring of WPBR following DNA extraction. Beyond its practical utility, this assay establishes valuable baseline data for targeted disease surveillance in the context of evolving climate conditions. Full article