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The alpine mining area of the Qilian Mountains features a fragile ecosystem, severe soil degradation due to mining disturbances, and slow natural recovery. To clarify the ecological restoration potential of rhizosphere microorganisms associated with native dominant plants, this study investigated the community structure, diversity, and functional differentiation patterns of rhizosphere bacterial and fungal communities associated with seven native dominant plant species in the Tianzhu mining area. Using Illumina NovaSeq 6000 high-throughput sequencing, we amplified the bacterial 16S rRNA V3–V4 region and the fungal ITS1 region. A total of 24 sequencing libraries (seven plant species + bare soil, three replicates each) were analyzed. Bioinformatics analyses examined ASV distributions, alpha/beta diversity, species composition, and differentially enriched taxa, followed by functional predictions. Bacterial alpha diversity (Chao1: 623.39–1553.25; Shannon: 7.49–9.67) varied significantly among plant species, with Allium przewalskianum (AP) showing the highest bacterial richness and diversity (Chao1 = 1553.25 ± 35.89, Shannon = 9.67 ± 0.02). Fungal alpha diversity also showed significant variation (Chao1:69.66–488.56; Shannon: 3.24–4.96), with Dasiphora fruticosa (DF) exhibiting the highest fungal diversity (Chao1 = 488.56 ± 18.71, Shannon = 7.32 ± 0.06). At the phylum level, Proteobacteria (32.22–50.32%) and Actinobacteriota (15.04–23.19%) were core bacterial groups, and Ascomycota (45.54–96.07%) dominated fungal communities. PERMANOVA confirmed significant differences in community composition among plant species (bacteria: R² = 0.78, p < 0.001; fungi: R² = 0.84, p < 0.001). Different plant species were associated with distinct predicted functional taxa, which may serve as candidate biomarkers for soil remediation. However, all functional interpretations are predictive and require experimental validation. In conclusion, rhizosphere microbial community composition and predicted functional profiles differed among native plant species, providing correlative evidence and candidate targets for future vegetation–microbe synergy studies in alpine mining area restoration. Full article

Atmospheric bacteria and fungi are key components of urban bioaerosols, and their community structures are closely related to urban air quality, bioaerosol concentration, and environmental driving factors. However, the temporal dynamics and environmental drivers of bacterial and fungal community structures remain poorly characterized in megacities such as Shanghai, China. From November 2024 to November 2025, we conducted a year-long, cross-seasonal bioaerosol sampling and high-throughput DNA sequencing campaign to investigate the seasonal and diel variations, environmental covariation, and meteorological responses of atmospheric bacteria and fungi in Shanghai. The results show that seasonal transitions cannot significantly alter the α-diversity of bacterial or fungal communities, but significantly shift their community compositions, exhibiting a stronger differentiation for fungi than bacteria (PERMANOVA R² = 0.133 vs. 0.054, p = 0.001). At the diel scale, bacterial communities exhibit weak diurnal variation, whereas fungal communities display significantly higher nocturnal Chao1 richness and Shannon diversity, along with distinct compositional separation. Cladosporium and Alternaria are enriched during the day, while saprotrophic basidiomycetes such as Irpex and Trametes are more abundant at night. Fungal composition covaries most strongly with meteorological gradients governed by boundary layer height, clear-sky surface downward solar radiation, temperature, relative humidity, atmospheric pressure and visibility, whereas bacterial–environment associations are weaker. The Relative Exposure-Relevant Proportion (RERP), dominated by Cladosporium and Alternaria, is higher during daytime and negatively associated with relative humidity (β = −0.23, q = 0.001). During a strong cold-air event, bacterial communities shifted rapidly following immediate air mass replacement and high wind shear before stabilizing, whereas fungal communities underwent a more gradual and cumulative turnover. The RERP also elevated during this event, accompanied by a greater contribution from Talaromyces. These findings reveal contrasting dynamics between airborne bacteria and fungi under both background and transient synoptic disturbances, providing crucial observational insights for bioaerosol modeling and risk prediction in urban environments. Full article

Cadmium (Cd) pollution threatens global ecosystems and human health owing to its high toxicity, long-term persistence, and dual irreversibility of environmental geochemical behavior and biological toxicological effects. The interaction between phosphate-solubilizing fungi (PSF) and clay minerals governs the biogeochemical transformation, chemical speciation, and migration fate of soil Cd. However, the dose-dependent mechanisms underlying Cd²⁺ removal by Aspergillus niger (A. niger) and montmorillonite remain unclear. In this study, three Cd²⁺ stress levels were simulated, and four A. niger-montmorillonite composite systems were established. Key physicochemical and metabolic indicators, including pH, available phosphorus (AP) concentration, oxalic acid concentration, acid phosphatase (ACP) activity, and Cd²⁺ removal rate, were determined. The results showed that the single A. niger treatment achieved the optimal Cd removal performance among all composite treatment groups. Severe Cd²⁺ stress induced abundant oxalic acid and ACP secretion, which simultaneously mobilized phosphorus and facilitated Cd removal via phosphate precipitation and oxalate complexation. Low-to-medium montmorillonite dosage temporarily alleviated Cd²⁺ toxicity, whereas high montmorillonite dosage restricted fungal metabolic exudates and, together with acid-mediated mineral-Cd interactions, triggered antagonistic rather than synergistic Cd removal. This study clarifies how montmorillonite dosage reshapes the metabolic defense of A. niger, providing theoretical references for optimizing microbe–montmorillonite composite remediation formulations. Full article

Wild Polygala crotalarioides is an ethnomedicinal plant traditionally used for neurological health. Endophytic fungi associated with medicinal plants are increasingly recognized as sources of bioactive natural products; however, their diversity and biological activities in wild P. crotalarioides remain poorly understood. We used high-throughput sequencing and culture-dependent methods to explored the diversity, community composition, and bioactivities of endophytic fungi associated with wild P. crotalarioides. Culturable isolates were identified via ITS sequencing and further screened for AChE-inhibitory and antioxidant activities. Our results revealed that a total of 818 fungal OTUs were detected, revealing pronounced tissue-specific community differentiation. Stem tissues harbored the highest fungal diversity, richness, and number of unique OTUs. Ascomycota and Basidiomycota dominated fungal communities across all tissues, while distinct biomarker taxa were enriched in different organs. Functional annotation indicated marked tissue-dependent variation in trophic composition. Among 108 culturable isolates, Penicillium sp. PRP024 and Trichoderma sp. PRP008 exhibited the strongest AChE inhibitory activities (>80%), whereas Fusarium sp. PSP053, Diaporthe sp. PSM027 and Exserohilum sp. PSP042 showed notable antioxidant activities. Wild P. crotalarioides hosts highly diverse and tissue-specific endophytic fungal communities. Several isolates exhibited promising acetylcholinesterase inhibitory and antioxidant activities, highlighting medicinal plant-associated endophytic fungi as potential sources of antioxidative natural products. Full article

Melilotus officinalis (L.) Lam. (yellow sweet clover) is a medicinally valuable Fabaceae species with recognized antioxidant and antimicrobial properties, yet the impact of cultivation system on its secondary metabolism remains poorly characterized for Central Asian populations. This study compared wild and in vitro-grown Melilotus officinalis from northern Kazakhstan (Astana city), examining phenolic composition, organic acids, antioxidant capacity, and antimicrobial activity as functions of cultivation system. Hydroethanolic extracts were analyzed by HPLC-DAD-ESI-Orbitrap MS/MS and UFLC-PDA, while antioxidant activity was assessed by TBARS and ABTS assays and antimicrobial activity by broth microdilution against eight bacterial and two fungal strains. Thirteen phenolic compounds were tentatively identified, revealing higher total flavonoid content in in vitro plants, dominated by apigenin di-C-pentoside isomers and vicenin-3, whereas wild plants showed greater diversity of phenolic acids and flavonols, including kaempferol and quercetin glycosides. Despite lower total phenolics, wild extracts more effectively inhibited lipid peroxidation, while ABTS radical scavenging was comparable between sources, and antimicrobial effects were strain-specific. Oxalic acid was approximately three-fold higher in in vitro material, a biochemical feature relevant for downstream use. These findings indicate that cultivation system substantially shapes the secondary metabolite profile and bioactivity of this regionally important medicinal species. Full article

Antimicrobial resistance is a growing global health challenge, highlighting the need for new bioactive compounds from medicinal plants. Vepris nobilis is traditionally used in East Africa for treating infections and respiratory disorders; however, its essential oil (EO) composition and antimicrobial mechanisms remain poorly characterized. This study investigated the chemical composition and antimicrobial activity of V. nobilis EO, along with an in silico evaluation of its major constituent, germacrene D. The EO was extracted by hydrodistillation and analyzed using gas chromatography-mass spectrometry (GC–MS). Its antimicrobial activity was evaluated against 26 bacterial and 4 fungal strains using disc diffusion, broth microdilution, and MBC/MFC (Minimum Bactericidal Concentration/Minimum Fungicidal Concentration) assays. Germacrene D showed stronger activity than the EO, particularly against both multidrug resistant (MDR) and non-MDR Gram-negative bacterial strains (MIC = 10 µg/mL), with bactericidal and fungicidal effect. Molecular docking of germacrene D against two clinically relevant enzymes—dehydrosqualene synthase (CrtM) from Staphylococcus aureus and SWISS-modeled sterol 14-α-demethylase (CYP51) from Penicillium funiculosum—suggested potential interactions with both targets, with a favorable predicted binding affinity for CrtM (−7.654 kcal/mol) and for CYP51 (−5.898 kcal/mol). These findings provide preliminary insights into a possible antimicrobial mechanism, although experimental validation is needed to confirm this hypothesis. ADMET analysis suggested favorable drug-like properties despite limited solubility. These findings provide scientific support for the traditional use of V. nobilis leaves in the treatment of respiratory infections and highlight germacrene D as a promising lead compound for further antimicrobial development. Full article

Seed-associated microorganisms influence seed quality, seedling establishment, and plant health and also constitute a major source of seed-borne pathogens. Cold atmospheric plasma (CAP) has emerged as a promising alternative to chemical seed treatments because of its antimicrobial activity, although its effects on fungal communities associated with developing seedlings remain poorly understood. Here, Arabidopsis thaliana seeds from two ecotypes (Columbia and Landsberg erecta) were exposed to CAP for 5 or 15 min. Seed decontamination efficiency was assessed by culturing on malt extract agar and nephelometric analyses, while fungal communities associated with seedlings derived from treated and untreated seeds were characterized by ITS1 amplicon sequencing. CAP efficiently reduced fungal contamination without affecting seed germination. CAP altered the composition of fungal communities associated with developing seedlings, but the magnitude of these changes depended on seed batch and ecotype. Dominant taxa markedly declined after treatment, whereas several low-abundance taxa increased in relative abundance. These findings demonstrate that CAP is an effective pesticide-free technology for seed decontamination and can also reshape fungal communities associated with developing seedlings, highlighting broader ecological consequences of plasma-based seed treatments. Full article

Chlorpyrifos (CPF) is the most commonly used organophosphorus insecticide in agriculture globally. This has raised concerns due to its persistence, bioaccumulation, neurotoxicity, and environmental and human health effects. Until 2020, CPF was the most commonly used pesticide in European Union (EU) food production. CPF is also used in other parts of the world, though it has been discontinued in the EU, as national pesticide surveillance programs indicate it is found in soil, water, and food. This type of persistence is potentially harmful to farmers, consumers, and animals because CPF is toxic. Markedly, CPF has the potential to change the microbiota composition of soils, i.e., fungal, bacterial, and actinomycete communities, and inhibit the mineralization of nitrogen. The key CPF activity is associated with the inhibition of acetylcholinesterase (AChE), leading to reproductive, neurotoxic, and genotoxic effects. Microbial degradation, especially when applied by means of bacteria, has become one of the promising alternatives to the traditional physicochemical means since it is inexpensive, does not harm the environment and may possibly be fully detoxified. This review summarizes the latest developments in the study of CPF-degrading bacteria, enzyme pathways, microbial diversity, and the evaluation of the environmental impact of microbial remediation. Recent research findings, genomic research developments, and potential applications of CPF-degrading bacteria are addressed. In addition, this study reveals the current knowledge gaps, presents biotechnological challenges, and suggests future directions in the application of field-scale studies, focusing on the application of microbial solutions in sustainable agriculture. Full article

Belowground multitrophic communities and their potential associations are important biological foundations for the maintenance and recovery of soil ecosystem functions. However, it remains unclear how soil micro-food web composition and network complexity are linked to soil ecosystem multifunctionality across different post-cropland restoration states. In this study, we used a space-for-time substitution approach and selected cropland and three post-cropland restoration states in the Taihang Mountains, including shrub–grassland, Populus spp. plantation, and Robinia pseudoacacia plantation, each with five plots, to examine changes in bacterial, fungal, and nematode communities, soil micro-food web network complexity, and soil ecosystem multifunctionality in topsoil and subsoil. Compared with cropland, bacterial diversity was higher in the shrub–grassland, Populus spp. and R. pseudoacacia plantations, whereas fungal diversity showed a marked decline in the Populus spp. plantation. Furthermore, the topsoil of the R. pseudoacacia plantation exhibited much higher micro-food web network complexity and soil multifunctionality than cropland, whereas differences among land-use types were relatively small in the subsoil. Structural equation modeling indicated that vegetation type, soil depth, soil moisture content, microbial diversity, nematode diversity, and soil micro-food web network complexity jointly explained 94% of the variation in soil ecosystem multifunctionality (R² = 0.94). Further random forest analysis identified soil depth as the most important predictor of soil ecosystem multifunctionality, followed by soil micro-food web network complexity; among biological variables, fungal diversity, bacterial diversity, omnivorous-predatory nematode diversity, and herbivorous nematode diversity also showed relatively high importance. Overall, these results suggest that changes in soil ecosystem multifunctionality across post-cropland restoration states were strongly soil-depth-dependent, and that soil micro-food web diversity and network complexity can serve as important biological indicators for assessing restoration outcomes. Full article

The comprehensive utilization of lignocellulose is still constrained by the inefficiency of its degradation. The application of a synthetic microbial community represents a promising strategy to promote straw decomposition. By employing multi-omics coupling techniques to explore the microbial community and functional composition of various straw-associated environments, we identified core microbial taxa driving straw decomposition and subsequently constructed three microbial communities: a bacterial community, a fungal community, and a cross-kingdom community. In particular, the bacterial community exhibited intrinsic synergistic effects, increasing its straw weight loss by 10.8–57.3% compared to single-constituent strains. Liquid fermentation experiments further verified that the bacterial community possessed excellent straw degradation performance, achieving net degradation rates of 26.4% within 3 days and 33.7% within 30 days under 1% (w/v) tobacco straw conditions. The bacterial community exhibited cellulolytic and ligninolytic enzyme activities. Metagenomic analysis revealed that the bacterial community was dominated by Paenibacillus (42.3–70.9%), followed by Paenarthrobacter (7.1–31.7%) and Microbacterium (6.5–26.2%). CAZy annotation revealed that the bacterial community harbored numerous lignocellulose-degrading genes, including those encoding glycoside hydrolases (GHs, 51.2%), carbohydrate esterases (CEs, 17.7%), and auxiliary activities (AAs, 5.7%). Non-targeted metabolomics analysis identified 1024 differentially expressed metabolites that were involved in alanine, aspartate, and glutamate metabolism; butanoate metabolism; and cofactor biosynthesis. These results indicate that a community constructed with multi-omics coupling techniques can effectively degrade lignocellulose, which provides meaningful guidance for constructing synthetic microbial consortia aimed at lignocellulose decomposition. Full article

Post-Byzantine portable icons are complex, multilayered heritage objects whose preservation may be influenced by interactions among their constituent materials, environmental conditions, and associated microorganisms. This study represents the first multidisciplinary investigation of this kind in Greece and examined five painted faces belonging to four post-Byzantine icons using a multidisciplinary approach combining environmental monitoring, stereomicroscopic and cross-sectional examination, Fourier transform infrared (FTIR) and micro-FTIR spectroscopy, scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM–EDS), culture-dependent microbiology, molecular identification, biofilm assessment, amplicon-based metabarcoding, and bacterial functional prediction. The results revealed substantial material and microbial heterogeneity among the examined icons and individual sampling locations. Material characterization revealed differences in the preparation layers, textile reinforcements, pigments, and surface coatings, including calcite, calcium sulfates, kaolinite, Prussian blue, Pb- and Fe-rich pigments, and HgS. Cultivable microorganisms showed variable biofilm-forming capacities. To address the minimal-sampling constraints inherent to cultural heritage objects, amplicon-based metabarcoding was used as a complementary approach to broaden microbial community characterization beyond the fraction recoverable by cultivation. Metabarcoding revealed diverse bacterial and fungal DNA signatures; however, these signatures indicate microbial association and do not, by themselves, demonstrate microbial viability, metabolic activity, or active biodeterioration. No single material- or conservation-related variable consistently explained the observed microbial patterns. Overall, the findings highlight the importance of considering microbial occurrence within the broader context of material composition, environmental conditions, and conservation state. This multidisciplinary approach provides a useful framework for contextualizing potential biological risk and supporting evidence-based preventive conservation strategies for painted wooden heritage objects. Full article

Organic amendments can improve soil C storage, nutrient availability, and crop production, particularly in purple soils with low organic matter and weak nutrient retention. They may also alter soil micro-food web processes. However, how different amendments affect bacteria–fungi–nematode associations remains unclear. We hypothesized that, relative to mineral fertilization alone, organic amendments would improve soil nutrient conditions, reshape bacterial and fungal communities, and increase microbivorous nematode abundance, whereas combined organic–mineral inputs would increase multitrophic co-occurrence network complexity. In a long-term wheat–maize rotation, soils were sampled in both seasons in 2023 under seven treatments: no fertilization (NF), mineral fertilization (NPK), manure (OM), straw return (RSD), mineral fertilization combined with manure (OMNPK), mineral fertilization combined with straw return (RSDNPK), and mineral fertilization combined with biochar (BCNPK). Among the organic amendment treatments, only RSD reduced wheat and maize yields relative to NPK. Fertilization mainly affected microbial community composition and nematode trophic structure, while microbial α diversity changed little. Network organization differed among fertilization regimes and between crop seasons. This study provides new insights into how long-term organic amendment regimes differentially regulate crop productivity, soil resource conditions, and soil micro-food webs, and advances our understanding of belowground multitrophic responses across wheat and maize seasons. Full article

The application of exogenous nutrient bags (ENBs) is critical for achieving high yields in morel mushroom cultivation; however, the high cost and lack of locally adapted formulations have become major constraints for the sustainable expansion of this industry. This study aimed to evaluate the effects of ten treatments, including a conventional formulation control, incorporating locally available agricultural by-products (rapeseed straw, organic fertilizer, alfalfa, and oats), on soil fertility, enzyme activity, microbial community structure, and ultimately the yield and quality of cultivated Morchella sextelata in Jianzha County, Qinghai. A randomized complete block design was established, and soil physicochemical properties, microbial biomass carbon/nitrogen/phosphorus (MBC/MBN/MBP), and enzyme activities (urease, phosphatase, and catalase) were measured at 38, 62, and 137 days post-application, while bacterial and fungal community compositions were characterized via high-throughput sequencing of 16S rRNA and ITS2 genes. Our results demonstrated that the wa-60 treatment (30% wheat + 60% alfalfa) outperformed all the other formulations, delivering the highest yield (1.32 ± 0.08 kg/m²) and a 28.6% increase over the control (1.03 ± 0.06 kg/m²; p < 0.01), while maintaining a high total amino acid content (19.8 g/100 g). Soil analysis revealed that wa-60 notably enhanced urease activity (peaking at 85 µg/g/h at day 137) and alkaline phosphatase activity (322.55 µg/g/h), alongside significant increases in MBC and MBN. Microbiome profiling further demonstrated that wa-60 selectively increased the relative abundance of various taxa, particularly the bacterial phylum Bacteroidota and the fungal phylum Mortierellomycota. Correlation analyses indicated strong positive associations among these enriched taxa (primarily at the genus level), enhanced enzyme activities, and improved soil nutrient availability. Collectively, these findings establish that the wa-60 formulation, leveraging locally sourced alfalfa, represents a cost-effective and high-performance strategy for morel cultivation in the Qinghai Plateau, providing a microbial–ecological basis for optimizing ENB design and offering a practical pathway for recycling agricultural waste in edible mushroom production. Full article

Pulque is a traditional Mexican beverage produced by the spontaneous fermentation of “aguamiel”, the sap of several Agave species. Fermentation is driven by adding a previously fermented inoculum, locally known as “semilla”, whose microbial community contributes to the sensory and physicochemical properties of the beverage. The objective of this study was to provide a preliminary characterization of the microbial taxonomic composition and functional potential of pulque inoculant prepared from Agave mapisaga and Agave salmiana using shotgun metagenomic sequencing. Six inoculum samples were sequenced on the DNBSEQ using 150 bp paired-end reads. Metagenomic DNA was extracted using a CTAB-based protocol and analyzed in the Galaxy platform. The workflow included quality filtering, host-sequence removal, taxonomic classification with Kraken2, assembly with MEGAHIT, and functional annotation with eggNOG Mapper. Bacterial communities in inoculum from A. mapisaga and A. salmiana sap were dominated by Acetobacter (68.1% and 58.3%) and Leuconostoc (19.5% and 21.9%). Komagataeibacter was more abundant in A. mapisaga inoculum (3.8%), whereas Zymomonas was more abundant in A. salmiana inoculum (11.7%). The greatest species-level difference was observed for Zymomonas mobilis, whose mean relative abundance was 6.4-fold higher in A. salmiana. Fungal communities were dominated by Saccharomyces (91.4% and 72.7%) and Kluyveromyces (6.6% and 25.5%) in A. mapisaga and A. salmiana, respectively. Across all replicates, the most abundant species were Acetobacter sp. AC2005 (23.9%), Saccharomyces paradoxus (17.0%), and Zymomonas mobilis (12.9%), together accounting for approximately 54% of the total relative abundance. Kluyveromyces marxianus was 3.9-fold more abundant in A. salmiana inoculum, whereas Saccharomyces paradoxus was 1.26-fold more abundant in A. mapisaga inoculum. Alpha-diversity analysis indicated higher bacterial diversity in A. mapisaga inoculum, with a Shannon index of 2.74 and 35 exclusive species, whereas A. salmiana inoculum showed greater fungal diversity, with a Shannon index of 0.68. These differences were not statistically significant (p > 0.05). However, beta-diversity analysis suggested substantial separation between the microbial communities associated with the two Agave species (R² ≈ 0.92). Functional annotation identified genes potentially associated with carbohydrate metabolism, sucrose degradation, and secondary metabolite biosynthesis. These findings suggest that the agave species used as the sap source may influence the taxonomic composition and functional potential of microbial communities involved in pulque fermentation. Full article

This study presents the first comprehensive characterization of the airborne microbiome in a zoological garden and its comparison with the surrounding atmospheric environment. The aim of this study was to evaluate potential human health hazards associated with occupational and visitor exposure in zoo environments across 24 sampling locations. The assessment included measurements of particulate matter (PM) and gaseous pollutants, microbiological contamination of air, surfaces, settled dust, and selected items of personal protective equipment (PPE). In addition, the cytotoxic potential of settled dust samples was evaluated using A549 human lung epithelial cells. The highest concentrations of airborne PM ranged from 0.250 mg/m³ for PM₁ to 0.278 mg/m³ for PM₁₀. The concentrations of chemical contaminants varied depending on the sampling location. Airborne bacterial counts ranged from 1.1 × 10² to 3.0 × 10² colony-forming units (CFU)/m³ in employee areas and from 2.2 × 10³ to 1.5 × 10⁴ CFU/m³ in visitor areas. The average microbial contamination of surfaces in both employee and visitor areas was 4.3 CFU/cm². Amplicon sequencing revealed that the airborne microbiome was dominated by bacterial taxa belonging to Bacillota, Pseudomonadota, and Actinomycetota, as well as fungal taxa representing the phyla Ascomycota and Basidiomycota. Settled dust samples exhibited variable cytotoxicity toward A549 cells, with half-maximal inhibitory concentration (IC₅₀) values ranging from 13.1 to 53.5 mg/mL. The findings provide novel insights into the molecular composition of zoo-associated airborne microbial communities and their potential implications for environmental health risk assessment and hygiene management practices in zoological gardens. Full article