Search Results (73)

Umbilical cord mesenchymal stromal cells (UC-MSCs) are a key element of regenerative medicine due to their ability to secrete growth factors that stimulate proliferation and angiogenesis, and modulate the inflammatory response. Despite their widespread use, the influence of the perinatal microenvironment on their biological properties remains poorly understood. The aim of this study was to assess the influence of pH and blood gas parameters in umbilical cord blood on the global transcriptomic profile of UC-MSCs and to analyze the correlation between the metabolic status of the newborn and the expression of key trophic factors: EGF, FGF2, FGFR1, FGFR3, GDNF, HGF, IGF1, NES, NGF, and PGF. Methods: The study was conducted in two stages. In the first phase, transcriptomic screening was performed using Affymetrix HuGene 2.0 ST microarray on cells isolated from three environmental groups defined by cord blood pH: acidic (pH < 7.35), physiological (7.35–7.39), and alkaline (pH ≥ 7.4). In the second phase, the results were validated using qPCR on an expanded study group (N = 50). Gene expression levels (RQ) were related to blood gas parameters (pH, pCO₂, pO₂, cHCO₃) and the presence of clinical features of threatened neonatal asphyxia. Results: Microarray analysis revealed that environmental pH acts as a molecular phenotypic switch. Under low pH conditions (<7.35), a shift in cell profile from proliferative to structural–migratory was observed. Significant overexpression of genes responsible for extracellular matrix (ECM) organization and adhesion (e.g., COMP, DCN, LUM, FMOD) was observed, while pathways related to cell cycle and cell division (↓CDK1, AURKA, TOP2A) were downregulated. qPCR validation confirmed these observations, demonstrating a strong positive correlation between blood pH and the expression of regenerative mediators: FGFR1 (r = 0.28), EGF (r = 0.30), NGF (r = 0.39), and IGF1 (r = 0.30). A negative correlation was also found between carbon dioxide pressure (pCO₂) and the expression of NGF, FGFR1, and EGF. A significant clinical finding was that in newborns diagnosed with threatened asphyxia, EGF, FGFR1, and NGF gene expression was significantly reduced, indicating impaired trophic potential of the cells in response to metabolic stress. Conclusions: These results indicate that cord blood gas parameters are critical regulators of the genetic activity of UC-MSCs. Metabolic and respiratory acidosis not only inhibit the cells’ proliferative potential but also force them into a matrix remodeling mode, permanently modifying their transcriptomic profile. This suggests that the neonatal acid–base status may serve as an objective indicator of the “biological quality” of isolated stromal cells, which has significant implications for their future applications in cell therapies. Full article

Soil depth and habitat degradation can reshape fungal communities in salt-affected wetlands, but their effects on fungal ecological processes remain insufficiently understood. This study examined soil fungi in the Halahai Provincial Nature Reserve and adjacent converted farmland in the western Songnen Plain, Northeast China, where salt-affected meadow soils correspond mainly to Solonetz. Four habitat types—reed wetland, meadow steppe, degraded Suaeda saline patch, and converted farmland—were sampled at 0–20 cm and 20–40 cm soil depths. Soil properties, fungal diversity, taxonomic composition, environmental associations, niche breadth, assembly processes, and FUNGuild-based trophic modes were analyzed using ITS sequencing. Degraded Suaeda soils showed the strongest salinity–alkalinity stress, with pH values of 10.34–10.30 and electrical conductivity of 1.70–1.75 dS·m⁻¹. Fungal richness was highest in surface-converted farmland, with a Sobs value of 423.33, and lowest in deeper degraded Suaeda soil, with a Sobs value of 86.00. Ascomycota dominated most groups, especially degraded Suaeda soils, where its relative abundance reached 75.29–76.80%. ANOSIM confirmed significant community dissimilarity among habitat-depth groups (R = 0.56878, p = 0.001). Specialists accounted for 68.07% of fungal taxa, and stochastic processes, especially drift and dispersal limitation, contributed substantially to assembly. These results indicate that soil depth, salinity–alkalinity, and habitat conversion jointly regulate fungal community structure and ecological processes in degraded soda saline–alkali wetlands. Full article

Mixed plantations of Pinus sylvestris var. mongolica with native shrubs are widely established in semiarid sandy landscapes, yet soil microbial responses may differ among mixed-planting modes depending on the companion shrub species. We compared soil bacterial and fungal communities across three approximately 9-year-old mixed-planting modes in the Mu Us Sandy Land, where P. sylvestris var. mongolica was combined with Juniperus sabina (Ps–Js), Salix psammophila (Ps–Sp), or Corethrodendron fruticosum (Ps–Cf). Planting configuration was associated with shifts in soil physicochemical conditions. Bacterial α-diversity did not differ among modes, whereas fungal α-diversity was higher in Ps–Sp. Community composition diverged across modes for both domains, and LEfSe identified configuration-specific taxa. Null-model analyses showed that bacterial assembly was consistently dominated by stochastic components, whereas the relative contributions of fungal assembly processes varied among mixed-planting modes. Functional inference further suggested mode-associated differences in fungal trophic guild composition, with Ps–Cf showing significantly higher ectomycorrhizal abundance and Ps–Sp showing higher representation of saprotroph-associated guilds; by contrast, predicted bacterial functional profiles were broadly comparable among modes. Together, these results indicate that bacterial and fungal communities showed different response patterns among mixed-planting modes: bacterial communities showed compositional differentiation but little variation in α-diversity and consistently stochastic assembly, whereas fungal communities showed mode-related changes in α-diversity, the relative contributions of assembly processes, and trophic guild composition. These findings provide a microbial basis for considering shrub-species selection when designing P. sylvestris var. mongolica mixed plantations in semiarid sandy ecosystems. Full article

Phenolics in Sphagnum can inhibit its microbial decomposition. Climate warming and drainage have driven vascular plants, such as Ericaceae, to expand into Sphagnum-dominated peatland. However, the impact of fine root invasion by Rhododendron auriculatum Hemsl. on Sphagnum decomposition and changes in phenolic compounds remains unclear. This study compared Sphagnum decomposition in a Sphagnum palustre L.-dominated peatland and an R. auriculatum (Sapling)–S. palustre peatland by examining the microscopic structure of S. palustre and microbial community composition. Decomposition was higher in the R. auriculatum–S. palustre peatland. On this site, bacterial metabolic types such as aerobic chemoheterotrophy and chemoheterotrophy had higher relative abundances, as did fungal trophic modes, including those with combined ectomycorrhizal, ericoid mycorrhizal, and saprotrophic functions. Acid phosphatase, laccase, total nitrogen (TN), C/N ratio (C:N), and pH differed significantly across decomposition stages. Microbial communities are affected by physicochemical factors and enzyme activities. Untargeted metabolomics revealed more downregulated than upregulated phenolics, cinnamic acids, and tannins, indicating loss of phenolic compounds. In summary, R. auriculatum fine root invasion altered enzyme activities and physicochemical properties, driving the restructuring of bacterial and fungal trophic modes and accelerating S. palustre cell wall and hyaline cell decomposition. Full article

Sewage sludge management poses major environmental challenges due to increasing production and concerns about contaminants and microbial risks. Vermicomposting offers a sustainable biological treatment, yet the extent to which different earthworm species shape microbial outcomes remains poorly understood. Here, we examined how gut transit by three epigeic (Eisenia andrei, E. fetida, and Dendrobaena hortensis) and two anecic (Lumbricus friendi and L. terrestris) earthworm species alters bacterial and fungal communities in fresh sewage sludge. Using 16S rRNA and ITS amplicon sequencing combined with multivariate, differential-abundance, and functional prediction analyses, we compared sludge and earthworm cast bacteriomes and mycobiomes. Earthworm gut transit caused pronounced species-specific restructuring of bacterial and fungal community composition, diversity, and functional profiles, with clear separation between sludge and cast communities. Functional analyses indicated coordinated shifts in bacterial metabolic potential and fungal trophic modes consistent with enhanced biosynthetic and decomposer functions. Pathogen profiles were reshaped in a host-dependent manner, with low overall abundances and selective changes rather than uniform suppression. These findings demonstrate that vermicomposting outcomes depend strongly on earthworm species and microbial kingdom, highlighting the importance of earthworm lifestyle diversity when evaluating the ecological safety and agronomic potential of sludge-derived amendments. Full article

Analyzing microplastics in marine organisms is essential for understanding the ecological and toxicological impacts of marine microplastic pollution in coastal food webs. This study investigated microplastic ingestion in three edible invertebrate species commonly found on Vietnamese sandy beaches, wedge clam Donax sp., hermit crabs Pagurus sp., and horn-eyed ghost crabs Ocypode ceratophthalmus, which differ in feeding modes and mobility, using micro-Fourier Transform Infrared spectroscopy (µ-FTIR) with a detection limit of 20 µm. Results showed that all three species ingested microplastics, with ingestion patterns varying according to species-specific traits and habitat-related feeding behaviors. The highly mobile crabs Ocypode ceratophthalmus (omnivore) and Pagurus sp. (scavenger) were found to partially reflect the polymer pollution in their ambient environment. The higher ingestion rate and diversity of polymer types observed in sedentary Donax sp. suggest that this species could serve as a potential bioindicator for microplastic pollution, given its mixed suspension and deposit feeding habits that integrate pollution from both the water column and beach sediments. Overall, these results reveal widespread microplastic ingestion among edible beach fauna, highlighting potential ecological and human health concerns, and emphasizing the need for targeted pollution management and increased public awareness. Advancing our understanding will require larger datasets and controlled experiments to more robustly assess species-specific responses and the likelihood of trophic transfer. Full article

Land-use change strongly affects soil microbiota, yet the role of agroecological systems in shaping soil fungal communities remains poorly understood in tropical soils. We evaluated the diversity, trophic modes, community composition, and co-occurrence networks of culturable soil fungal taxa across a land-use gradient in the Colombian Andes–Amazon transition zone. Agroecological systems—including improved pasture (IP), cacao and copoazu agroforestry systems (CaAS and CoAS), secondary forest with agroforestry enrichment (SFAE), and a moriche palm swamp ecosystem (MPSE)—were compared with dominant land-uses (degraded pasture, DP and old-growth forest, OF). Fungi were isolated using the soil dilution plate method and identified based on morphological and molecular characteristics, and soil physicochemical properties were measured to evaluate their relationships with fungal community patterns. A total of 420 isolates were assigned to 93 fungal species. Alpha-diversity metrics revealed significantly higher fungal richness in OF and MPSE, and higher Shannon diversity in agroforestry and forest-based systems, whereas DP exhibited the lowest values. Ordination analyses showed clear differences in fungal community composition, with CoAS displaying the most distinct assemblage. Agroecological and forest-based systems favored saprotrophic and symbiotrophic modes. Co-occurrence network analyses indicated that MPSE, OF, and IP supported more complex and modular fungal networks. Soil pH and total phosphorus (TP) were key drivers of fungal community composition, whereas exchangeable calcium, TP, soil organic carbon, and base saturation were associated with network attributes. Overall, our findings highlight the importance of agroecological management for soil fungal diversity and network organization in Amazonian transition landscapes. Full article

Fungi are a critical component of microbial biomass in agricultural soils, but their distribution across soil depths under different cover crops remains poorly understood. We used high-throughput sequencing of fungal ITS1 amplicons to characterize fungal communities across four soils depths (0–2, 2–4, 4–10, and 10–20 cm) in experimental field plots under four cover crop treatments: winter fallow reference (REF), cereal rye (CRYE), wild pennycress (WPEN), and a mixture of pea, crimson clover, radish, and oat (PCRO). There was no significant interaction between soil depth and cover crop treatment on both alpha diversity and beta diversity. CRYE and PCRO cover crops had low abundance of Fusarium, a genus including many important plant pathogens, and different fungal community composition relative to REF. Fungal diversity was significantly higher at 4–10 cm compared to 0–2 cm depth, but fungal richness was not affected by soil depth. Fungal community composition differed significantly between 0–4 and 10–20 cm soil depths. The relative abundance of Mortierella and unclassified Basidiomycota increased with increasing soil depth while that of Calvatia, Cryptococcus, Fusarium, and Idriella decreased with increasing soil depth. Most fungal taxa were assigned to more than one guild, but the few taxa that were classified as strict saprophytes decreased with increasing soil depth while those classified as strict symbionts increased with increasing soil depth. These differences were associated with low pH and high content of OM, K, S, P, and Zn in the topsoil layer compared to the deeper soil layer. The findings may inform the development of targeted soil management practices to promote beneficial fungi, but additional studies covering multiple study sites and sampling dates are needed for clarity. Full article

Integrated multi-trophic aquaculture (IMTA) has emerged as an ecological intensification strategy capable of enhancing nutrient utilization and improving environmental stability in mariculture systems, yet the microbial mechanisms driving nutrient transformations remain insufficiently understood. This study investigated how culture mode (IMTA vs. monoculture) shape water quality, sediment microbial communities, and nutrient cycling processes in a shrimp–sea urchin system by combining water-quality monitoring, nutrient analysis, 16S rRNA high-throughput sequencing, and redundancy analysis. IMTA significantly increased turbidity, chlorophyll-a, phosphate, ammonium, and nitrite compared with monoculture, while physico-chemical parameters remained stable. Sediment microbiota in IMTA exhibited substantially higher alpha diversity and showed a clear compositional separation from monoculture communities. At the genus level, IMTA sediments were enriched in Vibrio, Motilimonas, and Ruegeria, distinguishing them from monoculture systems. At the phylum level, IMTA was characterized by increased abundances of Proteobacteria and Bacteroidota, accompanied by a marked decline in Spirochaetota. Functional predictions indicated that microbial communities were predominantly characterized by pathways related to amino acid and carbohydrate metabolism, as well as nutrient remineralization. RDA and correlation analyses further identified turbidity, chlorophyll-a, phosphate, ammonium, and nitrite as the principal drivers of microbial divergence. Overall, the findings demonstrate that IMTA reshapes sediment microbial communities toward more efficient nutrient-processing assemblages, thereby promoting active nitrogen and phosphorus transformations and improving biogeochemical functioning relative to monoculture. These results provide mechanistic insight into how IMTA supports nutrient recycling and environmental sustainability in modern mariculture systems. Full article

The aim of this study was to determine fungal diversity and composition in an area of high host diversity and identify the organisms involved in the appearance of symptoms in Pinus needles. Asymptomatic and symptomatic live needle samples were obtained from different Pinus spp. in an arboretum with confirmed presence of brown spot needle blight. The samples were analysed using high-throughput sequencing of fungal ITS2rDNA. Ascomycota dominated all samples, with Lophodermium as the most abundant genus, although it showed lower representation in symptomatic needles. Other genera with recognised pathogenic potential, including Lecanosticta, Pestalotiopsis, Cyclaneusma, Rhizosphaera, Neophysalospora, and Cenangium, were also detected, whereas the Dothistroma genus was absent despite its presence in the region. Alpha diversity was higher in asymptomatic needles, with a significant difference only for the Shannon index, while Bray–Curtis dissimilarity revealed significant shifts in community composition between needle types. Functional guilds were dominated by pathotroph–saprotroph trophic mode, and the functional guild ‘plant pathogen’ was the most abundant across samples. These findings identify fungal genera associated with symptomatic and asymptomatic needles and provide guidance for future targeted isolation and detailed morphological and molecular identification using more resolutive techniques, enabling a deeper understanding of pathogenic community presence and their potential synergistic interactions. Full article

Soil fungi play an indispensable role in maintaining soil ecosystem functions. However, how forest succession and soil depth interactively shape fungal community composition and diversity remains poorly understood. To address this, we investigated fungal communities across four successional stages and two soil depths (0–10 cm and 40–60 cm) in a subalpine forest on the eastern Qinghai–Tibetan Plateau using Illumina high-throughput sequencing. Results showed that the soil fungal community composition of different trophic modes varied significantly with both succession and soil depth. The α-diversity of symbiotic and saprotrophic fungi responded to succession in a depth-dependent manner, while β-diversity across all trophic modes was primarily driven by species turnover. Soil properties and vegetation factors collectively explained 69.85–82.91% of the variation in soil fungal community composition, with their effects being dependent on both soil depth and trophic mode. Specifically, in topsoil, the β-diversity of symbiotic fungi was influenced only by soil property heterogeneity, whereas that of saprotrophic and pathogenic fungi was shaped by both vegetation and soil property heterogeneity. In subsoil, symbiotic fungal β-diversity was co-regulated by vegetation and soil properties heterogeneity, while saprotrophic fungal β-diversity was driven solely by soil properties heterogeneity. This study demonstrates that soil depth modulates the successional dynamics of soil fungal communities and highlights the trophic-dependent drivers of fungal assembly in forest soils. Full article

Ziziphus lotus (L.) Lam., (Rhamnaceae) a resilient shrub native to Moroccan’s arid regions, functions as a keystone species by creating microhabitats that buffer temperature extremes, retain soil moisture, and accumulate organic matter. However, its role in structuring soil fungal diversity and community composition in these environments remains largely unexplored. This study investigated the spatial distribution of fungal communities associated with Z. lotus in barley-planted and non-planted fields. Soil samples were collected at 0, 3, and 6 m from shrub clusters during the barley harvest. The fungal community was dominated by Ascomycota (93.5%). Alpha diversity indices (Shannon–Wiener and Simpson) were significantly higher near shrub bases (0 and 3 m) compared to more distant soils (6 m), indicating a clear decline in diversity with distance (0 m vs. 6 m: p = 0.0012; 3 m vs. 6 m: p = 0.0007). Soil physicochemical parameters, including calcium carbonate content, nitrate, and salinity, significantly influenced fungal diversity (p ≤ 0.05). Beta diversity analysis revealed significant spatial differentiation in fungal community composition (PERMANOVA: p = 0.001). Overall, fungal richness and diversity were highest near shrub. Genera such as Cladosporium, Fusarium, and Alternaria were more abundant near shrub bases, while taxa like Didymellaceae and Alfaria were specially restricted. Functional predictions indicated dominance of fungi with mixed trophic modes (pathotroph–saprotroph–symbiotroph), suggesting ecological plasticity. Despite barley cultivation, the fungal community structure remained largely similar between the planted and non-planted fields. Overall, our findings underscore the ecological importance of Z. lotus as a reservoir of stress-tolerant fungi and as a potential keystone species for restoring degraded arid ecosystems. Full article

First discovered in 1977, Abies ziyuanensis (Pinaceae) is listed as an endangered species by the International Union for Conservation of Nature (IUCN); its population continues to decline. Analyzing the rhizospheric fungal communities in the two largest populations of A. ziyuanensis within the Yinzhu Laoshan National Nature Reserve in Guangxi Zhuang Autonomous Region, China, and factors influencing the rhizosphere will establish a theoretical framework for the reintroduction of A. ziyuanensis. This study used ITS rRNA gene high-throughput sequencing and statistical data analysis to compare the functional diversity and structure of the molecular ecological network of rhizospheric fungal communities between A. ziyuanensis populations in Yinzhu Laoshan mountain in Guangxi at two sites, Shenbaotang and Sanjiaohutang. A total of 1755 OTUs were identified from the rhizospheric samples of 30 A. ziyuanensis; these were classified into seven trophic modes and 81 functional guilds. The most important functional types corresponded to the fungal phyla Ascomycota, Mortierellomycota, and Basidiomycota. Changes in the structure of the functional molecular ecological network of the rhizospheric fungal communities of A. ziyuanensis were mainly related to soil nutrient conditions and soil water content, with AK and TK being the most critical. The functional molecular ecological networks of the rhizosphere of A. ziyuanensis differed among populations; distinct functional-gene profiles were detected in the rhizosphere microbiomes of different A. ziyuanensis populations. These findings provide insight into the role of unique rhizospheric fungi in the growth and environmental adaptation of A. ziyuanensis, and for the discovery of superior rhizosphere-promoting fungi. Full article

The order Pezizales (Ascomycota) consists of cup and truffle fungi growing in a wide range of habitats and geographical zones worldwide, exhibiting diverse nutritional behaviors. In Israel, morphological studies have designated most Pezizales as saprotrophs. We re-screened Pezizales mushrooms collected in northern Israel between 2020–2022 using molecular tools based on DNA sequences of partial large subunit rRNA (28S), internal transcribed spacer (ITS), and partial heat shock protein (Hsp90) regions, along with macro images of each freshly collected samples. Trophic mode was determined through available literature and δ¹³C and δ¹⁵N stable isotope analysis along with a quadratic discriminator analysis (QDA) model to predict trophic modes: 112 collections were positively identified with identification of 23 genera; 23 taxa were resolved to the species level, 11 to approximate species, and 15 to the genus level. Helvella was the most species-rich genus; 25 species and species approximations were newly reported for Israel. Further molecular phylogenetic studies are needed to resolve species identity of the Israeli Pezizales. Most Pezizales collections were determined by trophic mode studies to be ectomycorrhizal, with a few saprotrophs. The QDA model yielded several samples with undefined nutritional behavior or a different trophic mode than previously inferred, suggesting that more in-depth study is needed to understand their trophic ecology. This study improves knowledge regarding species diversity, ecology, and evolution of Israeli Pezizales. Full article

Euglena gracilis is a metabolically versatile microalga capable of thriving under photoautotrophic (light, no ethanol), mixotrophic (light with 1% v/v ethanol), and heterotrophic (dark with 1% v/v ethanol) conditions. Here, we applied untargeted LC-MS metabolomics (Agilent 1290 LC, 6545XT QTOF-MS; Agilent Technologies, Santa Clara, California, USA) to investigate its trophic-mode-dependent metabolic adaptations and assess its biotechnological potential. Metabolites were separated on a C18 column and analyzed in both positive and negative ion modes. Multivariate analyses (PCA and sPLS-DA) revealed clear and reproducible metabolic separations among growth modes (p < 0.001). Photoautotrophic cultures were enriched in phenolic acids, flavonoids, and lipid classes associated with oxidative stress protection. Mixotrophy induced a broader spectrum of upregulated metabolite classes, including saccharolipids, macrolactams, and triterpenoids, reflecting a hybrid metabolism combining photosynthesis and ethanol utilization. Heterotrophic cultures showed elevated levels of polyamines and amino acids (e.g., putrescine, proline), indicative of redox regulation and stress adaptation in dark, ethanol-rich conditions. Class-level comparisons identified distinct and shared metabolite categories, with photoautotrophy favoring antioxidant biosynthesis and mixotrophy supporting metabolic diversity. These findings provide metabolite-level insights into the extraordinary plasticity of E. gracilis and offer a framework for optimizing cultivation strategies to enhance the targeted production of high-value bioproducts. Full article