Search Results (645)

Studies of microbial degradation of historic woods are essential to help protect and preserve these important cultural properties. The USS Cairo is a historic Civil War gunboat and one of the first steam-powered and ironclad ships used in the American Civil War. Built in 1861, the ship sank in the Yazoo River of Mississippi in 1862 after a mine detonated and tore a hole in the port bow. The ship remained on the river bottom and was gradually buried with sediments for over 98 years. After recovery of the ship, it remained exposed to the environment before the first roofed structure was completed in 1980, and it has been displayed under a tensile fabric canopy with open sides at the Vicksburg National Military Park in Vicksburg, Mississippi. Concerns over the long-term preservation of the ship initiated this investigation to document the current condition of the wooden timbers, identify the fungi that may be present, and determine the elemental composition resulting from past wood-preservative treatments. Micromorphological characteristics observed using scanning electron microscopy showed that many of the timbers were in advanced stages of degradation. Eroded secondary cell walls leaving a weak framework of middle lamella were commonly observed. Soft rot attack was prevalent, and evidence of white and brown rot degradation was found in some wood. DNA extraction and sequencing of the ITS region led to the identification of a large group of diverse fungi that were isolated from ship timbers. Soft rot fungi, including Alternaria, Chaetomium, Cladosporium, Curvularia, Xylaria and others, and white rot fungi, including Bjerkandera, Odontoefibula, Phanerodontia, Phlebiopsis, Trametes and others, were found. No brown rot fungi were isolated. Elemental analyses using induced coupled plasma spectroscopy revealed elevated levels of all elements as compared to sound modern types of wood. High concentrations of boron, copper, iron, lead, zinc and other elements were found, and viable fungi were isolated from this wood. Biodegradation issues are discussed to help long-term conservation efforts to preserve the historic ship for future generations. Full article

Organic manure and grass mulching are widely recognized as modifiers of soil microbial communities and nutrient dynamics; however, the combined effects of these practices on nitrogen fractionation and microbial functionality in orchard ecosystems remain poorly understood. This study conducted a comprehensive evaluation of soil nitrogen fractions, enzymatic activity, microbial diversity and functional traits in walnut orchards under three management practices: organic manure (OM), grass mulching combined with manure (GM), and chemical fertilization (CF) in China’s Loess Plateau. The results revealed that OM and GM significantly enhanced soil nutrient pools, with GM elevating total nitrogen by 1.96-fold, soil organic carbon by 97.79%, ammonium nitrogen by 128%, and nitrate nitrogen by 54.56% relative to CF. Furthermore, the OM significantly increased the contents of total hydrolysable nitrogen, amino sugar nitrogen, amino acid nitrogen, ammonia nitrogen, hydrolysable unidentified nitrogen, non-acid-hydrolyzable nitrogen compared to the CF and GM treatments. Meanwhile, ASN and AN had significant effects on mineral and total nitrogen. The OM and GM had higher activities of leucine aminopeptidase enzymes (LAP), α-glucosidase enzyme, β-glucosidase enzyme (βG), and N-acetyl-β-D-glucosidase enzyme (NAG). Microbial community analysis revealed distinct responses to different treatments: OM and GM enhanced bacterial Shannon index, while suppressing fungal diversity, promoting the relative abundance of copiotrophic bacterial phyla such as Proteobacteria and Chloroflexi. Moreover, GM favored the enrichment of lignocellulose-degrading Ascomycota fungi. Functional annotation indicated that Chemoheterotrophy (43.54%) and Aerobic chemoheterotrophy (42.09%) were the dominant bacterial metabolic pathways. The OM significantly enhanced the abundance of fermentation-related genes. Additionally, fungal communities under the OM and GM showed an increased relative abundance of saprotrophic taxa, and a decrease in the relative abundances of potential animal and plant pathogenic taxa. The Random forest model further confirmed that βG, LAP, and NAG, as well as Basidiomycota, Mortierellomycota, and Ascomycota served as pivotal mediators of soil organic nitrogen fraction. Our findings demonstrated that combined organic amendments and grass mulching can enhance soil N retention capacity, microbial functional redundancy, and ecosystem stability in semi-arid orchards. These insights support the implementation of integrated organic management as a sustainable approach to enhance nutrient cycling and minimize environmental trade-offs in perennial fruit production systems. Full article

Urban lawns are a predominant form of vegetation in sports grounds and greenbelts. Nitrogen (N) fertilization is widely used to sustain lawn productivity. However, it also promotes nitrous oxide (N₂O) emissions, a potent greenhouse gas. The microbial mechanisms underlying N₂O emissions from fertilized lawn soils remain poorly understood. In this study, we conducted a controlled incubation experiment with four N application rates [0 (N0), 100 (N100), 200 (N200), and 300 kg·ha⁻¹·yr⁻¹ (N300)] to investigate N₂O emissions and associated microbial processes in urban lawn soil. Biological inhibitors combined with high-throughput sequencing were used to quantify the inhibitor-sensitive fraction of fungi and bacteria contributing to N₂O emissions. Our results showed that N fertilizer significantly increased N₂O emissions, with the highest emission observed under N200. The fungi inhibitor-sensitive fraction accounted for ~45% of total N₂O emissions, significantly higher than that of bacteria (~31%). Dominant fungal phyla included Ascomycota, Basidiomycota, and Zygomycota, with N fertilization significantly increasing the relative abundance of Ascomycota and decreasing that of Basidiomycota. Redundancy analysis revealed strong positive correlations between Ascomycota abundance and N₂O emissions across N treatments. At the genus level, Pyrenochaetopsis, Myrothecium, and Humicola were positively associated with N₂O production and identified as key functional taxa. These findings demonstrate that moderate N fertilization can disproportionately stimulate fungal-driven N₂O emissions in urban lawns. The results provide a scientific basis for optimizing N fertilization strategies in green spaces, with implications for N policy and sustainable landscape management. Full article

In the Red List of Threatened Species, released by International Union for Conservation of Nature (IUCN), Paphiopedilum helenae has been classified as an endangered species. It exhibits exceptional decorative value and germplasm resource potential. To elucidate the ecological adaptation of this species and the characteristics of its rhizosphere microbiome, bacterial 16S rRNA and fungal ITS sequences of three wild populations of P. helenae were investigated using Illumina high-throughput sequencing technology and the microbial community structures and diversities were systematically compared. These three populations were spanned across distinct geographical locations in Longzhou County, Guangxi. The results showed that the bacterial community in the rhizosphere soil of P. helenae comprised 31 phyla, primarily including Actinobacteriota, Proteobacteria, Chloroflexi and Acidobacteriota. On the other hand, the fungal community consisted of 10 phyla, dominated by Ascomycota and Basidiomycota. There were significant differences in the diversity of rhizosphere microbes across different populations of P. helenae. The LG population had the highest bacterial richness (Chao index: 2912.71 ± 131.73; p < 0.05) and diversity (Shannon index: 6.40 ± 0.06; p < 0.01), while the MQ population had the lowest diversity (Shannon index: 3.47 ± 0.24; p < 0.01) of fungi. The degree of variation in fungal β-diversity was significantly higher than that of bacteria. Soil organic matter (SOM) and available nitrogen (AN) contents were the core factors shaping the microbial communities in the rhizosphere soil of P. helenae, which jointly explained 49.87% and 16.39% of variations in the bacterial and fungal communities. Furthermore, population-specific enrichment of functionally significant microorganisms was evident. Population MQ was enriched with plant growth-promoting and stress-resistant fungi, such as Geminibasidium, Trichoderma, etc. Population LG was enriched with oligotrophic bacteria (e.g., Patescibacteria), while population SL exhibited an overwhelming dominance of Ascomycota (93.25%) and enrichment of pathogenic fungal genus Nigrospora. This research revealed the variations in the functional adaptation strategy of P. helenae and the microbial communities in the rhizosphere soils across different geographical locations. This suggests that microbial community imbalance in rhizosphere soil may be one of the factors leading to the endangerment of this plant species. The study proposed a differentiated protection strategy for endangered plant species based on microbial resources. The results provide a theoretical basis for development of a “microorganism-assisted protection” strategy for ecological restoration and sustainable utilization of endangered orchid plants. Full article

Caves and other subterranean ecosystems are characterized by stable, low temperatures, high humidity, and limited nutrient input, creating unique environments for extremophilic microorganisms. Among them, fungi play key roles in organic matter degradation, mineral interactions, and biogeochemical cycling, yet the diversity and adaptations of cold-adapted fungi in cave habitats remain insufficiently explored. This study investigated psychrophilic and psychrotolerant fungi inhabiting the stone surfaces of Ravništarka Cave in Eastern Serbia. Biofilm samples were collected from nine sites and analyzed using culture-based isolation on both nutrient-rich and diluted media, followed by incubation at 10 °C, 25 °C, and 37 °C. Fungal identification combined morphological characteristics with molecular analyses of the ITS region and BenA gene, while ecological roles were assigned using FUNGuild. A total of 41 fungal species were documented, spanning Ascomycota (53.1%), Basidiomycota (43.7%), and Mortierellomycota (3.1%) phyla. The genus Penicillium exhibited the greatest species richness, with 14 taxa documented, including P. chrysogenum, P. glandicola, and P. solitum, all previously associated with cold or oligotrophic environments. The psychrotolerant species Mortierella alpina was the only representative of Mortierellomycota. Ecological guild assignment revealed fungi functioning at different trophic levels, highlighting their multifunctional ecological roles in extreme subterranean habitats. Full article

Endophytic fungi represent key microbial symbionts that colonize internal plant tissues without causing apparent disease, playing vital roles in host growth, stress resistance, and biosynthesis of bioactive compounds. Carpesium lipskyi C. Winkl., a medicinal plant endemic to the Gaoligong Mountains in Yunnan, remains largely unexplored regarding its endophytic fungal composition. In this study, a total of 737 amplicon sequence variants (ASVs) were identified through high-throughput sequencing, spanning 9 phyla, 36 classes, 67 orders, 137 families, 206 genera, and 277 species. The dominant phyla were Ascomycota, Basidiomycota, and Glomeromycota. Alpha diversity in stems and leaves followed a unimodal distribution along the elevational gradient, in contrast to root endophytic communities, which showed no significant correlation with altitude. Peak diversity occurred at 2734 m, indicating a non-linear altitude-diversity relationship. Altitude, along with stable precipitation and temperature (2600–3210 m), significantly influenced fungal diversity. Medicinal fungi such as Cladosporium sp., Meyerozyma guilliermondii, Phialocephala fortinii, and Rhodotorula mucilaginosa were found in either roots or stems. This is the first comprehensive assessment of endophytic fungi in C. lipskyi from this region, providing a foundation for future ecological and pharmacological studies. Full article

Microalgae cultivation is often limited by the high cost and inefficiency of harvesting, making it a major barrier to large-scale resource recovery. Traditional methods such as centrifugation or chemical flocculation are expensive and environmentally unsustainable. As a biological alternative, filamentous fungi can form pellets or hyphal networks that entrap microalgae cells via bio-flocculation, facilitating easier separation from the culture medium. This study aimed to optimize culture conditions for fungal pellet formation and develop effective microalgae–fungal composites for improved harvesting. Fungal isolates including Aspergillus niger, A. fumigatus, A. flavus, and unidentified strains were screened for their pelleting capacity and nutrient removal efficiency. Through OVAT analysis, key factors such as pH, agitation speed, carbon source, and C:N ratio were found to significantly influence pellet formation. One isolate (FP) showed strong potential, forming pellets under stationary conditions and performing best at neutral to alkaline pH. Molecular analysis identified FP as a fungal consortium containing members of Ascomycota, Mucoromycota, Basidiomycota, and Rozellomycota. When applied to cocoa pulp wastewater, the microalgae–fungi composites outperformed monocultures in reducing NH₄⁺-N, COD, and PO₄³⁻-P. Interestingly, microalgae delayed fungal sporulation. These findings highlight the potential of fungal consortia in enhancing both microalgae harvesting and wastewater bioremediation. Full article

This study investigates the diversity and provides a preliminary evaluation of the enzymatic potential of culturable fungi present in two-phase olive mill waste (TPOMW), a lignocellulose- and phenolic-rich agro-industrial by-product generated in large quantities in olive oil-producing countries. Ninety-four isolates, representing 31 species of the phyla Ascomycota, Basidiomycota, and Mucoromycota, were obtained and identified by using ITS, 28S, tef1-α, tub2, rpb2, act, and/or cal sequences. Among the identified taxa, two new Trichoderma species within the Harzianum clade, namely Trichoderma amurcicola (phylogenetically related to T. simile and T. guizhouense) and Trichoderma olivarum (phylogenetically related to T. simmonsii), were described following a multilocus phylogenetic analysis combined with a study of their morphoanatomical features. A rather high phylogenetic divergence was detected in Candida boidinii, Pleurostoma richardsiae, and Mucor circinelloides, while Cladosporium limoniforme, Mucor pseudolusitanicus, Stagonosporopsis ailanthicola, and Talaromyces nanjingensis were recorded for the first time in TPOMW. A preliminary screening revealed 29 species with cellulolytic and/or xylanolytic activities; 26 species displayed dye decolorization capacity, while ligninolytic and laccase activities were restricted to a few taxa. The most promising degraders of lignocellulosics included strains of Cladosporium limoniforme, C. ramotenellum, Fuscoporia ferrea, Peniophora lycii, and Pseudophlebia setulosa. Fungi detected in TPOMW are promising biotechnological tools to be exploited in the frame of circular economy applications. Full article

Forest ecosystems undergo seasonal shifts in bacterial and fungal communities, but little is known about the specific microbiota associated with Quercus robur–Boletus edulis systems. This study represents the first examination of seasonal changes in soil microbiota in pedunculate oak habitats in Galicia (NW Spain) and their relationship with Boletus edulis and Boletus reticulatus mycelium prevalence and concentration. Soil microbiota richness, diversity, and composition, as well as seasonal variation in Boletus mycelium, were assessed using DNA metabarcoding and qPCR, respectively. Sampling was conducted in autumn at two 30–40-year-old Q. robur stands. Bacterial communities were dominated by Acidobacteria (34%) and Proteobacteria (33%), with Acidobacterium (12%), Paludibaculum (9%), and Edaphobacter (7%) identified as most abundant. Fungal communities were primarily Basidiomycota (93%), led by Russula (46%). For both bacteria and fungi, the highest OTU richness was observed in September, followed by a significant decrease in October and a partial recovery in November. Boletus species were found to exhibit positive correlations with specific bacteria (e.g., Massilia, Rhizobium) and fungi (e.g., Amanita, Clavaria, Inocybe, Scleroderma, Suillus and Mortierella), suggesting a potential influence of these microbes on mycelium development. This study provides novel insights into the seasonal dynamics of soil microbiota and their potential role in Boletus ecology, thereby advancing understanding of host–microbe interactions in temperate forests. Full article

Karst rivers are increasingly contaminated by both heavy metals and nanoplastics, yet their combined impact on riparian litter decomposition remains unresolved. We conducted a 90-day microcosm experiment using Miscanthus floridulus leaf litter collected from the Donghe River, Jishou, China, and exposed it to Pb (1 mg L⁻¹), polystyrene nanoplastics (10 and 100 µg L⁻¹), and their combinations. Pb alone modestly inhibited mass loss (61.0%) and respiration, while NP10 significantly accelerated decomposition (67.0%), and NP100 suppressed it (60.4%); co-exposure produced non-monotonic, concentration-dependent effects. Enzyme stoichiometry revealed that all treatments intensified nitrogen limitation but alleviated carbon limitation through reduced microbial activity. Bacterial communities, dominated by Pseudomonadota, exhibited remarkably stable phylum-level composition, high network complexity, and identical keystone taxa across all treatments, indicating strong functional redundancy and resilience. In contrast, fungal communities suffered severe declines in Basidiomycota abundance, collapsed network stability, and a single keystone taxon, underscoring their vulnerability. βNTI–RC_bray analyses demonstrated that stochastic processes (>50%) overwhelmingly governed both bacterial and fungal assembly, with only marginal deterministic shifts. Collectively, our findings highlight that bacteria—not fungi—serve as the primary decomposers under Pb–NP co-stress and that stochastic assembly, coupled with bacterial redundancy, buffers ecosystem function against emerging mixed pollutants in subtropical riverine systems. Full article

Background/Objectives: We evaluated eukaryotic diversity in two cores obtained from abyssal sediments collected at depths of 4280 m and 4444 m in the equatorial Atlantic, between the Fernando de Noronha and São Pedro and São Paulo archipelagos, using a DNA metabarcoding approach applied to environmental DNA (eDNA) samples. Results: In total, we detected 248,905 DNA reads that were assigned to 65 amplicon sequence variants (ASVs) in the two core sediments (176,073 DNA reads and 59 ASVs were detected in sediment obtained at 4280 m depth, and 72,832 DNA reads and 14 ASVs were detected in the core at 4444 m). These represented three Kingdoms and five phyla: Fungi (Ascomycota and Basidiomycota), Viridiplantae (Chlorophyta and Streptophyta) and Chromista (Ciliophora), in rank abundance order. Ascomycota was the dominant phylum, followed by Basidiomycota. Didymella sp., Cladosporium sp., Scopulariopsis sp., Alternaria eichhorniae, Curvularia sp., Hortaea werneckii, Penicillium sp. (Ascomycota) and Malassezia globosa (Basidiomycota) were the most abundant taxa. Pseudochlorella pyrenoidosa (Chlorophyta) was the most abundant representative of Viridiplantae detected, and Spirotrachelostyla tani (Ciliophora) was the only Chromista detected, both present as minor components of the assigned eukaryotic diversity and only in the 4280 m core. The eukaryotic assemblages displayed moderate diversity indices, and those from the deeper core (4444 m depth) displayed the highest diversity values. Few assigned taxa were present in both samples. The two cores differed in their geological characteristics, consistent with their location in different depositional basins. The core obtained at 4280 m depth, located further north and more isolated from the adjacent continent by two fracture zones, appears to receive less terrigenous sediment input. In contrast, the core obtained at 4444 m depth is under greater continental influence and receives more terrigenous input from the continent. These geological and geographic differences may contribute to the varying eukaryotic eDNA diversities found. Results: Our metabarcoding study revealed the presence of a sediment eukaryotic community dominated by fungi. This included assigned ASVs representing groups with different ecological roles, such as cosmopolitan and phytopathogenic members and extremophiles, some of which may be able to survive and function in the polyextreme deep-sea abyssal conditions. Abyssal sediments present a potential habitat for studying organisms at the edge of viable conditions for life on Earth. eDNA metabarcoding provides a promising technique for detecting cryptic and uncultured biodiversity compared to traditional approaches, opening avenues for further ecological, evolutionary and biotechnological studies. Full article

Edible mushrooms represent great promise for the future of food and medicine due to their excellent nutritional, functional, and therapeutic properties. Macrofungi synthesize numerous bioactive compounds, among which proteins stand out for their remarkable diversity, both in terms of structure and their nutritional and functional roles. Fungi from the phylum Basidiomycota have a high protein content, characterized by a complete and balanced amino acid composition. Proteins and peptides from mushrooms have both nutritional and functional roles, with numerous health benefits, such as antimicrobial, antiviral, antioxidant, anticancer, hypotensive, angiotensin-converting enzyme (ACE) inhibition, immunomodulatory, and enzymatic activities. Functional proteins include lectins, immunomodulatory proteins, enzymes (laccase, cellulase, ribonuclease), enzyme inhibitors, ribosome-inactivating proteins, and hydrophobins. In addition to traditional cultivation, mushrooms can be grown as mycelium on solid substrates or in submerged culture, followed by protein separation and extraction. The main trends in protein biosynthesis from Basidiomycota involve both improving the properties of the producing strains and optimizing the cultivation methods in submerged culture and on solid substrates. Moreover, new techniques in the fields of genomics, proteomics, and metabolomics will enable increasingly promising results. This paper provides a systematic overview of the types and properties of proteins from edible mushrooms, with a focus on the main beneficial effects of their consumption. Full article

In this study, we focused on four major coniferous species in the eastern part of Inner Mongolia, namely Larix gmelinii var. principis-rupprechtii (Mayr) Pilg., Larix gmelinii (Rupr.) Kuzen., Pinus tabuliformis Carrière and Pinus sylvestris var. mongolica Litv. and carried out a systematic study on their ectomycorrhiae (EM) fungi. The present study was based on high-throughput sequencing. Based on the high-throughput sequencing data, analyzed by bioinformatics and statistical methods, the results showed that (1) a total of 150 operational taxonomic units (OTUs) were obtained, which belonged to 26 evolutionary branches of Basidiomycota and Ascomycota, respectively. Among them, Tricholoma, Tomentella-thelephora, Suillus-rhizopogon, Wilcoxina, Piloderma, Pustularia, Hygrophorus, Sebacina and Amphinema-tylospora are the EM fungi shared by four conifer species. (2) The species diversity and community composition of EM fungi differed significantly among tree species and sample plots, while soil total nitrogen (N) content and nitrogen/phosphorus (N/P) ratio were the main factors affecting community structure. (3) The Neutral Community Model (NCM) and β-Nearest Taxon Index (β-NTI) showed that stochastic processes dominated the construction of EM fungal communities. The results of this study revealed the geographical distribution pattern and maintenance mechanisms of EM fungal communities of four coniferous species in the eastern part of Inner Mongolia, which provides a scientific basis for the restoration practice of disturbed ecosystems and the sustainable development of the regional economy. Full article

Pinellia ternata, a traditional Chinese herb, suffers from soil degradation and nutrient imbalance, which significantly decrease both yield and quality. Here, the application of microbial organic fertilizer (MOF) in the cultivation of P. ternata results in high yields and quality under two soil conditions, whether grown in greenhouse or open-field environments. The application of MOF enhanced seedling emergence rates and photosynthetic efficiency, significantly improving various agronomic traits, and increasing the content of flavonoids and total alkaloids in tubers, with a stronger effect observed at a dosage of 75 g/m². Moreover, available phosphorus, available potassium, catalase, and urease levels were significantly improved. Further, 16S and ITS sequencing revealed that bacteria diversity was not affected by all treatment, while the fungi unweighted UniFrac index showed significant decline in the MOF treatment. The abundance of bacterial Acidobacteriota and Proteobacteria varied with continuous cropping soil, whereas abundance of fungi Ascomycota, Basidiomycota, and Mortierellomycota was changed in the first cropping of P. ternata. These findings suggest that applying MOF improves the microbial communities of the rhizosphere soil of P. ternata, enhancing soil enzyme activities and decomposing organic and inorganic matter. This, in turn, contributes to the yield and quality of P. ternata. Full article

An experiment was conducted to evaluate the effects of mixed lactic acid bacteria (LAB) plus fibrolytic enzymes (xylanase + β-glucanase) on bacterial and fungal communities in terminal and aerobically exposed whole-plant corn silage ensiled in a temperate zone. Short-season corn forage was either uninoculated (C) or inoculated (I) with a mixture of LAB containing 1.5 × 10⁵ colony-forming units (cfu)/g Lentilactobacillus hilgardii, 1.5 × 10⁵ cfu/g of Lentilactobacillus buchneri, and 1.0 × 10⁵ cfu/g Pediococcus pentosaceus plus a combination of xylanase + β-glucanase. Silage samples were taken after ensiling in bag silos for 418 days (terminal silage; TS), with subsamples of TS subsequently exposed to air for 14 days (aerobically exposed silage; AS). Regardless of treatment, Firmicutes, Proteobacteria, Cyanobacteria, and Actinobacteria were the predominant phyla in the bacterial microbiome, whilst Ascomycota and Basidiomycota were the predominant phyla in the fungal microbiome in both TS and AS. Lactobacillus, Acetobacter, and Bacillus were the most abundant bacterial genera, whilst Candida, Aspergillus, Vishniacozyma, Pichia, and Issatchenkia were the most abundant fungal genera. Use of silage additive did not change bacterial or fungal alpha or beta diversity during ensiling or aerobic exposure, but decreased (p < 0.01) the relative abundance (RA) of Proteobacteria in both TS and AS, increased (p < 0.01) RA of Firmicutes in AS, but did not affect the RA of fungal phyla in either TS or AS. At the genus level, the additive significantly decreased (p < 0.01) RA of Acetobacter in both TS and AS. The silage additive used in this study significantly affected the composition of multiple microbial genera during ensiling and aerobic exposure by shifting bacterial communities towards enhanced aerobic stability. Full article