Search Results (33)

This study aimed to evaluate solid-state fermentation (SSF) as a sustainable approach for the simultaneous detoxification of olive pomace (OP) and the production of industrially relevant enzymes. OP, a semisolid byproduct of olive oil extraction, is rich in lignocellulose and phenolic compounds, which limit its direct reuse due to phytotoxicity. A native strain of Aspergillus sp., isolated from OP, was employed as the biological agent, while grape pomace (GP) was added as a co-substrate to enhance substrate structure. Fermentations were conducted at two scales, Petri dishes (20 g) and a fixed-bed bioreactor (FBR, 2 kg), under controlled conditions (25 °C, 7 days). Key parameters monitored included dry and wet weight loss, pH, color, phenolic content, and enzymatic activity. Significant reductions in color and polyphenol content were achieved, reaching 68% in Petri dishes and 88.1% in the FBR, respectively. In the FBR, simultaneous monitoring of dry and wet weight loss enabled the estimation of fungal biotransformation, revealing a hysteresis phenomenon not previously reported in SSF studies. Enzymes such as xylanase, endopolygalacturonase, cellulase, and tannase exhibited peak activities between 150 and 180 h, with maximum values of 424.6 U·g⁻¹, 153.6 U·g⁻¹, 67.43 U·g⁻¹, and 6.72 U·g⁻¹, respectively. The experimental data for weight loss, enzyme production, and phenolic reduction were accurately described by logistic and first-order models. These findings demonstrate the high metabolic efficiency of the fungal isolate under SSF conditions and support the feasibility of scaling up this process. The proposed strategy offers a low-cost and sustainable solution for OP valorization, aligning with circular economy principles by transforming agro-industrial residues into valuable bioproducts. Full article

The long-term monocropping of red kidney beans in agricultural fields can lead to the occurrence of soil-borne diseases. Alterations in the composition of the soil microbial community are a primary cause of soil-borne diseases and a key factor in continuous cropping obstacles. Research exploring how different cultivation modes can modify the diversity and composition of the rhizosphere microbial community in red kidney beans, and thus mitigate the effects of continuous cropping obstacles, is ongoing. This study employed three cultivation modes: the continuous monocropping of red kidney beans, continuous monocropping of soybeans, and red kidney bean–soybean intercropping. To elucidate the composition and diversity of rhizosphere microbial communities, we conducted amplicon sequencing targeting the V3-V4 hypervariable regions of the bacterial 16S rRNA gene and the ITS1 region of fungal ribosomal DNA across distinct growth stages. The obtained sequencing data provide a robust basis for estimating soil microbial diversity. We observed that, under the intercropping mode, the composition of both bacteria and fungi more closely resembled that of soybean monocropping. The monocropping of red kidney beans increased the richness of rhizosphere bacteria and fungi and promoted the accumulation of pathogenic microorganisms. In contrast, intercropping cultivation and soybean monocropping favored the accumulation of beneficial bacteria such as Bacillus and Streptomyce, reduced pathogenic fungi including Alternaria and Mortierell, and exhibited less microbial variation across different growth stages. Compared to the monocropping of red kidney beans, these systems demonstrated more stable microbial structure and composition. The findings of this study will inform sustainable agricultural practices and soil management strategies. Full article

This study explored how potted treatments (with and without Scleroderma bovista inoculation) shape rhizosphere microbial diversity in hazel across five soils using split-root cultivation. Three treatments (control, split-root, split-root with S. bovista) were analyzed for root growth and microbial dynamics. S. bovista inoculation consistently enhanced root parameters (number, tips) in all soils. Potted treatments (with and without S. bovista inoculation) altered microbial features (OTU/ASV), with only 0.9–3.3% of features remaining unchanged. At the class level, potting increased Agaricomycetes abundance while reducing Sordariomycetes, a trend amplified by S. bovista. Potting decreased species richness estimates (ACE and Chao1), while both treatments lowered diversity index (Shannon index). Potted treatments without S. bovista inoculation drove stronger shifts in species composition than inoculation. Findings reveal potting and S. bovista synergistically recruit symbiotic fungi via root exudates, establishing disease-suppressive communities that selectively inhibit pathotrophic fungi (particularly plant pathogen Coniothyrium and fungal parasite Cladobotryum) while roughly maintaining non-pathogenic saprotrophic microbes essential for organic matter decomposition. This work provides insights for optimizing hazel orchard management and ectomycorrhizal agent development. Full article

Fungi are one of the major components of the eukaryotic microbial community in marine ecosystems, playing a significant role in organic matter cycling and food web dynamics. However, the diversity and roles of fungi in marine sediments remain poorly documented. To elucidate the diversity and spatial distribution of fungal communities in the marine sediments of an estuary–coast continuum across three distinct salinity regions in Zhanjiang Bay, China, the variations in fungal diversity, abundance, community structure, and distribution in the sediments were investigated through the application of high-throughput amplicon sequencing using the internal transcribed spacer (ITS) primers. Additionally, the FUNGuild database was employed to assess the potential functional traits of fungi. A total of 1242 ASV sequences, affiliated to 144 genera and five phyla, were identified. Ascomycota (68.97%) and Basidiomycota (6.41%) were the dominant fungal groups, together accounting for 75.38% of the total relative abundance of the fungal community. Significant differences were observed in the α-diversity indices (Shannon index and richness) and β-diversity of fungal communities across the three distinct salinity regions. The fungal molecular network exhibited primarily positive species interactions, with notable structural differences across salinity gradients. The low-salinity group had a large network with high modularity; the medium-salinity group a small, simple network with high centralization, and the high-salinity group a compact, moderately complex network. Symbiotrophs, saprotrophs, and pathotrophs, being the three trophic types with the highest proportions, were estimated based on ITS. A redundancy analysis (RDA) indicated that salinity was the primary factor influencing the distribution of Ascomycota communities, while the distributions of Basidiomycota, Chytridiomycota, Mucoromycota, and Rozellomycota were more strongly affected by environmental factors such as chlorophyll a, chemical oxygen demand (COD), pH, and temperature. Our work provides new scientific data on the diversity, composition, and distribution of fungal communities in Zhanjiang Bay, which helps to understand the biodiversity of fungi in the estuary–coast ecosystems. Full article

Dermatophytes are widely distributed in the environment, with an estimated prevalence of 20–25% of the the global population yearly. These fungi are keratinophilic and keratinolytic and cause the infection of keratin-rich structures such as skin, hair, and nails. The pattern of this infectious disease covers a wide spectrum from exposed individuals without symptoms to those with acutely inflammatory or non-inflammatory, chronic to invasive, and even life-threatening symptoms. This review summarizes current information on the pathogenicity, virulence factors, and drug resistance mechanisms associated with dermatophytes. A greater number of virulence factors of these fungi are important for the occurrence of infection and the changes that occur, including those regarding adhesins, the sulfite efflux pump, and proteolytic enzymes. Other virulence factors include mechanisms of evading the host defense, while the development of resistance to antifungal drugs is increasing, resulting in treatment failure. The investigation of host-pathogen interactions is essential for developing a more complete understanding of the mechanisms underlying dermatophyte pathogenesis and host response to inform the use of diagnostics methods and antifungal therapeutics to minimize the high fungal burden caused by dermatophytes and to control the spread of resistance. Full article

Clean tillage frequently causes the loss of soil nutrients and weakens microbial ecosystem service functions. In order to improve orchard soil nutrient cycling, enhance enzyme activities and microbial community structure in a “Jiro” sweet persimmon orchard, sod culture management was carried out to clarify the relationship among soil nutrient, microbial communities, and fruit yield and quality in persimmon orchard. The results showed that sod culture management increased the content of organic matter, total organic carbon, nitrogen, phosphorus, and potassium in the soil, thus improving soil fertility. Compared with clean tillage orchards, sod culture methods significantly increased soil enzyme activities and microbial biomass carbon (MBC) content. The abundance-based coverage estimator (ACE) and the simplest richness estimators (Chao l) indices of the bacterial community and all diversity and richness indices of the fungal community significantly increased in the sod culture orchard, which indicated that sod culture could increase the richness and diversity of the soil microbial community. The dominant bacterial phyla were Proteobacteria (32.21~41.13%) and Acidobacteria (18.76~23.86%), and the dominant fungal phyla were Mortierellomycota (31.11~83.40%) and Ascomycota (3.45~60.14%). Sod culture drove the composition of the microbial community to increase the beneficial microbiome. Correlation analyses and partial least squares path modeling (PLS-PM) comparative analyses showed that the soil chemical properties (mainly including soil organic matter content, total organic carbon content, total potassium content, and total nitrogen content), soil enzyme activities and soil microorganisms were strongly correlated with fruit yield and quality. Meanwhile, soil nutrient, soil enzyme, and soil microbes had also influenced each other. Our results showed that long-term ryegrass planting could improve soil fertility, enzyme activities, and microbial community compositions. Such changes might lead to a cascading effect on the fruit yield and quality of “Jiro” sweet persimmons. Full article

Endophytic fungi that reside internally in healthy, asymptomatic plants often benefit their hosts by promoting plant growth and/or providing plant protection against abiotic and biotic stresses. However, only a small fraction of the estimated 1.5 million fungal endophytes have been identified. In this study, a total of 369 isolates of fungal endophytes in 59 distinct taxa were isolated from stem samples of Cornus florida (flowering dogwood). All isolates belonged to species of phyla Ascomycota and Basidiomycota distributed across five orders and 11 genera. Isolates belonging to the same family clustered together in a phylogenetic tree generated from a cluster analysis using MEGA 7 software. Diversity indices of the fungi revealed a rich and diverse community that included several species associated with leaf spots, blight, cankers, and/or dieback diseases. Pathogenicity tests confirmed 16 fungal endophytes as C. florida pathogens, including some well-known destructive pathogens Botryosphaera dothidea, Colletotrichum acutatum, and C. gleosporoides. Isolates of the fungal endophytes possess the capacity to produce extracellular hydrolytic enzymes (cellulase, amylase, pectinase, laccase, chitinase, and protease) that are known to function in tissue penetration, plant colonization, nutrient acquisition, and disease suppression in both plant pathogens and endophytes These results support the interchangeable pathogenic–endophytic roles for some taxa. Full article

An amplicon-based metagenomic survey of archaea, fungi, and bacteria was performed on Livingston Island, Maritime Antarctica. In many of the samples, patterns of antagonism between these three superkingdoms were observed in the form of an inversely proportional dependence of the richnesses of the three types of microorganisms. The antagonism was quantified—based on the observed numbers of the total tags and the numbers of the operational taxonomic units (OTUs), and on four alpha diversity parameters—using the Shannon, the Simpson, the Chao1, and the ACE indices. We found that the most discriminative results in the antagonism measuring were obtained when the numbers of the OTUs and the ACE community richness estimator were compared. The antagonism between archaea and fungi was most potent, followed by that of archaea and bacteria. The fungi–bacteria antagonism was slightly detectable. Pearson and Spearman correlation analyses also showed a statistically significant negative correlation between the fungal and archaeal effective tags, while the correlation between archaeal and bacterial diversity was positive. Indications of the order of primary microbial succession in barren ecological niches were also observed, demonstrating that archaea and bacteria are the pioneers, followed by fungi, which would displace archaea over time. Full article

In 2019, the bark beetle Ips amitinus (native to central Europe) was identified in south-western Siberia at a distance exceeding 2500 km east of its previously known easternmost location in the European part of Russia. In Siberia, its invasive populations are characterised by high abundance and harmfulness. Here, I. amitinus accomplishes primary attacks on standing vital trees of Pinus sibirica with a lethal outcome. This invasion has already resulted in massive dieback in stands of pine over a large geographic territory. By, 2021, the invaded area was estimated to cover at least 31,200 km². The objectives of this study were to investigate fungi associated with/vectored by I. amitinus in its invasive area in south-western Siberia and wood decay fungi that cause root and butt rots to P. sibirica. This led to the following conclusions: (i) DNA analysis of sixty adult beetles of Ips amitinus collected from P. sibirica in south-west Siberia revealed the presence of 143 fungal taxa; (ii) species richness was significantly higher in beetles collected from dead branches than from (more recently infested) dying branches; (iii) fungal communities were >90% dominated by yeasts, among which the most common were Nakazawaea holstii, Kuraishia molischiana, and N. ambrosiae; (iv) entomopathogenic Beauveria bassiana s.l. was the most common fungus isolated from dead/mycosed beetles of I. amitinus, followed by Lophium arboricola and four Ophiostoma spp.; and (v) Heterobasidion parviporum was the most common decay fungus detected, which was causing heart rot in stems of P. sibirica. Full article

The endophytic fungal diversity of Cirsium kawakamii, a herb indigenous to Taiwan, was analyzed in this study. In addition, some fungal isolates were evaluated for the risk they pose as plant pathogens. In total, 1836 endophytic fungi were isolated from C. kawakamii from Hehuanjian, Puli Township, and Tatachia. They were classified into 2 phyla, 8 classes, 40 families, and 68 genera. Colletotrichum, Fusarium, Phomopsis, and Xylaria, (Ascomycota, Sordariomycetes) were the dominant genera. The genus accumulation curve (based on the bootstrap estimator) was non-asymptotic, with estimated richness significantly exceeding the richness captured by our sampling to date. Considering the collection time, the data indicated significant differences in the proportions of the C. kawakamii endophyte genus from Hehuanjan, Puli Township (across two seasons), and Tatachia. The Shannon and Gini–Simpson indices revealed variations in diversity, with C. kawakamii endophytes (Puli Township in winter) significantly reducing alpha diversity compared with other seasons and locations. Meanwhile, the Gini–Simpson index suggested that there were no significant differences in richness among the four sampling sites. The PCA results unveiled distinct community structures across different locations and seasons, explaining 46.73% of the total variation in fungal community composition significantly affected diversity and richness. In addition, a considerable number of Fusarium isolates exhibited harmful properties towards wheat, potatoes, and apples. It is postulated that these fungi belong to the Fusarium tricinctum species complex (FTSC). Full article

The chytrid fungal pathogens Batrachochytrium salamandrivorans (Bsal) and B. dendrobatidis (Bd) are driving amphibian extinctions and population declines worldwide. As their origins are believed to be in East/Southeast Asia, this region is crucial for understanding their ecology. However, Bsal screening is relatively limited in this region, particularly in hotspots where Bd lineage diversity is high. To address this gap, we conducted an extensive Bsal screening involving 1101 individuals from 36 amphibian species, spanning 17 natural locations and four captive facilities in the biodiversity-rich Guangxi Zhuang Autonomous Region (GAR). Our PCR assays yielded unexpected results, revealing the complete absence of Bsal in all tested samples including 51 individuals with Bd presence. To understand the potential distribution of Bsal, we created niche models, utilizing existing occurrence records from both Asia and Europe. These models estimated potential suitable habitats for Bsal largely in the northern and southwestern parts of the GAR. Although Bsal was absent in our samples, the niche models identified 10 study sites as being potentially suitable for this pathogen. Interestingly, out of these 10 sites, Bd was detected at 8. This suggests that Bsal and Bd could possibly co-exist in these habitats, if Bsal were present. Several factors seem to influence the distribution of Bsal in Asia, including variations in temperature, local caudate species diversity, elevation, and human population density. However, it is climate-related factors that hold the greatest significance, accounting for a notable 60% contribution. The models propose that the specific climatic conditions of arid regions, primarily seen in the GAR, play a major role in the distribution of Bsal. Considering the increased pathogenicity of Bsal at stable and cooler temperatures (10–15 °C), species-dependent variations, and the potential for seasonal Bd-Bsal interactions, we emphasize the importance of periodic monitoring for Bsal within its projected range in the GAR. Our study provides deeper insights into Bsal’s ecological niche and the knowledge generated will facilitate conservation efforts in amphibian populations devastated by chytrid pathogens across other regions of the world. Full article

The decomposition of animal bodies is a process defined by specific stages, described by the state of the body and participation of certain guilds of invertebrates and microorganisms. While the participation of invertebrates in decomposing is well-studied and actively used in crime scene investigations, information on bacteria and fungi from the scene is rarely collected or used in the identification of important factors such as estimated time of death. Modern molecular techniques such as DNA metabarcoding allow the identification and quantification of the composition of microbial communities. In this study, we used DNA metabarcoding to monitor fungal succession during the decomposition of juvenile pigs in grasslands of New Jersey, USA. Our findings show that decomposition stages differ in a diversity of fungal communities. In particular, we noted increased fungal species richness in the more advanced stages of decomposition (e.g., bloat and decay stages), with unique fungal taxa becoming active with the progression of decay. Overall, our findings improve knowledge of how fungi contribute to forensically relevant decomposition and could help with the assessment of crime scenes. Full article

The priming effect (PE) occurs when fresh organic matter (FOM) supplied to soil alters the rate of decomposition of older soil organic matter (SOM). The PE can be generated by different mechanisms driven by interactions between microorganisms with different live strategies and decomposition abilities. Among those, stoichiometric decomposition results from FOM decomposition, which induces the decomposition of SOM by the release of exoenzymes by FOM-decomposers. Nutrient mining results from the co-metabolism of energy-rich FOM with nutrient-rich SOM by SOM-decomposers. While existing statistical approaches enable measurement of the effect of community composition (linear effect) on the PE, the effect of interactions among co-occurring populations (non-linear effect) is more difficult to grasp. We compare a non-linear, clustering approach with a strictly linear approach to separately and comprehensively capture all linear and non-linear effects induced by soil microbial populations on the PE and to identify the species involved. We used an already published data set, acquired from two climatic transects of Madagascar Highlands, in which the high-throughput sequencing of soil samples was applied parallel to the analysis of the potential capacity of microbial communities to generate PE following a ¹³C-labeled wheat straw input. The linear and clustering approaches highlight two different aspects of the effects of microbial biodiversity on SOM decomposition. The comparison of the results enabled identification of bacterial and fungal families, and combinations of families, inducing either a linear, a non-linear, or no effect on PE after incubation. Bacterial families mainly favoured a PE proportional to their relative abundances in soil (linear effect). Inversely, fungal families induced strong non-linear effects resulting from interactions among them and with bacteria. Our findings suggest that bacteria support stoichiometric decomposition in the first days of incubation, while fungi support mainly the nutrient mining of soil’s organic matter several weeks after the beginning of incubation. Used together, the clustering and linear approaches therefore enable the estimation of the relative importance of linear effects related to microbial relative abundances, and non-linear effects related to interactions among microbial populations on soil properties. Both approaches also enable the identification of key microbial families that mainly regulate soil properties. Full article

Soil salinization is one of the most compelling environmental problems on a global scale. Fungi play a crucial role in promoting plant growth, enhancing salt tolerance, and inducing disease resistance. Moreover, microorganisms decompose organic matter to release carbon dioxide, and soil fungi also use plant carbon as a nutrient and participate in the soil carbon cycle. Therefore, we used high-throughput sequencing technology to explore the characteristics of the structures of soil fungal communities under different salinity gradients and whether the fungal communities influence CO₂ emissions in the Yellow River Delta; we then combined this with molecular ecological networks to reveal the mechanisms by which fungi adapt to salt stress. In the Yellow River Delta, a total of 192 fungal genera belonging to eight phyla were identified, with Ascomycota dominating the fungal community. Soil salinity was the dominant factor affecting the number of OTUs, Chao1 index, and ACE index of the fungal communities, with correlation coefficients of −0.66, 0.61, and −0.60, respectively (p < 0.05). Moreover, the fungal richness indices (Chao1 and ACE) and OTUs increased with the increase in soil salinity. Chaetomium, Fusarium, Mortierella, Alternaria, and Malassezia were the dominant fungal groups, leading to the differences in the structures of fungal communities under different salinity gradients. Electrical conductivity, temperature, available phosphorus, available nitrogen, total nitrogen, and clay had a significant impact on the fungal community structure (p < 0.05). Electrical conductivity had the greatest influence and was the dominant factor that led to the difference in the distribution patterns of fungal communities under different salinity gradients (p < 0.05). The node quantity, edge quantity, and modularity coefficients of the networks increased with the salinity gradient. The Ascomycota occupied an important position in the saline soil environment and played a key role in maintaining the stability of the fungal community. Soil salinity decreases soil fungal diversity (estimate: −0.58, p < 0.05), and soil environmental factors also affect CO₂ emissions by influencing fungal communities. These results highlight soil salinity as a key environmental factor influencing fungal communities. Furthermore, the significant role of fungi in influencing CO₂ cycling in the Yellow River Delta, especially in the environmental context of salinization, should be further investigated in the future. Full article

Lakeshore wetlands are important terrestrial ecosystems worldwide, and the lakeshore wetlands of the Tibetan Plateau are sensitive to climate change. Therefore, in the context of global warming, studying the effects of temperature rise on surface soil microbial communities is essential for wetland biodiversity conservation. In this study, we used metagenomic sequencing to examine changes in the structure of surface soil microbial communities and their metabolic pathways in the Niaodao lakeshore wetland (NLW) in Qinghai Lake at 1.2 °C warming. Under natural control and warming conditions, Proteobacteria and Actinobacteria were the most dominant bacterial phyla, and Ascomycota and Basidiomycota were the predominant fungal phyla. Soil pH, electrical conductivity, and temperature affected the relative abundances of the dominant soil microbes. Effect size estimation in a linear discriminant analysis revealed 11 differential pathways between warming and natural conditions. Warming considerably enhanced the peptidoglycan biosynthetic pathways but inhibited the ATP-binding cassette transporter pathway. Warming treatment affected α-diversity indices, with an increase in the Shannon, Chao1, and richness indices and a decrease in the Simpson index compared with the index changes for the natural control conditions. Analysis of similarities showed significant differences between warming and control samples. Overall, temperature rise altered surface soil microbial community structure and increased surface soil microbial diversity and abundance in NLW. Full article