Fungal Species Research Articles

MFPSP: Identification of fungal species-specific phosphorylation site using offspring competition-based genetic algorithm

Protein phosphorylation is essential in various signal transduction and cellular processes. To date, most tools are designed for model organisms, but only a handful of methods are suitable for predicting task in fungal species, and their performance still leaves much to be desired. In this study, a novel tool called MFPSP is developed for phosphorylation site prediction in multi-fungal species. The amino acids sequence features were derived from physicochemical and distributed information, and an offspring competition-based genetic algorithm was applied for choosing the most effective feature subset. The comparison results shown that MFPSP achieves a more advanced and balanced performance to several state-of-the-art available toolkits. Feature contribution and interaction exploration indicating the proposed model is efficient in uncovering concealed patterns within sequence. We anticipate MFPSP to serve as a valuable bioinformatics tool and benefiting practical experiments by pre-screening potential phosphorylation sites and enhancing our functional understanding of phosphorylation modifications in fungi. The source code and datasets are accessible at https://github.com/AI4HKB/MFPSP/.

Quantification of fungal biomass in mycelium composites made from diverse biogenic side streams

AbstractMycelium composite materials are comprised of renewable organic substrates interconnected by fungal mycelium, allowing full biodegradability after use. Due to their promising material properties, adaptability, and sustainable nature, these biomaterials are investigated intensively. However, one crucial aspect that has hardly been covered so far is the proportion of fungal biomass in the composites, which would be necessary to assess its contribution to the material characteristics. Since a complete physical separation of mycelium and substrate is not feasible, we approached this issue by isolating the fungal DNA and relating it to the mass of mycelium with the help of quantitative PCR. Overall, 20 different combinations of fungi and biogenic side streams were evaluated for their handling stability, and growth observations were related to the quantification results. Ganoderma sessile was able to form stable composites with almost all substrates, and a positive correlation between mycelial biomass and composite stability could be found. However, the amount of mycelium required for fabricating firm materials strongly depends on the combination of substrate and fungal species used. Less than five mass percent of fungal biomass can suffice to achieve this, as for example when combining Trametes versicolor with sugar beet pulp, whereas a mass fraction of twenty percent leads to crumbly materials when using Pleurotus pulmonarius on green waste. These results indicate that the mycelial biomass is an important factor for the composite’s stability but that the properties of the fungal hyphae, as well as those of the substrate, are also relevant. The presented quantification method not only allows to estimate fungal growth during composite production but can also improve our understanding of how the mycelium influences the material.

Microbial Indoor Air Quality Within Greenhouses and Polytunnels Is Crucial for Sustainable Horticulture (Malopolska Province, Poland Conditions)

Sustainable horticulture is crucially based on the greenhouse production of vegetables under controlled conditions. In this study, we wanted to learn how cultivated plants may impact indoor air quality and whether the workers can be exposed to bioaerosols in a similar way in these settings. The study objective was to test the hypothesis that the microbial concentrations, distribution of bioaerosol particle sizes, and composition of the airborne microbiome are specific to greenhouses, polytunnels, and open-air sites. The air samples were collected to assess the concentration of total culturable bacteria (TCB), fungi, actinomycetes, and β-haemolytic bacteria and for the identification of bacterial and fungal strains. Higher concentrations of TCB and fungi were found in the greenhouse (log 3.71 and 3.49 cfu m−3, respectively) than in polytunnels (log 2.60–2.48 and 2.51–2.31 cfu m−3, respectively) during the vegetation of cucumbers. These airborne microbes were represented by a significant contribution of the respirable fraction with a distinct contribution of fine particles in size below 4.7 µm. Cultivation of cucumbers resulted in the higher emission of airborne microorganisms in contrast with growing herbs such as oregano and basil. In total, 35 different bacteria and 12 fungal species, including pathogenic or allergenic agents, were identified within the studied sites. The workers can be exposed to increased concentrations of TCB and fungi in the greenhouse during the plant vegetation. It might be recommended to properly manage greenhouses and polytunnels, dispose of dust sources, and maintain appropriate ventilation to sustain relevant air quality.

Identification and Characterization of Fungi in Hibiscus sabdariffa (zobo) Drink Produced and Hawked in Eket Metropolis, Nigeria

Zobo drink is an affordable local soft beverage derived from the calyx of Hibiscus sabdariffa, a herbaceous medicinal plant that thrives in tropical regions. The characterization and identification of fungi present in Zobo drinks produced and sold by vendors in Eket, Akwa Ibom State, was the aim of this study. Hawked Zobo drinks packaged in plastic bottles were purchased from ten different hawkers, two each from five locations. The pH values of the samples were determined and the total fungal count. The pour plate technique, using Sabouraud Dextrose Agar (SDA) was used to determine the total fungal count. Macroscopic and microscopic features were used to characterize the isolates obtained from the samples. The microscopic identification was done by preparing a wet mount of isolated colonies and observing under a microscope. The rate of growth, colony colour, colour changes, colour of reverse colonies, odour and texture of surface were observed and compared with previous work done on fungi. Results showed that the pH of the freshly obtained and stored samples was 3.9 and 2.8 respectively. The average number of colonies for samples stored in the refrigerator ranged from 0.54 x 105 to 0.91 x 105 cfu/ml while that of the freshly obtained samples ranged from 1.26 x 105 to 1.64x105 cfu/ml at 10-3 dilution. A total of 43.6% Aspergillus spp., 29.5% Candida spp. 15.4% Penicillium spp. and 11.5% Rhizopus spp. were identified. With increased acidity in the refrigerated samples, the number reduced to 41.2% Aspergillus spp., 27.4% Candida spp. 15.7% Penicillium spp. and 15.7% Rhizopus spp. The fungi species isolated are known to produce mycotoxins with potential immunosuppressive and cytotoxic effect. These microorganisms could have been introduced to the drinks at various stages of production, during transportation, through the ingredients utilized in the manufacturing process, or even during the cultivation of the Hibiscus sabdariffa plant. This issue can be mitigated by implementing effective manufacturing practices throughout the production process.

A case report of Penicillium chorioretinitis in a Border Collie dog

Systemic fungal pathogens typically gain entry through a single portal and disseminate to affect multiple body systems. Infections caused by fungal Penicillium species are rare in dogs, and these cases have a poor prognosis. An unknown Penicillium species was isolated from the right eye of a middle‐aged Border Collie without evidence of systemic disease. Due to financial limitations, an extensive diagnostic evaluation could not be performed. Histopathology alone failed to identify the specific causative agent; however, fungal culture on aqueous humor provided the definitive diagnosis. This case highlights the advantage of collecting ocular fluids after enucleation to diagnose atypical fungal infections.

Prevalence and Etiology of Otomycosis in West Libya

Fungal otitis media is a frequently case facing otolaryngologists due to its recurrence and long-Fungal otitis media is a frequent condition faced by otolaryngologists due to its recurrence and long-term treatment period. The infection starts in the outer ear canal and may reach the inner ear. The aim of this study was to isolate and identify the fungal species causing inflammation of the auditory canal, identify the main causes and contributing factors to the spread and increased incidence of ear fungal infection, and determine the relationship between otomycosis occurrence and age, gender, and diabetes. Additionally, the study aimed to compare the incidence of otomycosis among different areas. A total of 205 ear swabs were collected from patients visiting national clinics and hospitals. The samples were cultured on Sabouraud dextrose agar and Czapek-Dox agar and incubated at 30°C for a week. Nine fungal species belonging to four genera were isolated: Aspergillus spp., Alternaria spp., Penicillium spp., and Candida spp. The current study showed a predominance of Aspergillus spp. isolates, with a rate of 82.67%, making it the main cause of fungal ear infection; however, Penicillium spp. was the least prevalent. Among the fungal species, A. niger was dominant, with a prevalence rate of 41.16%. The prevalence of ear infection was higher in females (62.82%) than in males (37.17%), and the infection was most common in the age group from one to twenty years (39.35%), while it was less frequent in older age groups. In coclusion, The study concluded that otomycosis is widely prevalent in western Libya, with Aspergillus niger as the predominant etiological agent.

Combining the Powerful Antioxidant and Antimicrobial Activities of Pomegranate Waste Extracts with Whey Protein Coating-Forming Ability for Food Preservation Strategies

Different solvents water, ethanol and ethanol/water (6:4 v/v), were compared in the extraction of pomegranate peels and seeds (PPS) in terms of recovery yields, antioxidant properties, and antimicrobial action against typical spoilage bacterial and fungal species. The best performing extract (ethanol/water (6:4 v/v) was shown to contain mostly ellagic acid and punicalagin as phenolic compounds (5% overall) and hydrolysable tannins (16% as ellagic acid equivalents) and was able to inhibit the growth of the acidophilic Alicyclobacillus acidoterrestris at a concentration as low as 1%. The preservation of the organoleptic profile of A. acidoterrestris-inoculated apple juice with extract at 1% over 20 days was also observed thanks to the complete inhibition of bacterial growth, while the extract at 0.1% warranted a significant (40%) inhibition of the enzymatic browning of apple smoothies over the first 30 min. When incorporated in whey proteins’ isolate (WPI) at 5% w/w, the hydroalcoholic extract conferred well appreciable antioxidant properties to the resulting coating-forming hydrogel, comparable to those expected for the pure extract considering the amount present. The WPI coatings loaded with the hydroalcoholic extract at 5% were able to delay the browning of cut fruit by ca. 33% against a 22% inhibition observed with the sole WPI. In addition, the functionalized coating showed an inhibition of lipid peroxidation of Gouda cheese 2-fold higher with respect to that observed with WPI alone. These results open good perspectives toward sustainable food preservation strategies, highlighting the potential of PPS extract for the implementation of WPI-based active packaging.

Increasing Phylogenetic Clustering of Arbuscular Mycorrhizal Fungal Communities in Roots Explains Enhanced Plant Growth and Phosphorus Uptake.

Temporal variation during the assembly of arbuscular mycorrhizal (AM) fungal communities within plant roots have been posited as critical drivers of the plant-fungal symbiotic outcomes. However, functional implications of these dynamics for the host plant remain poorly understood. We conducted a controlled pot experiment with Sorghum bicolor to investigate how temporal shifts in AM fungal community composition and phylogenetic diversity influence plant growth and phosphorus responses to the symbiosis. We characterised the root-colonising AM fungal communities across three time points and explored their community assembly processes by analysing their phylogenetic diversity and employing joint species distribution modelling with the Hierarchical Modelling of Species Communities (HMSC) framework. We found strong AM fungal turnover through time with a high phylogenetic signal, indicating recruitment of phylogenetically clustered AM fungal species in the host. This temporal phylogenetic clustering of communities coincided with marked increases in plant biomass and phosphorus responses to the AM fungal symbiosis, suggesting that host selection for specific fungi may be a key determinant of these benefits.

Exploring the Molecular Basis of Anticancer Activity in Various Moss Species Against Colorectal Cancer Cells

Background: Mushrooms are shown to protect against the side effects of cancer. Therefore, mushrooms with proven anticancer properties and active ingredients are fascinating in the search for new cancer drugs. Objective: In this study, the effects of extracts from Hericium coralloides (M1), Lactarius deliciosus (M2), Lepista nuda (M3), Pleurotus ostreatus (M4), and Suillus collitinus (M5) together on HCT116 were investigated. Mesenchymal stem cells (MSCs) were used to study the effect on healthy cells. Methods: MTT was used to determine cell viability. Dose-response curves were generated, the IC50 values of the compounds were calculated, and the effect of the extracts was compared using it. The FTIR was used to analyze the quantitative changes of the cellular components. Results and Discussion: The evaluation of the IC50 values of all fungal species showed that they reduced the cell viability of HCT116 cells. In contrast, no significant reduction in cell viability was observed in MSCs. Changes in the ratio of cell membrane lipids, proteins, and cell nucleic acids between control and fungal-treated HCT116 cells were detected by FTIR. Many of the chemotherapeutic agents are of plant origin, and many resources should still be explored to inhibit the side effects of cancer therapy. Conclusion: The data obtained through this experiment will serve as a reference for studies to be a new source of anticancer drugs in modern pharmacology.

Molecular and morphoanatomical characterization of Urocystis heteropogonis sp. nov.: a novel smut fungus infecting Heteropogon contortus.

A new species of smut fungus, Urocystis heteropogonis, was discovered infecting Heteropogon contortus in Shawar Valley, Swat district, Khyber Pakhtunkhwa, Pakistan. The study aimed to characterize this fungus based on its morpho-anatomical and molecular features and clarify its phylogenetic position within the genus Urocystis. Urocystis heteropogonis was identified as a novel species, distinct from other Urocystis species. Morphologically, it is characterized by larger spore balls (14-69 × 11-45μm) and central spores that are 14-28 × 11-20μm in size, with each spore containing1-8 central spores. The spore walls measure 0.9-2.5μm in thickness and the species differs in infection patterns compared to other Urocystis species. Phylogenetic analysis based on the ITS and LSU regions of nuclear ribosomal DNA (nrDNA) further confirmed the novelty of the species, placing it within a distinct clade alongside U. agropyri, U. occulta, U. piptatheri, and U. tritici. The discovery of Urocystis heteropogonis adds to the diversity of smut fungi infecting grasses and highlights the need for further research into its ecological and agricultural implications. Future studies should focus on the disease's spread, management, and potential impact on host populations.

Green Synthesis of Silver Nanoparticles Using Doxycycline: Evaluation of Antimicrobial Potential and Organ-specific Toxicity

Silver nanoparticles (Ag-NPs) have wide applicability as antimicrobial, biomedical, and anti-cancer drug delivery systems. This study aimed to synthesize Ag-NPs using green methodology to assess their antimicrobial properties and toxicity. Ag-NPs were prepared using doxycycline, an antibiotic serving as a reducing and capping agent. The synthesized Ag-NPs were characterized by ultraviolet-visible spectrophotometry, X-ray diffraction, scanning electron microscopy, and Fourier-transform infrared spectrometry. The antimicrobial efficacy of doxycycline-mediated Ag-NPs was assessed on Candida species in vitro and for toxicity in male albino mice in vivo. The Ag-NPs showed a surface plasmon resonance at 411 nm, indicating a 90 nm average size and spherical shape. Toxicity was tested on mouse organs (liver, kidney, spleen, heart and stomach) using three Ag-NP doses (50, 100, 200 mg/kg) over 14 days. The synthesized Ag-NPs produced large inhibition zones against two well-known fungal species, C. albicans and C. tropicalis, demonstrating their antimicrobial potential. The Ag-NPs showed varying degrees of toxicity in different mouse organs, depending on the administered dose, with more pronounced adverse effects observed at higher concentrations. Periodic administration of Ag-NPs at low-dose volumes holds promise as a safe approach to their use as antimicrobial agents. Low-dose Ag-NPs are minimally toxic and show strong antimicrobial efficacy.

Characterization, Genome Sequencing, and Development of a Rapid PCR Identification Primer for Fusarium oxysporum f. sp. crocus, a New forma specialis Causing Saffron Corm Rot

Saffron corm rot (SCR), the most serious disease affecting saffron, has been confirmed to be caused by Fusarium oxysporum in previous studies. Compared to other fungal species, F. oxysporum exhibits host specialization, a special phenomenon associated with the secreted in xylem (SIX) genes. This study examined the pathogenicity specialization of F. oxysporum isolated from saffron corms with SCR disease. The results showed that this F. oxysporum strain was strongly pathogenic to saffron corms, causing SCR; weakly pathogenic to the corms of freesia, which is in the Iridaceae family along with saffron; and not pathogenic to watermelon, melon, and tomato. Other formae speciales of F. oxysporum were not pathogenic to saffron corms. This suggests that F. oxysporum saffron strains exhibit obvious pathogenicity specialization for Iridaceae spp. Subsequently, the F. oxysporum saffron strain (XHH35) genome was sequenced, and a comparative genomics study of XHH35 and three other formae speciales was conducted using OrthoVenn3. XHH35 contained 90 specific genes absent in the other three formae speciales. These genes are involved in certain key biological processes and molecular functions. Based on BLAST homology searching, the F. oxysporum saffron strain (XHH35) genome was predicted to contain seven SIX genes (SIX 4, SIX 6, SIX 7, SIX 10, SIX 11, SIX 12, and SIX 14) highly homologous to F. oxysporum f. sp. lycopersici, which was verified using polymerase chain reaction (PCR) amplification. The corresponding individual phylogenetic tree indicated that the F. oxysporum saffron strain (XHH35) showed a separate branch with different formae speciales. This study is the first-ever report of F. oxysporum f. sp. crocus, a new forma specialis. Based on the specificity of its SIX genes, the SIX 10 gene was selected to further establish a rapid identification technique for F. oxysporum f. sp. crocus, which will be useful in future research.

The contribution of tropical long-term studies to mycology.

Fungi are arguably the most diverse eukaryotic kingdom of organisms in terms of number of estimated species, trophic and life history strategies, and their functions in ecosystems. However, our knowledge of fungi is limited due to a distributional bias; the vast majority of available data on fungi have been compiled from non-tropical regions. Far less is known about fungi from tropical regions, with the bulk of these data being temporally limited surveys for fungal species diversity. Long-term studies (LTS), or repeated sampling from the same region over extended periods, are necessary to fully capture the extent of species diversity in a region, but LTS of fungi from tropical regions are almost non-existent. In this paper, we discuss the contributions of LTS of fungi in tropical regions to alpha diversity, ecological and functional diversity, biogeography, hypothesis testing, and conservation-with an emphasis on an ongoing tropical LTS in the Pakaraima Mountains of Guyana. We show how these contributions refine our understanding of Fungi. We also show that public data repositories such as NCBI, IUCN, and iNaturalist contain less information on tropical fungi compared to non-tropical fungi, and that these discrepancies are more pronounced in fungi than in plants and animals.

Functional diversity of the above-ground fungal community under long-term integrated, organic and biodynamic Vineyard Management

Abstract Background Sustainable agriculture increasingly emphasizes the importance of microbial communities in influencing plant health and productivity. In viticulture, understanding the impact of management practices on fungal communities is critical, given their role in disease dynamics, grape and wine quality. This study investigates the effects of integrated, organic, and biodynamic management practices on the diversity and function of fungal communities in a vineyard located in Geisenheim, Germany, focusing on above-ground parts such as bark, leaves, and grapes. Results Our findings indicate that while overall fungal species richness did not significantly differ among management systems across various compartments, the composition of these communities was distinctly influenced by the type of management system. In particular, leaf and grape compartments showed notable variations in fungal community structure between integrated and organic/biodynamic management. No differences were observed between organic and biodynamic management. Integrated management demonstrated a significantly higher abundance of mycoparasites in comparison to organic and biodynamic management, primarily attributed to the increased presence of Sporobolomyces roseus, Sporobolomyces ellipsoideus and Rhodotorula glutinis. Conclusions The findings highlight the importance of management practices in shaping fungal community composition and function in vineyards. Although overall species richness remained unaffected, community composition and functional diversity varied, highlighting the potential for strategic microbiome management to enhance vineyard sustainability and plant health.

Preharvest Natural Multitoxin Contamination of Winter Wheat Genotypes in Hungary with Special Attention to Aflatoxins and HT-2 Toxin

Toxigenic fungi are among the most significant disease-causing agents in wheat. DON is the most common Fusarium mycotoxin, and for a long time, it was the only toxin researched. However, multitoxin data from wheat samples have drawn attention to the fact that much more toxins can be involved in the wheat toxin story than we supposed earlier. For resistance breeding, we need a more detailed approach to identify toxins that occur above the limit and identify the source of the fungal species that produces them. This study analyzed local wheat varieties for fungal infections and natural multitoxin contamination. Eighteen winter wheat genotypes were tested for fungal contaminations across three different locations in 2021 and 2022. Fourteen different mycotoxins—deoxynivalenol, aflatoxins (B1, B2, G1, and G2), fumonisins (B1 and B2), sterigmatocystin, ochratoxin A, zearalenone, T-2, HT-2, and diacetoxyscirpenol—were analyzed using HPLC/triple-quad MS. Toxigenic species such as Fusarium, Aspergillus, and Penicillium had low rates of occurrence, but the toxin contamination was often surprisingly high. Many samples without corresponding fungal infections were also identified as containing mycotoxins. Therefore, the identified fungal infection is less useful for forecasting toxin level. In conclusion, mycotoxin contamination is decisive. Most samples were contaminated by one or more mycotoxins. Although the mycotoxin concentrations typically remained below EU limits, some samples exhibited higher levels, particularly aflatoxins and Ht-2 toxin. Significant variations were observed across year, location, and genotype. For several toxins, significant genotype differences were identified, supporting the hypothesis that resistance may be a useful and suitable control measure. Stability of toxin contamination across years and locations is a very valuable trait; genotypes were identified with low toxin levels and stability (low variance) to all mycotoxins tested. It seems that, in addition to DON, more attention should be given to aflatoxin B1, B2, and G1, which provided similar concentrations. The HT-2 toxin was present in many samples surpassing EU limits. This is the first report on the dangerous occurrence of preharvest-origin aflatoxins and the HT-2 toxin of wheat in Hungary.

The biosynthesis and impacts of cytokinins on growth of the oyster mushroom, Pleurotus ostreatus

ABSTRACT While a lot is known about cytokinins (CKs) and their actions at the molecular and cellular levels in plants, much less is known about the function of CKs in other kingdoms such as fungi. CKs have been detected in a wide range of fungal species where they play roles ranging from enhancing the virulence of phytopathogens to fortifying plant growth when secreted from fungal symbionts. However, the role of CKs where they concern fungal physiology, apart from plant associations, remains largely uncharacterized. Profiling by UHPLC-HRMS/MS (ultrahigh-performance liquid chromatography–high-resolution tandem mass spectrometry) revealed that Pleurotus ostreatus (oyster mushroom) produces CKs in vitro in both liquid and solid cultures. During fungal growth, CK profiling patterns were consistent with previous suggestions that tRNA degradation products might play a role in the physiological development of fungi. It confirms that those products are CKs that act as fungal growth regulators. Moreover, P. ostreatus was shown to respond to exogenous applications of aromatic and isoprenoid CKs, and their effects were dependent on the dose and CK type in a biphasic manner consistent with hormone action. N 6-benzyladenine (BAP), kinetin (KIN), N 6-isopentenyladenine (iP), and trans-zeatin (tZ) bioassays all revealed hormesis-type responses. Accordingly, at low doses, mycelium colony diameter, biomass accumulation, and changes in morphology were stimulated, whereas at high doses only inhibitory effects were observed. Thus, CKs may act as “mycohormones” and consequently have potential for applications in fungal agriculture and medicinal compound production.

Ochratoxin A in Poultry Supply Chain: Overview of Feed Occurrence, Carry-Over, and Pathognomonic Lesions in Target Organs to Promote Food Safety

Ochratoxin A (OTA) is a mycotoxin produced by fungi species belonging to the genera Aspergillus spp. and Penicillium spp. The proliferation of OTA-producing fungal species may occur due to inadequate practices during both the pre-harvest and post-harvest stages of feed. Consequently, poultry species may be exposed to high concentrations of this mycotoxin that can be transferred to animal tissues due to its carry-over, reaching dangerous concentrations in meat and meat products. Therefore, this review aims to propose a comprehensive overview of the effects of OTA on human health, along with data from global studies on the prevalence and concentrations of this mycotoxin in avian feeds, as well as in poultry meat, edible offal, and eggs. Moreover, the review examines significant gross and histopathological lesions in the kidneys and livers of poultry linked to OTA exposure. Finally, the key methods for OTA prevention and decontamination of feed are described.

Microbial Bioremediation of Spent Engine Oil: Current Advances, Challenges, and Future Directions

Study’s Excerpt Recent advancements in microbial bioremediation of spent engine oil (SEO) are presented. Specifically, the efficiency of bacterial and fungal species in degrading SEO hydrocarbons are reviewed. Key factors that influence degradation rates, such as strain specificity and environmental parameters in relation to different microorganisms are also highlighted. Full Abstract The extensive pollution of soil and water by spent engine oil (SEO) presents a considerable environmental hazard, especially because of its poisonous and recalcitrant characteristics. Traditional remediation approaches typically fall short in managing these toxins successfully, leading to an increased interest in bioremediation as a sustainable option. This review aims to compile current achievements/advancements in the microbial bioremediation of SEO, with emphasis on the effectiveness of several bacterial and fungal species in degrading the hydrocarbons in SEO under diverse environmental settings. Various studies published in the last decade (accessible via Google Scholar, Google, Scopus, and PubMed), reporting on microbial degradation rates on SEO, the impact of environmental conditions, and the efficacy of microbial consortia were objectively selected and analysed. Key findings showed that various genera such as Alcaligenes, Acinetobacter, Bacillus, Candida, Flavobacterium, Pseudomonas, and Rhodococcus were the most commonly reported microorganisms with potential SEO remediation because they have been reported to significantly degrade and used hydrocarbons in SEO as an energy source. Notably, Pseudomonas alcaligenes and Klebsiella aerogenes exhibited significant degradation rates of SEO, up to 68%, over 21 days under optimal conditions; Acinetobacter, Bacillus, Micrococcus, Flavobacterium, and Pseudomonas were found to exhibit a total hydrocarbon reduction of 86.7% over 60 days; while species like Ochrobactrum thiophenivorans were found to effectively degrade waste lubricating oil. However, there are significant differences in degradation rates among the reported species due to physiological factors such as temperature, pH, and available nutrients. Hence, it is inferential to conclude that microbial bioremediation shows promise in SEO management but its effectiveness is highly dependent on the type of microbial strain used and optimizing environmental conditions. Therefore, this review identifies several key knowledge gaps and proposed future research directions, such as the integration of bioremediation with emerging technologies to improve and ensure efficiency and scalability in real-world applications.

Deep Learning-Based Classification of Macrofungi: Comparative Analysis of Advanced Models for Accurate Fungi Identification

This study focuses on the classification of six different macrofungi species using advanced deep learning techniques. Fungi species, such as Amanita pantherina, Boletus edulis, Cantharellus cibarius, Lactarius deliciosus, Pleurotus ostreatus and Tricholoma terreum were chosen based on their ecological importance and distinct morphological characteristics. The research employed 5 different machine learning techniques and 12 deep learning models, including DenseNet121, MobileNetV2, ConvNeXt, EfficientNet, and swin transformers, to evaluate their performance in identifying fungi from images. The DenseNet121 model demonstrated the highest accuracy (92%) and AUC score (95%), making it the most effective in distinguishing between species. The study also revealed that transformer-based models, particularly the swin transformer, were less effective, suggesting room for improvement in their application to this task. Further advancements in macrofungi classification could be achieved by expanding datasets, incorporating additional data types such as biochemical, electron microscopy, and RNA/DNA sequences, and using ensemble methods to enhance model performance. The findings contribute valuable insights into both the use of deep learning for biodiversity research and the ecological conservation of macrofungi species.

Moving beyond species: fungal function in house dust provides novel targets for potential indicators of mold growth in homes

BackgroundIncreased risk of asthma and other respiratory diseases is associated with exposures to microbial communities growing in damp and moldy indoor environments. The exact causal mechanisms remain unknown, and occupant health effects have not been consistently associated with any species-based mold measurement methods. We need new quantitative methods to identify homes with potentially harmful fungal growth that are not dependent upon species. The goal of this study was to identify genes consistently associated with fungal growth and associated function under damp conditions for use as potential indicators of mold in homes regardless of fungal species present. A de novo metatranscriptomic analysis was performed using house dust from across the US, incubated at 50%, 85%, or 100% equilibrium relative humidity (ERH) for 1 week.ResultsGene expression was a function of moisture (adonis2 p < 0.001), with fungal metabolic activity increasing with an increase in moisture condition (Kruskal–Wallis p = 0.003). Genes associated with fungal growth such as sporulation (n = 264), hyphal growth (n = 62), and secondary metabolism (n = 124) were significantly upregulated at elevated ERH conditions when compared to the low 50% ERH (FDR-adjusted p ≤ 0.001, log2FC ≥ 2), indicating that fungal function is influenced by damp conditions. A total of 67 genes were identified as consistently associated with the elevated 85% or 100% ERH conditions and included fungal developmental regulators and secondary metabolite genes such as brlA (log2FC = 7.39, upregulated at 100% compared to 85%) and stcC (log2FC = 8.78, upregulated at 85% compared to 50%).ConclusionsOur results demonstrate that moisture conditions more strongly influence gene expression of indoor fungal communities compared to species presence. Identifying genes indicative of microbial growth under damp conditions will help develop robust monitoring techniques for indoor microbial exposures and improve understanding of how dampness and mold are linked to disease.-X5AkW-U2mftBzktcaxDSrVideo