Impact of microbial-based biopreparations on soil quality, plant health, and fruit chemistry in raspberry cultivation.

Application of microbial-based biopreparations as a pre-harvest strategy offers a method to obtain sustainable agricultural practices and could be an important approach for advancing food science, promoting sustainability, and meeting global food market demands. The impact of a bacterial-fungal biopreparation mixture on soil-plant-microbe interactions, fruit chemical composition and yield of 7 raspberry clones was investigated by examining the structural and functional profiles of microbial communities within leaves, fruits, and soil. Biopreparation addition caused the enhancement of the microbiological utilization of specific compounds, such as d-mannitol, relevant in plant-pathogen interactions and overall plant health. The biopreparation treatment positively affected the nitrogen availability in soil (9-160%). The analysis of plant stress marker enzymes combined with the evaluation of fruit quality and chemical properties highlight changes inducted by the pre-harvest biopreparation application. Chemical analyses highlight biopreparations' role in soil and fruit quality improvement, promoting sustainable agriculture. This effect was dependent on tested clones, showing increase of soluble solid content in fruits, concentration of polyphenols or the sensory quality of the fruits. The results of the next-generation sequencing indicated increase in the effective number of bacterial species after biopreparation treatment. The network analysis showed stimulating effect of biopreparation on microbial communities by enhancing microbial interactions (increasing the number of network edges up to 260%) of and affecting the proportions of mutual relationships between both bacteria and fungi. These findings show the potential of microbial-based biopreparation in enhancing raspberry production whilst promoting sustainable practices and maintaining environmental homeostasis and giving inshght in holistic understanding of microbial-based approaches for advancing food science monitoring.

Airborne fungal communities are more susceptible to anthropogenic activities than bacteria.

Airborne microorganisms (AM) have significant environmental and health implications. Extensive studies have been conducted to investigate the factors influencing the composition and diversity of AM. However, the knowledge of AM with anthropogenic activities has not reach a consensus. In this study, we took advantage of the dramatic decline of outdoor anthropogenic activities resulting from COVID-19 lockdown to reveal their associations. We collected airborne particulate matter before and during the lockdown period in two cities. The results showed that it was fungal diversity and communities but not bacteria obviously different between pre-lockdown and lockdown samples, suggesting that airborne fungi were more susceptible to anthropogenic activities than bacteria. However, after the implementation of lockdown, the co-occurrence networks of both bacterial and fungal community became more complex, which might be due to the variation of microbial sources. Furthermore, Mantel test and correlation analysis showed that air pollutants also partly contributed to microbial alterations. Airborne fungal community was more affected by air pollutants than bacterial community. Notably, some human pathogens like Nigrospora and Arthrinium were negatively correlated with air pollutants. Overall, our study highlighted the more impacts of anthropogenic activities on airborne fungal community than bacterial community and advanced the understanding of associations between anthropogenic activities and AM.

Metabolic homeostasis in fungal infections from the perspective of pathogens, immune cells, and whole-body systems.

SUMMARYThe ability to overcome metabolic stress is a major determinant of outcomes during infections. Pathogens face nutrient and oxygen deprivation in host niches and during their encounter with immune cells. Immune cells require metabolic adaptations for producing antimicrobial compounds and mounting antifungal inflammation. Infection also triggers systemic changes in organ metabolism and energy expenditure that range from an enhanced metabolism to produce energy for a robust immune response to reduced metabolism as infection progresses, which coincides with immune and organ dysfunction. Competition for energy and nutrients between hosts and pathogens means that successful survival and recovery from an infection require a balance between elimination of the pathogen by the immune systems (resistance), and doing so with minimal damage to host tissues and organs (tolerance). Here, we discuss our current knowledge of pathogen, immune cell and systemic metabolism in fungal infections, and the impact of metabolic disorders, such as obesity and diabetes. We put forward the idea that, while our knowledge of the use of metabolic regulation for fungal proliferation and antifungal immune responses (i.e., resistance) has been growing over the years, we also need to study the metabolic mechanisms that control tolerance of fungal pathogens. A comprehensive understanding of how to balance resistance and tolerance by metabolic interventions may provide insights into therapeutic strategies that could be used adjunctly with antifungal drugs to improve patient outcomes.

Characteristics and driving forces of the soil microbial community during 35 years of natural restoration in abandoned areas of the Daxin manganese mine, China.

The restoration of mining wastelands, particularly in karst regions contaminated by heavy metals, is an environmental challenge in need of urgent attention. Soil microbes play a vital role in nutrient cycling and ecosystem recovery, yet the long-term evolution of soil microbial communities in such settings remains poorly understood. This study explored the dynamics and influencing factors of soil microbial communities during 35 years of natural restoration in abandoned manganese (Mn) mine areas in Guangxi Province, China. The results revealed that the concentrations of Mn, Cd, Zn, and Cu were significantly (p < 0.05) reduced by 80.4-85.3%, 55.3-70.0%, 21.0-38.1%, and 29.4-49.4%, respectively, in the mid-late restoration periods (R19 and R35) compared with R1. The α diversities of the bacterial and fungal communities significantly increased in the middle-late restoration periods (R19 and R35), indicating increased microbial diversity as restoration progressed. The bacterial community structure exhibited more pronounced changes than did the fungal community structure, with significant shifts observed in dominant phyla such as Proteobacteria, Actinobacteria, Acidobacteriota, and Ascomycota. Notably, the relative abundances of Rhizobiales, Burkholderiales, and Hypocreales increased gradually with succession. Co-occurrence network analysis revealed that bacterial interactions became stronger over time, whereas interactions between bacteria and fungi weakened. Mantel tests and partial least squares path modeling (PLS‒PM) identified soil pH, heavy metals (Mn, Cd, Zn, and Cu), and nutrients (SOM and TN) as key drivers shaping the microbial community composition. These factors were more strongly correlated with bacterial communities than with fungal communities, underscoring the different responses of microbial groups to environmental changes during natural restoration. These findings enhance our understanding of the ecological processes governing microbial community succession in heavy metal-contaminated soils undergoing natural restoration.

Community structure of soil microorganisms and endophytes of honeysuckle at different ecological niche specificities.

BACKGROUND: The plant microbiome is one of the key determinants of healthy plant growth. However, the complexity of microbial diversity in plant microenvironments in different regions, especially the relationship between subsurface and aboveground microorganisms, is not fully understood. The present study investigated the diversity of soil microorganisms in different regions and the diversity of microorganisms within different ecological niches, and compared soil microorganisms and endophytic microorganisms. METHODS: 16 S and ITS sequencing was used to sequence the soil and endophytes microbiome of honeysuckle. Alpha diversity analysis and principal component analysis (PCoA) were used to study the soil and endophyte microbial communities, and the function of endophyte bacteria and fungi was predicted based on the PICRUST2 process and FUNGuild. RESULTS: In total, there were 382 common bacterial genera and 139 common fungal genera in the soil of different producing areas of honeysuckle. There were 398 common bacterial genera and 157 common fungal genera in rhizosphere soil. More beneficial bacteria were enriched in rhizosphere soil. Endophytic bacteria were classified into 34 phyla and 770 genera. Endophytic fungi were classified into 11 phyla and 581 genera, among which there were significant differences in the dominant genera of roots, stems, leaves, and flowers, as well as in community diversity and richness. Endophytic fungal functions were mainly dominated by genes related to saprophytes, functional genes that could fight microorganisms were also found in KEGG secondary functional genes. CONCLUSION: More beneficial bacteria were enriched in rhizosphere soil of honeysuckle, and the microbial network of the rhizosphere is more complex than that of the soil. Among the tissues of honeysuckle, the flowers have the richest diversity of endophytes. The endogenous dominant core bacteria in each part of honeysuckle plant have a high degree of overlap with the dominant bacteria in soil. Functional prediction suggested that some dominant core bacteria have antibacterial effects, providing a reference for further exploring the strains with antibacterial function of honeysuckle. Understanding the interaction between honeysuckle and microorganisms lays a foundation for the study of growth promotion, quality improvement, and disease and pests control of honeysuckle from the perspective of microorganisms.

A taxon-rich and genome-scale phylogeny of Opisthokonta.

Ancient divergences within Opisthokonta-a major lineage that includes organisms in the kingdoms Animalia, Fungi, and their unicellular relatives-remain contentious. To assess progress toward a genome-scale Opisthokonta phylogeny, we conducted the most taxon rich phylogenomic analysis using sets of genes inferred with different orthology inference methods and established the geological timeline of Opisthokonta diversification. We also conducted sensitivity analysis by subsampling genes or taxa from the full data matrix based on filtering criteria previously shown to improve phylogenomic inference. We found that approximately 85% of internal branches were congruent across data matrices and the approaches used. Notably, the use of different orthology inference methods was a substantial contributor to the observed incongruence: analyses using the same set of orthologs showed high congruence of 97% to 98%, whereas different sets of orthologs resulted in somewhat lower congruence (87% to 91%). Examination of unicellular Holozoa relationships suggests that the instability observed across varying gene sets may stem from weak phylogenetic signals. Our results provide a comprehensive Opisthokonta phylogenomic framework that will be useful for illuminating ancient evolutionary episodes concerning the origin and diversification of the 2 major eukaryotic kingdoms and emphasize the importance of investigating effects of orthology inference on phylogenetic analyses to resolve ancient divergences.

Comparing NGS-Based identification of bloodstream infections to traditional culture methods for enhanced ICU care: a comprehensive study.

Background: Accurate identification of infectious diseases using molecular techniques, such as PCR and NGS, is well-established. This study aims to assess the utility of Bactfast and Fungifast in diagnosing bloodstream infections in ICU settings, comparing them against traditional culture methods. The objectives include evaluating sensitivity and specificity and identifying a wide range of pathogens, including non-culturable species. Methods: We collected 500 non-duplicate blood samples from ICU patients between January 2023 and December 2023. Specimens underwent traditional culture, MALDI-TOF, VITEK®2 compact system, and NGS-based Bactfast and Fungifast analyses. Results: Out of the 500 samples, 26.8% (n=134) showed bacterial growth via traditional culture methods, while 4.8% (n=24) were positive for fungal growth. MALDI-TOF and VITEK®2 compact system yielded comparable results, identifying 26.4% (n=132) of specimens with bacterial growth. NGS-based Bactfast detected bacterial presence in 38.2% (n=191) of samples, including non-culturable bacteria missed by traditional methods. However, NGS-based Fungifast showed concordant fungal detection rates with culture methods. Among identified pathogens by culture method included Klebsiella pneumoniae 20.89% (n=28), Enterococcus faecalis 18.65% (n=25), Escherichia coli 15.67% (n=21), Pseudomonas aeruginosa 12.68% (n=17), Acinetobacter baumannii 10.44% (n=14), various Streptococcus species 7.46% (n=10), Mycobacterium tuberculosis 6.71% (n=9), Mycobacterium abscessus 4.47% (n=6), and Salmonella spp 2.98% (n=4). Non-culture-based NGS identified additional (n=33) pathogens, including Klebsiella pneumoniae 27.27% (n=9), Bacteroides fragilis 21.21% (n=7), Aerococcus viridans 15.15% (n=5), Elizabethkingia anopheles 12.12% (n=4), Aeromonas salmonicida 9% (n=3), Clostridium 9% (n=3), and Bacteroides vulgatus 6% (n=2). Candida albicans was reported in 5% (n=24) of samples by both methods. Conclusion: NGS-based Bactfast and Fungifast demonstrate high sensitivity in identifying a wide array of bacterial and fungal pathogens in ICU patients, outperforming traditional culture methods in detecting non-culturable organisms. These molecular assays offer rapid and comprehensive diagnostic capabilities, potentially improving clinical outcomes through timely and accurate pathogen identification.

Seasonal dynamics in leaf litter decomposing microbial communities in temperate forests: a whole-genome- sequencing-based study.

Leaf litter decomposition, a crucial component of the global carbon cycle, relies on the pivotal role played by microorganisms. However, despite their ecological importance, leaf-litter-decomposing microorganism taxonomic and functional diversity needs additional study. This study explores the taxonomic composition, dynamics, and functional role of microbial communities that decompose leaf litter of forest-forming tree species in two ecologically unique regions of Europe. Twenty-nine microbial metagenomes isolated from the leaf litter of eight forest-forming species of woody plants were investigated by Illumina technology using read- and assembly-based approaches of sequences analysis. The taxonomic structure of the microbial community varies depending on the stage of litter decomposition; however, the community's core is formed by Pseudomonas, Sphingomonas, Stenotrophomonas, and Pedobacter genera of Bacteria and by Aureobasidium, Penicillium, Venturia genera of Fungi. A comparative analysis of the taxonomic structure and composition of the microbial communities revealed that in both regions, seasonal changes in structure take place; however, there is no clear pattern in its dynamics. Functional gene analysis of MAGs revealed numerous metabolic profiles associated with leaf litter degradation. This highlights the diverse metabolic capabilities of microbial communities and their implications for ecosystem processes, including the production of volatile organic compounds (VOCs) during organic matter decomposition. This study provides important advances in understanding of ecosystem processes and the carbon cycle, underscoring the need to unravel the intricacies of microbial communities within these contexts.

Networks as tools for defining emergent properties of microbiomes and their stability.

The potential promise of the microbiome to ameliorate a wide range of societal and ecological challenges, from disease prevention and treatment to the restoration of entire ecosystems, hinges not only on microbiome engineering but also on the stability of beneficial microbiomes. Yet the properties of microbiome stability remain elusive and challenging to discern due to the complexity of interactions and often intractable diversity within these communities of bacteria, archaea, fungi, and other microeukaryotes. Networks are powerful tools for the study of complex microbiomes, with the potential to elucidate structural patterns of stable communities and generate testable hypotheses for experimental validation. However, the implementation of these analyses introduces a cascade of dichotomies and decision trees due to the lack of consensus on best practices. Here, we provide a road map for network-based microbiome studies with an emphasis on discerning properties of stability. We identify important considerations for data preparation, network construction, and interpretation of network properties. We also highlight remaining limitations and outstanding needs for this field. This review also serves to clarify the varying schools of thought on the application of network theory for microbiome studies and to identify practices that enhance the reproducibility and validity of future work. Video Abstract.

Antibiotics Amoxicillin, Ampicillin and Their Mixture-Impact on Bacteria, Fungi, Ostracods and Plants.

Ampicillin (AMP) and amoxicillin (AMX) are popular antibiotics, which are penicillin derivatives, and are used in both human and veterinary medicine. In the conducted study, AMP, AMX and their mixtures did not cause major changes in the total bacterial counts in soil samples, and even an increase in the bacterial counts from 3,700,000 to 6,260,000 colony-forming units (cfu) per gram of soil dry weight (g of soil DW) was observed for minimal amounts of these drugs in the soil. The total abundance of fungi, on the other hand, increased from values ranging from 17,000 to 148,000 cfu∙g-1 of soil DW to a level of 32,000 to 131,000 cfu∙g-1 of soil DW. The tested antibiotics and their mixtures had no significant effect on the mortality and growth of H. incongruens. AMX and the AMP + AMX mixture also showed no effect on the plant fresh weight yield, plant aboveground part length and dry weight content of wheat seedlings. In contrast, AMP caused an increase in the plant fresh weight yield and wheat seedling length compared to the control. The drug also caused a slight decrease in the seedling dry weight content. Both AMP and AMX showed inhibitory effects on the plant root length at the highest concentrations of the compounds.

Packing Incubation and Addition of Rot Fungi Extracts Improve BTEX Elimination from Air in Biotrickling Filters.

The removal of benzene, toluene, ethylbenzene, and xylene (BTEX) from air was investigated in two similar biotrickling filters (BTFs) packed with polyurethane (PU) foam, differing in terms of inoculation procedure (BTF A was packed with pre-incubated PU discs, and BTF B was inoculated via the continuous recirculation of a liquid inoculum). The effects of white rot fungi enzyme extract addition and system responses to variable VOC loading, liquid trickling patterns, and pH were studied. Positive effects of both packing incubation and enzyme addition on biotrickling filtration performance were identified. BFF A exhibited a shorter start-up period (approximately 20 days) and lower pressure drop (75 ± 6 mm H2O) than BTF B (30 days; 86 ± 5 mm H2O), indicating the superior effects of packing incubation over inoculum circulation during the biotrickling filter start-up. The novel approach of using white rot fungi extracts resulted in fast system recovery and enhanced process performance after the BTF acidification episode. Average BTEX elimination capacities of 28.8 ± 0.4 g/(m3 h) and 23.1 ± 0.4 g/(m3 h) were reached for BTF A and BTF B, respectively. This study presents new strategies for controlling and improving the abatement of BTEX in biotrickling filters.

Diabetic foot exacerbates gut mycobiome dysbiosis in adult patients with type 2 diabetes mellitus: revealing diagnostic markers.

Type 2 diabetes mellitus (T2DM) is globally recognized as a significant health concern, with diabetic foot (DF) identified as a severe long-term complication that can lead to tissue death or amputation. The discovery of the impact of mycobiota, a diverse group of multicellular eukaryotes in the gut microbiome, on the onset of endocrine disorders holds great significance. Therefore, this research aimed to examine variations in fungal mycobiome and identify potential biomarkers for T2DM and T2DM-DF. Fecal and blood samples were collected from 33 individuals with T2DM, 32 individuals with T2DM-DF, and 32 healthy individuals without any health conditions (HC). Blood samples were used for laboratory parameters analysis, while total DNA was extracted from fecal samples and sequenced using Illumina 18s rRNA. Bioinformatics tools were employed to analyze fungal abundance and diversity, revealing differentially expressed fungal species and signature fungi that distinguished between T2DM, T2DM-DF, and HC groups. Firstly, significant alterations in some laboratory parameters were observed among the three groups, which also differed between T2DM and T2DM-DF. The diversity of gut fungi in T2DM and T2DM-DF significantly differed from that of the HC group; however, more pronounced changes were observed in T2DM-DF. Additionally, two significantly altered phyla, Ascomycota and Basidiomycota, were identified with higher Ascomycota abundance but lower Basidiomycota abundance in both the T2DM and T2DM-DF compared to the HC group. Furthermore, the top 15 fungi showing significant changes at the species level included a notable decrease in Rhodotorula_mucilaginosa abundance in patients with T2DM compared to HC and a substantial increase in unclassified_g_Candida abundance specifically seen only among patients with T2DM-DF, but not among those diagnosed with T2DM or HC. Thirdly, KEGG was employed to analyze enzyme expression across the three groups, revealing a more pronounced alteration in gut fungal function within T2DM-DF compared to T2DM. Subsequently, to accurately identify signature fungi in each group, a random forest was utilized to rank the top 15 significant fungi. Notably, 11 fungi were identified as potential biomarkers for distinguishing T2DM or T2DM-DF from HC, while eight fungi could discriminate between T2DM and T2DM-DF. Furthermore, receiver operating characteristic curve (ROC) analysis demonstrated enhanced accuracy of predicted outcomes. These findings suggest that changes in fungal mycobiome are closely associated with the progression and complications of T2DM and DF, offering promising prospects for diagnosis and treatment.

Phytoremediation of mercury-contaminated Soil by Vigna radiata L. plant in companion with bacterial and fungal biofertilizers.

Mercury is one of the most toxic pollutants that has drawn the attention of scientists. This study investigates the phytoremediation capabilities of Vigna radiata L. in conjunction with microbial biostimulators. The inoculated seeds were cultivated in soil under controlled greenhouse conditions. The concentration of Hg, biomass, and photosynthetic pigments was investigated under amendment factor including EDTA, bacterial, fungal (Mycorrhiza and Trichoderma), biochar, and combined levels, as well as the pollution factor with three levels of HgCl2 as two factorial experiments. Results showed that Plant Growth-Promoting Microorganisms (PGPMs) influenced mercury absorption and distribution in different plant organs. Aside from biochar, all stimulators increased the plant's Hg concentration. Although EDTA greatly increased mercury accumulation in plants, it reduced biomass. Fungal and bacterial treatments increased total mercury in the plant but decreased its concentration in the leaves. The combination of bacteria and fungi resulted in the highest mercury absorption, while the biochar in combination with PGPMs produced the greatest biomass. Analysis of mercury concentration in seeds indicated that V radiata effectively prevented its contamination in seeds. The results disclosed that microbial combinations of bacteria and fungi could increase the plant's potential to cope with heavy metal pollution. This improvement is due to the different roles of these two organisms, like nitrogen fixation by bacteria and phosphorus absorption by mycorrhiza fungi. Moreover, biochar as a soil amendment and microorganism carrier was noticed. Finally, considering the plant's inherent capacity to stabilize mercury in the roots, phytostabilization with the benefit of combined levels of biochar and microorganisms can be introduced as the best approach.

Investigating PCB degradation by indigenous fungal strains isolated from the transformer oil-contaminated site: degradation kinetics, Bayesian network, artificial neural networks, QSAR with DFT, molecular docking, and molecular dynamics simulation.

The widespread prevalence of polychlorinated biphenyls (PCBs) in the environment has raised major concerns due to the associated risks to human health, wildlife, and ecological systems. Here, we investigated the degradation kinetics, Bayesian network (BN), quantitative structure-activity relationship-density functional theory (QSAR-DFT), artificial neural network (ANN), molecular docking (MD), and molecular dynamics stimulation (MS) of PCB biodegradation, i.e., PCB-10, PCB-28, PCB-52, PCB-138, PCB-153, and PCB-180 in the soil system using fungi isolated from the transformer oil-contaminated sites. Results revealed that the efficacy of PCB biodegradation best fits the first-order kinetics (R2 ≥ 0.93). The consortium treatment (29.44-74.49%) exhibited more efficient degradation of PCBs than those of Aspergillus tamarii sp. MN69 (27.09-71.25%), Corynespora cassiicola sp. MN69 (23.76-57.37%), and Corynespora cassiicola sp. MN70 (23.09-54.98%). 3'-Methoxy-2, 4, 4'-trichloro-biphenyl as an intermediate derivative was detected in the fungal consortium treatment. The BN analysis predicted that the biodegradation efficiency of PCBs ranged from 11.6 to 72.9%. The ANN approach showed the importance of chemical descriptors in decreasing order, i.e., LUMO > MW > IP > polarity no. > no. of chlorine > Wiener index > Zagreb index > HOMU > Pogliani index > APE in PCB removal. Furthermore, the QSAR-DFT model between the chemical descriptors and rate constant (log K) exhibited a high fit and good robustness of R2 = 99.12% in predicting ability. The MD and MS analyses showed the lowest binding energy through normal mode analysis (NMA), implying stability in the interactions of the docked complexes. These findings provide crucial insights for devising strategies focused on natural attenuation, holding substantial potential for mitigating PCB contamination within the environment.

Fungal-mediated nanoparticles for industrial applications: synthesis and mechanism of action.

The advancement of safe, eco-friendly, and cost-efficient techniques for nanoparticle production is a crucial objective in nanotechnology. Among the various sustainable methods, the biological synthesis of nanoparticles utilizing fungi, bacteria, yeasts, and plants stands out. Fungi, in particular, are well suited for this task because of their capacity to secrete numerous enzymes and streamline subsequent processes. Using fungal strains for nanoparticle biosynthesis is both technologically appealing and economically viable. The utilization of fungal strains for nanoparticle biosynthesis is both technologically appealing and economically viable. Fungi have long been acknowledged as adept natural engineers capable of creating a wide array of nanoparticles with distinct properties and applications. This article provides an overview of fungus-mediated nanoparticle development, shedding light on the underlying mechanisms of their synthesis and the factors influencing their characteristics. Furthermore, the potential of fungus-mediated nanoparticles in the industrial domain has been explored. These findings emphasize the importance of different fungal species in nanoparticle synthesis, as well as the biocompatibility and environmental friendliness of fungus-mediated nanoparticles. By underscoring the essential role of fungi in connecting natural knowledge with innovative industrial applications, recent progress in enhancing nanoparticle production and optimizing synthesis conditions through fungi has been examined to underscore the feasibility of extensive industrial nanoparticle utilization via fungi.

Biotechnological approaches for suppressing Microcystis blooms: insights and challenges.

Cyanobacterial harmful algal blooms, particularly those dominated by Microcystis, pose significant ecological and health risks worldwide. This review provides an overview of the latest advances in biotechnological approaches for mitigating Microcystis blooms, focusing on cyanobactericidal bacteria, fungi, eukaryotic microalgae, zooplankton, aquatic plants, and cyanophages. Recently, promising results have been obtained using cyanobactericidal bacteria: not through the inoculation of cultured bacteria, but rather by nurturing those already present in the periphyton or biofilms of aquatic plants. Fungi and eukaryotic microalgae also exhibit algicidal properties; however, their practical applications still face challenges. Zooplankton grazing on Microcystis can improve water quality, but hurdles exist because of the colonial form and toxin production of Microcystis. Aquatic plants control blooms through allelopathy and nutrient absorption. Although cyanophages hold promise for Microcystis control, their strain-specificity hinders widespread use. Despite successful laboratory validation, field applications of biological methods are limited. Future research should leverage advanced molecular and bioinformatic techniques to understand microbial interactions during blooms and offer insights into innovative control strategies. Despite progress, the efficacy of biological methods under field conditions requires further verification, emphasizing the importance of integrating advanced multi-meta-omics techniques with practical applications to address the challenges posed by Microcystis blooms. KEY POINTS: • A diverse range of biotechnological methods is presented for suppressing Microcystis blooms. • Efficacy in laboratory experiments needs to be proved further in field applications. • Multi-meta-omics techniques offer novel insights into Microcystis dynamics and interactions.

A novel luciferase-based reporter tool to monitor the dynamics of carbon catabolite repression in filamentous fungi.

Filamentous fungi with their diverse inventory of carbohydrate-active enzymes promise a holistic usage of lignocellulosic residues. A major challenge for application is the inherent repression of enzyme production by carbon catabolite repression (CCR). In the presence of preferred carbon sources, the transcription factor CreA/CRE-1 binds to specific but conserved motifs in promoters of genes involved in sugar metabolism, but the status of CCR is notoriously difficult to quantify. To allow for a real-time evaluation of CreA/CRE-1-mediated CCR at the transcriptional level, we developed a luciferase-based construct, representing a dynamic, highly responsive reporter system that is inhibited by monosaccharides in a quantitative fashion. Using this tool, CreA/CRE-1-dependent CCR triggered by several monosaccharides could be measured in Neurospora crassa, Aspergillus niger and Aspergillus nidulans over the course of hours, demonstrating distinct and dynamic regulatory processes. Furthermore, we used the reporter to visualize the direct impacts of multiple CreA truncations on CCR induction. Our reporter thus offers a widely applicable quantitative approach to evaluate CreA/CRE-1-mediated CCR across diverse fungal species and will help to elucidate the multifaceted effects of CCR on fungal physiology for both basic research and industrial strain engineering endeavours.

Accumulated melanin in molds provides wavelength-dependent UV tolerance.

Fungal contamination poses a serious threat to public health and food safety because molds can grow under stressful conditions through melanin accumulation. Although ultraviolet (UV) irradiation is popular for inhibiting microorganisms, its effectiveness is limited by our insufficient knowledge about UV tolerance in melanin-accumulating molds. In this study, we first confirmed the protective effect of melanin by evaluating the UV sensitivity of young and mature spores. Additionally, we compared UV sensitivity between spores with accumulated melanin and spores prepared with melanin biosynthesis inhibitors. We found that mature spores were less UV-sensitive than young spores, and that reduced melanin accumulation by inhibitors led to reduced UV sensitivity. These results suggest that melanin protects cells against UV irradiation. To determine the most effective wavelength for inhibition, we evaluated the wavelength dependence of UV tolerance in a yeast (Rhodotorula mucilaginosa) and in molds (Aspergillus fumigatus, Cladosporium halotolerans, Cladosporium sphaerospermum, Aspergillus brasiliensis, Penicillium roqueforti, and Botrytis cinerea). We assessed UV tolerance using a UV-light emitting diode (LED) irradiation system with 13 wavelength-ranked LEDs between 250 and 365 nm, a krypton chlorine (KrCl) excimer lamp device, and a low pressure (LP) Hg lamp device. The inhibition of fungi peaked at around 270 nm, and most molds showed reduced UV sensitivity at shorter wavelengths as they accumulated pigment. Absorption spectra of the pigments showed greater absorption at shorter wavelengths, suggesting greater UV protection at these wavelengths. These results will assist in the development of fungal disinfection systems using UV, such as closed systems of air and water purification.

Structure and distribution of sensor histidine kinases in the fungal kingdom.

Two-component systems (TCSs) are diverse cell signaling pathways that play a significant role in coping with a wide range of environmental cues in both prokaryotic and eukaryotic organisms. These transduction circuitries are primarily governed by histidine kinases (HKs), which act as sensing proteins of a broad variety of stressors. To date, nineteen HK groups have been previously described in the fungal kingdom. However, the structure and distribution of these prominent sensing proteins were hitherto investigated in a limited number of fungal species. In this study, we took advantage of recent genomic resources in fungi to refine the fungal HK classification by deciphering the structural diversity and phylogenetic distribution of HKs across a large number of fungal clades. To this end, we browsed the genome of 91 species representative of different fungal clades, which yielded 726 predicted HK sequences. A domain organization analysis, coupled with a robust phylogenomic approach, led to an improved categorization of fungal HKs. While most of the compiled sequences were categorized into previously described fungal HK groups, some new groups were also defined. Overall, this study provides an improved overview of the structure, distribution, and evolution of HKs in the fungal kingdom.