The filamentous fungal pellet-relationship between morphology and productivity

Structure-activity relationship of self-immobilized mycelial pellets and their functions in wastewater treatment

Mycelial pellets (MPs) represent an emerging class of eco-friendly, self-immobilized bioactive materials characterized by high biological activity, superior porous structure, and unique biocompatibility. Based on structure-activity relationships, this paper reviews MPs' applications, mechanisms, and advantages in wastewater treatment, while updating fundamental theories on their production optimization, structure characteristics, and surface properties. Emphasis is placed on MPs' three principal functions in remediating pollution: biodegradation via high biological activity, adsorption through porous aggregated structure and superior surface features, and bio-carrier role based on the three-dimensional carbonaceous skeleton. Furthermore, the multifunctionality of MPs improves sludge settleability and dewaterability, as well as enhances aerobic granular sludge granulation and structural stability. Future research priorities include scalable low-cost production, mechanical reinforcement strategies, development of engineered strains and composites, and safe disposal of pollutant-laden MPs. This work provides valuable insights into the use of MPs in wastewater treatment and identifies critical directions for advancing MPs technology.

Cell walls of filamentous fungi - challenges and opportunities for biotechnology

The cell wall of filamentous fungi is essential for growth and development, both of which are crucial for fermentations that play a vital role in the bioeconomy. It typically has an inner rigid core composed of chitin and beta-1,3-/beta-1,6-glucans and a rather gel-like outer layer containing other polysaccharides and glycoproteins varying between and within species. Only a fraction of filamentous fungal species is used for the biotechnological production of enzymes, organic acids, and bioactive compounds such as antibiotics in large amounts on a yearly basis by precision fermentation. Most of these products are secreted into the production medium and must therefore pass through fungal cell walls at high transfer rates. Thus, cell wall mutants have gained interest for industrial enzyme production, although the causal relationship between cell walls and productivity requires further elucidation. Additionally, the extraction of valuable biopolymers like chitin and chitosan from spent fungal biomass, which is predominantly composed of cell walls, represents an underexplored opportunity for circular bioeconomy. Questions persist regarding the effective extraction of these biopolymers from the cell wall and their repurposing in valorization processes. This review aims to address these issues and promote further research on understanding the cell walls in filamentous fungi to optimize their biotechnological use. KEY POINTS: • The highly complex cell walls of filamentous fungi are important for biotechnology. • Cell wall mutants show promising potential to improve industrial enzyme secretion. • Recent studies revealed enhanced avenues for chitin/chitosan from fungal biomass.

Biomining of lunar regolith simulant EAC-1 A with the fungus Penicillium simplicissimum

BACKGROUND

On a future lunar habitat, acquiring needed resources in situ will inevitably come from the Lunar regolith. Biomining, i.e. the use of microorganisms to extract metals from the regolith, is sustainable and energy-efficient, making it highly promising for space exploration applications. Given the extensive use of filamentous fungi in industrial biotechnology, we investigated the ability of the fungus Penicillium simplicissimum to extract metals from the European Astronaut Centre lunar regolith simulant 1 (EAC-1 A), which will be used as the analogue soil at the European Lunar Exploration Laboratory (LUNA) facility at the European Space Agency (ESA) and German Aerospace Centre (DLR) site.

RESULTS

Biocompatibility tests demonstrated P. simplicissimum tolerance to high concentrations of EAC-1 A lunar regolith simulant (up to 60%), both on Earth gravity and Lunar simulated gravity via clinorotation. We reveal that a fungal bioleaching setup using low nutrient medium (20% PDB) enables P. simplicissimum to extract metals from EAC-1 A regolith over the course of 2 weeks at room temperature. Inductively coupled plasma mass spectrometry (ICP-MS) analysis of the leachate revealed the extraction of magnesium (up to 159 mg/L), calcium (151 mg/L), iron (68 mg/L), aluminium (32 mg/L), manganese (3 mg/L) as well as traces of titanium (0.02 mg/L). The recovered metal oxide powder from the leachate, obtained via centrifugation (14,500 g, 4,000 rpm), followed by filtration (0.22 μm) and drying at 60 °C overnight, achieved a promising average of 10 ± 3 g/L. Further analysis via SEM/EDS and XRD confirmed the presence of aluminium [as boehmite (AlO(OH))], magnesium, and iron [possibly as haematite (Fe2O3)] and magnetite [possibly as (Fe3O4)].

CONCLUSION

Our study demonstrates successful fungal biomining of lunar regolith simulant EAC-1 A and emphasizes the utilization of fungal-based approaches as promising ISRU technologies in future space exploration missions.

Engineering dispersed mycelium morphology in Aspergillus niger for enhanced mycoprotein production via CRISPR/Cas9-mediated genome editing

Filamentous fungi are widely utilized in industrial fermentation processes due to their high productivity, with mycelial morphology directly influencing fermentation broth viscosity and target product yield, which is a critical parameter for process optimization. Aspergillus niger, an FDA-approved safe filamentous fungus, typically forms tightly packed mycelial pellets in submerged cultures, which severely restricts its industrial application potential by limiting mass transfer efficiency. To address this challenge, CRISPR/Cas9 mediated genome editing coupled with fermentation optimization enhanced microbial protein production in A. niger. Endogenous α-1,3-glucan synthase genes (agsA, agsB) and galactosaminogalactan (GAG) synthase genes (sph3, uge3) were disrupted using CRISPR/Cas9, achieving complete dispersion of filamentous pellets in liquid media. This morphological engineering strategy resulted in a 77.52 % increase in biomass and 39.98 % enhancement in mycelial protein content compared to the wild-type strain (A. niger Li2). Transcriptomic analysis revealed that the engineered strain (A. niger AnΔABSU) exhibited upregulated transporter proteins (ABC transporters, MFS transporters, sugar transporters), accelerating nutrient uptake and energy metabolism; altered cell wall integrity pathways, including activation of the MAPK signaling cascade and increased sensitivity to cell wall stressors; enhanced amino acid biosynthesis, driven by upregulated gene expression in key metabolic pathways. Furthermore, response surface methodology (RSM) with Box-Behnken design optimized the fermentation medium, yielding 16.67 g/L biomass and 45.91 % protein content, representing 115.37 % and 67.01 % improvements over the unoptimized wild-type control. This study establishes a novel paradigm for constructing high-efficiency microbial protein cell factories via integrated morphological-engineering and fermentation optimization.

Biological and biochemical studies on cell surface functions in microorganisms used in brewing and fermentation industry

When brewing microorganisms, which include bacteria and fungi, act on solid cereal substrates, the microbial cell surface interacts with the substrate. When microorganisms use sugars and amino acids released by hydrolysis of the substrate, this occurs on the cell surface. Throughout my career, I have focused on functional studies of cell surface molecules such as solute transporters, cell wall components, and bio-surfactants and applied the knowledge obtained to the development of fermentation technologies. In this review, I describe (i) catabolite control by sugar transporters and energy generation coupled with amino acid decarboxylation in lactic acid bacteria; (ii) recruitment of a polyesterase by the fungal bio-surfactant proteins to polyesters and subsequent promotion of polyester hydrolysis; and (iii) hyphal aggregation via cell wall α-1,3-glucan and galactosaminogalactan in aspergilli and the development of a novel liquid culture method with hyphal dispersed mutants lacking these two polysaccharides.

Exploiting Self-Immobilized Fungi for Biovalorization of Oil Palm Sap to Organic Acids Through Repeated-Batch Fermentation

This study focused on utilizing agricultural waste, oil palm sap (OPS) as a sole nutrient source for organic acid production by self-immobilized fungi. Among the fungi cultured in OPS, Rhizopus oryzae TISTR 3336 was selected as it could form compact and adequate-size pellets (3-5 mm) and gave the highest total acid production yield of 0.31 ± 0.02 g/g-sugar under pH control. The optimal conditions were as follows: inoculum size of 106 spores/mL and shaking speed of 120 rpm. Using concentrated OPS gave higher final concentration of organic acids but reduced the production yield. The repeated-batch fermentation of OPS by self-immobilized fungi was successfully carried out for four cycles. The optimal initial sugar concentration was 40 g/L, giving the organic acid productions ranging of 19 to 35 g/L, with yields ranging of 0.47 to 0.87 g/g-sugar. This study has shown the efficient bioconversion of agricultural wastes into organic acids using self-immobilized fungi in the repeated-batch fermentation.

Regulation of citrinin biosynthesis in Monascus purpureus: Impacts on growth, morphology, and pigments production

Fungal hyphae self-assemble a variety of cellular macrostates, ranging from suspended mycelium to dense pellets, all inextricably linked to their productivity. In this study, using CRISPR/Cas technology, we constructed a ctnA knockout strain (ΔctnA) and an overexpression strain (A2) so as to investigate the effects of interfering with citrinin biosynthesis on the growth, morphology and pigmentation of M.purpureus. Results indicated that deletion of ctnA in M. purpureus RP2 led to increased mycelium length, delayed conidium formation, and a citrinin content of 22% of the wild-type strain. Conversely, ctnA overexpression in strain A2 resulted in delayed mycelial growth, normal conidium formation, and a citrinin content of 120% compared to the wild-type strain, with minimal effects on pigments content. Notably, the ΔctnA strain formed small, tightly structured pellets (mean diameter 1.2 ± 0.06 mm) and exhibited low citrinin content, promoting pigments production. Our findings suggest a complex interplay between citrinin biosynthesis and morphological development, providing insights for optimizing metabolite production in industrial applications.

Fungi: Pioneers of chemical creativity - Techniques and strategies to uncover fungal chemistry

Natural product discovery from fungi for drug development and description of novel chemistry has been a tremendous success. This success is expected to accelerate even further, owing to the advent of sophisticated technical advances of technical advances that recently led to the discovery of an unparalleled biodiversity in the fungal kingdom. This review aims to give an overview on i) important secondary metabolite-derived drugs or drug leads, ii) discuss the analytical and strategic framework of how natural product discovery and drug lead identification transformed from earlier days to the present, iii) how knowledge of fungal biology and biodiversity facilitates the discovery of new compounds, and iv) point out endeavors in understanding fungal secondary metabolite chemistry in order to systematically explore fungal genomes by utilizing synthetic biology. An outlook is given, underlining the necessity for a collaborative and cooperative scenario to harness the full potential of the fungal secondary metabolome.

Bioreactor contamination monitoring using off-gassed volatile organic compounds (VOCs)

Metabolically active cells emit volatile organic compounds (VOCs) that can be used in real time to non-invasively monitor the health of cell cultures. We utilized these naturally occurring VOCs in an adapted culture method to detect differences in culturing Chinese hamster ovary (CHO) cells with and without Staphylococcus epidermidis and Aspergillus fumigatus contaminations. The VOC emissions from the cell cultures were extracted and measured from the culture flask headspace using polydimethylsiloxane (PDMS)-coated Twisters, which were subjected to thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS) analysis. In our initial time points of 1 and 2 h, we detected VOC signatures that differentiated the cultures earlier than traditional plating techniques or visualization methods. Partial least squares-discriminant analysis (PLS-DA) models were built to differentiate the analytes from the CHO cells and S. epidermidis- and A. fumigatus-inoculated CHO cultures. A total of 41 compounds with a variable importance in projection (VIP) score greater than 1 was obtained across the models. Similarly, based on the PLS regression analyses to predict the cell concentration of S. epidermidis (R2 = 0.891) and A. fumigatus (R2 = 0.375), 15 and 20 relevant compounds were putatively identified, respectively; two known compounds overlapped between the two microbes. Some of the compounds were unidentified and future studies will determine the relationship between the VOCs and the metabolic changes in contaminated cultures.

Cutting-edge advances in strain and process engineering for boosting cellulase production in Trichoderma reesei

Low-cost production of cellulases is a key factor in advancing the commercialization of lignocellulosic biorefinery. Thus far, Trichoderma reesei is the leading cellulase producer for biorefinery applications. Over 70 years of research, considerable advancements have been made in comprehending the mechanisms underlying cellulases biosynthesis and secretion in T. reesei, as well as enzymatic cellulose hydrolysis. However, many unknowns still hinder the rational design of strains for robust cellulase production, with an optimized ratio of cellulolytic enzymes to reduce the required dosage for cellulose hydrolysis. Moreover, large-scale cellulase production relies on submerged fermentation, which suffers from several mass transfer limitations. As the mycelia grow, the fermentation broth rapidly develops non-Newtonian properties, necessitating energy-intensive mixing and aeration to facilitate oxygen transfer essential for strain growth. Herein, this paper critically reviews updated progress in these regards, highlights challenges, and outlines potential solutions.

Considerations for Domestication of Novel Strains of Filamentous Fungi

Fungi, especially filamentous fungi, are a relatively understudied, biotechnologically useful resource with incredible potential for commercial applications. These multicellular eukaryotic organisms have long been exploited for their natural production of useful commodity chemicals and proteins such as enzymes used in starch processing, detergents, food and feed production, pulping and paper making and biofuels production. The ability of filamentous fungi to use a wide range of feedstocks is another key advantage. As chassis organisms, filamentous fungi can express cellular machinery, and metabolic and signal transduction pathways from both prokaryotic and eukaryotic origins. Their genomes abound with novel genetic elements and metabolic processes that can be harnessed for biotechnology applications. Synthetic biology tools are becoming inexpensive, modular, and expansive while systems biology is beginning to provide the level of understanding required to design increasingly complex synthetic systems. This review covers the challenges of working in filamentous fungi and offers a perspective on the approaches needed to exploit fungi as microbial cell factories.

Cultivation of filamentous fungi in airlift bioreactors: advantages and disadvantages

Filamentous fungi or mycelia are a valuable bioresource to produce several biomolecules and enzymes, especially because of their biodegradation potential and for their key role of enablers of a circular bioeconomy. Filamentous fungi can be grown in submerged cultivation to maximise the volumetric productivity of the bioprocess, instead of using the more established and time-consuming solid-state cultivation. Multicellular mycelia are sensitive to shear stresses induced by mechanical agitation, and this aspect greatly affects their morphology in submerged cultivation (pelletisation) and the connected volumetric productivity. An efficient compromise is the growth of filamentous fungi in airlift bioreactors (ALR) where the volumetric oxygen transfer (KLa) is optimal, but the shear stress is reduced. In this review, we critically analysed the advantages and disadvantages of ALR-based cultivation of filamentous fungi, comparing these bioreactors also with stirred tank reactors and bubble column reactors; we focused on scientific literature that highlights findings for the cultivation of filamentous fungi for both the production of enzymes and the production of myco-biomass in ALR; we included studies for the control of the pelletisation of the fungal biomass in batch and semi-continuous cultivation, highlighting the interlinked hydrodynamics; finally, we included studies regarding the modifications of ALR in order to enhance filamentous fungi production. KEY POINTS: • ALR are efficient for batch and prolonged continuous cultivation of filamentous fungi. • ALR show both optimal gas hold-up and KLa with an airflow that has high superficial velocity and critical bubble diameter (1-6 mm). • Suspended mycelia aggregates (pellet) maintain a fluidised motion in ALR if their size/density can be controlled.

Rheology and Culture Reproducibility of Filamentous Microorganisms: Impact of Flow Behavior and Oxygen Transfer During Salt-Enhanced Cultivation of the Actinomycete Actinomadura namibiensis

Analyzing the relationship between cell morphology, rheological characteristics, and production dynamics of cultivations with filamentous microorganisms is a challenging task. The complex interdependencies and the commonly low reproducibility of heterogeneous cultivations hinder the bioprocess development of commercially relevant production systems. The present study aims to characterize process parameters in Actinomadura namibiensis shake flask cultures to gain insights into relationships between culture behavior and rheological characteristics during salt-enhanced labyrinthopeptin A1 production. Plate-plate (PP) and vane-cup rheometer measurements of viscous model fluids and culture broths are compared, revealing a more uniform distribution of broth when measured with the PP system. Additionally, rheological characteristics and culture performance of A. namibiensis cultures are evaluated using online data of the specific power input and the oxygen transfer rate. It is demonstrated that salt-enhancement labyrinthopeptin A1 production by the addition of 50 mM (NH4)2SO4 increases the apparent viscosity of the A. namibiensis culture by four-fold and significantly reduces the reproducibility of the culture resulting in a 46 h difference in lag-phase duration. This approach demonstrates that the culture behavior of complex filamentous cell morphologies is challenging to decipher, but online monitoring of rheology and oxygen transfer can provide valuable insights into the cultivation dynamics of filamentous microbial cultures.

Oxygen Consumption in Filamentous Pellets of Aspergillus niger: Microelectrode Measurements and Modeling

Filamentous fungi cultivated as biopellets are well established in biotechnology industries. A distinctive feature of filamentous fungi is that hyphal growth and fungal morphology affect product titers and require tailored process conditions. Within the pellet, mass transfer, substrate consumption, and biomass formation are intricately linked to the local hyphal fraction and pellet size. This study combined oxygen concentration measurements with microelectrode profiling and three-dimensional X-ray microtomography measurements of the same fungal pellets for the first time. This allowed for the precise correlation of micromorphological information with local oxygen concentrations of two Aspergillus niger strains (hyperbranching and regular branching). The generated results showed that the identified oxygen-penetrated outer pellet regions exhibited a depth of 90-290 µm, strain-specific, with the active part percentage in the pellet ranging from 18% to 69%, without any difference between strains. Using a 1D continuum diffusion consumption model, the oxygen concentration in the pellets was computed depending on the local hyphal fraction. The best simulation results were achieved by individually estimating the oxygen-related biomass yield coefficient of the consumption term within each examined pellet, with an average estimated value of 1.95 (± 0.72) kg biomass per kg oxygen. The study lays the foundation for understanding oxygen supply in fungal pellets and optimizing processes and pellet morphologies accordingly.

Culture media design and scaling-up of submerged fermentation for the nematophagous fungus Duddingtonia flagrans

Biological control, which utilizes nematophagous fungi to reduce gastrointestinal nematode populations, may effectively diminish the need for chemical anthelmintic treatments. However, the limited knowledge surrounding the mass production of chlamydospores hinders the widespread use of biological products as alternatives to traditional anthelmintics. This study aimed to evaluate the development of liquid culture media for the large-scale production of the nematophagous fungi Duddingtonia flagrans using a systematic procedure, progressing from microplates to bioreactor. The liquid culture media were successfully validated in a 13 L bioreactor, achieving a yield of 2.18x107 chlam/g per day, which is comparable to the standard process of solid-state fermentation (SSF). Moreover, the nematode predatory ability remained unaffected by the changes in scales and exhibited a superior efficacy of over 90%. Consequently, this study demonstrates that the submerged fermentation approach serves as a viable alternative for the mass production of nematophagous fungi like D. flagrans.

Unveiling the potential of Aspergillus terreus SJP02 for zinc remediation and its driving mechanism

In present study, 15 morphologically different fungi isolated from rhizopheric soils of an industrial area were screened for their Zn2+ removal efficiency from aqueous solution. Isolate depicting highest potential was molecularly identified as Aspergillus terreus SJP02. Effect of various process parameters viz. biosorbent dose, contact time, temperature, agitation rate, pH and initial Zn2+ concentration on the fungal sorption capacity were studied. The biosorbent exhibited maximum Zn2+ sorption capacity of 10.7 ± 0.2 mg g- 1 in 60 min. Desorption studies showed 71.46% Zn2+ recovery rate in 120 min with 0.01 N HNO3, indicating efficient metal recovery for reuse and subsequent reutilization of spent mycosorbents. Acid digestion study suggested adsorption being the primary mechanism accounting for 87% Zn2+removal. It was further confirmed by the FE-SEM and EDX analysis. FTIR analysis suggested involvement of amino, hydroxyl, carbonyl, and phosphate functional groups of fungal cell wall in adsorption. The experimental results were in accordance with the tested isotherm and kinetic models, and suggested the role of physical adsorption for Zn2+ removal. Noteworthy, the present study showed better sorption capacity in considerably shorter equilibration time compared to previous reports and advocate potential utilization of A. terreus SJP02 for bioremediation of Zn2+ contaminated wastewater at industrial scale.

Biocomposites Based on Mould Biomass and Waste Fibres for the Production of Agrotextiles: Technology Development, Material Characterization, and Agricultural Application

This study explores the potential use of mould biomass and waste fibres for the production of agrotextiles. First, 20 mould strains were screened for efficient mycelium growth, with optimized conditions of temperature, sources of carbon and nitrogen in the medium, and type of culture (submerged or surface). A method was developed for creating a biocomposite based on the mould mycelium, reinforced with commercial bleached softwood kraft (BSK) pulp and fibre additives (cotton, hemp). The best properties, including mechanical, water permeability, and air permeability, were shown by the biocomposites containing 10-20% Cladosporium cladosporioides mycelium grown in surface or submerged cultures, milled with BSK pulp, cotton, and hemp (10-20%). The mould mycelium was refined with cellulosic fibrous material, formed, pressed, and dried, resulting in a biomaterial with good mechanical parameters, low water permeability, and high air permeability. The biocomposite was fully biodegradable in soil after 10 days in field conditions. The use of the biocomposite as a crop cover shortened the germination time and increased the percentage of germinated onion, but had no effect on parsley seeds. This study shows the potential of using mould mycelium for the production of biomaterial with good properties for applications in horticulture.

The mechanism of short hypha formation and high protein production system mediated by cell wall integrity signaling pathway in Aspergillus niger

Aspergillus niger is a cell factory widely used in industries to produce proteases, organic acids, drugs, and other substances. The hyphal morphology of A. niger is a complex differentiated elongated tubular structure, which limits its basic research and application. In this study, the mpkA, bck1, steC, and Tpk2 genes were successfully deleted using a quick way to knock out genes based on the RNP (Ribonucleoprotein) complex. The study showed that the knockout of mpkA and bck1 kinase gene strains resulted in smaller, denser colonies, short rod-shaped hypha, and a significant increase in glucoamylase secretion. The mechanism of short hypha formation and high protein production for A. niger is the cell wall integrity signaling (CWIS) pathway. The CWIS pathway passed through the bck1-mkkA-mpkA tertiary kinase to deliver phosphorylation signals to the rlmA transcription factor, which regulated the expression of the cell wall synthesis gene agsA, thus regulating hyphal morphology. The mpkA kinase regulated the expression of the transcription factor amyR, which affected the expression of the genes glaA and amyA, thus enhancing the expression of proteins in A. niger. This study provides a strategy for the regulation of hyphal morphology and promotes the application of A. niger in industrial production.

Resource recovery and treatment of wastewaters using filamentous fungi

Industrial wastewater, often characterized by its proximity to neutral pH, presents a promising opportunity for fungal utilization despite the prevalent preference of fungi for acidic conditions. This review addresses this discrepancy, highlighting the potential of certain industrial wastewaters, particularly those with low pH levels, for fungal biorefinery. Additionally, the economic implications of biomass recovery and compound separation, factors that require explicit were emphasized. Through an in-depth analysis of various industrial sectors, including food processing, textiles, pharmaceuticals, and paper-pulp, this study explores how filamentous fungi can effectively harness the nutrient-rich content of wastewaters to produce valuable resources. The pivotal role of ligninolytic enzymes synthesized by fungi in wastewater purification is examined, as well as their ability to absorb metal contaminants. Furthermore, the diverse benefits of fungal biorefinery are underscored, including the production of protein-rich single-cell protein, biolipids, enzymes, and organic acids, which not only enhance environmental sustainability but also foster economic growth. Finally, the challenges associated with scaling up fungal biorefinery processes for wastewater treatment are critically evaluated, providing valuable insights for future research and industrial implementation. This comprehensive analysis aims to elucidate the potential of fungal biorefinery in addressing industrial wastewater challenges while promoting sustainable resource utilization.

Initial pH determines the morphological characteristics and secondary metabolite production in Aspergillus terreus and Streptomyces rimosus cocultures

The influence of the initial pH on the morphology and secondary metabolite production in cocultures and axenic cultures of Aspergillus terreus and Streptomyces rimosus was investigated. The detected secondary metabolites (6 of bacterial and 4 of fungal origin) were not found in the cultures initiated at pH values less than or equal to 4.0. The highest mean levels of oxytetracycline were recorded in S. rimosus axenic culture at pH 5.0. Initiating the axenic culture at pH 5.9 led to visibly lower product levels, yet the presence of A. terreus reduced the negative effect of non-optimal pH and led to higher oxytetracycline titer than in the corresponding S. rimosus axenic culture. The cocultivation initiated at pH 5.0 or 5.9 triggered the formation of oxidized rimocidin. The products of A. terreus were absent in the cocultures. At pH 4.0, the striking morphological differences between the coculture and the axenic cultures were recorded.

Adding-value to Ganoderma lingzhi by producing enzymes and antioxidant compounds under submerged fermentation using different culture media

Ganoderma lingzhi is widely reported for its medicinal properties, presenting several bioactive substances with potential pharmaceutical and industrial application. This study aimed to evaluate the production of mycelial biomass, extracellular enzymes and antioxidant compounds by G. lingzhi under submerged fermentation. G. lingzhi was cultured in Polysaccharide (POL) and Melin-Norkrans (MNM) media for 7 days. The cellulases, xylanases, pectinases, laccases, and proteases activities were quantified in the culture broth, while the antioxidant potential was evaluated for the mycelial biomass. G. lingzhi showed higher biomass production in MNM. However, it exhibited similar microstructural characteristics in both culture media. In the POL there was greater activity of CMCase (0.229 U/mL), xylanase (0.780 U/mL), pectinase (0.447 U/mL) and proteases (16.13 U/mL). FPase did not differ (0.01 U/mL), and laccase was detected only in MNM (0.122 U/mL). The biomass water extract from MNM showed high levels of phenolic compounds (951.97 mg AGE/100 g). DPPH• inhibition (90.55%) and reducing power (0.456) were higher in MNM medium, while ABTS•+ inhibition (99.95%) and chelating ability (54.86%) were higher in POL. Thus, the MNM medium was more favorable to the production of mycelial biomass and phenolic compounds, while the POL medium favored the synthesis and excretion of hydrolytic enzymes.

3D imaging and analysis to unveil the impact of microparticles on the pellet morphology of filamentous fungi

Controlling the morphology of filamentous fungi is crucial to improve the performance of fungal bioprocesses. Microparticle-enhanced cultivation (MPEC) increases productivity, most likely by changing the fungal morphology. However, due to a lack of appropriate methods, the exact impact of the added microparticles on the structural development of fungal pellets is mostly unexplored. In this study synchrotron radiation-based microcomputed tomography and three-dimensional (3D) image analysis were applied to unveil the detailed 3D incorporation of glass microparticles in nondestructed pellets of Aspergillus niger from MPEC. The developed method enabled the 3D analysis based on 375 pellets from various MPEC experiments. The total and locally resolved volume fractions of glass microparticles and hyphae were quantified for the first time. At increasing microparticle concentrations in the culture medium, pellets with lower hyphal fraction were obtained. However, the total volume of incorporated glass microparticles within the pellets did not necessarily increase. Furthermore, larger microparticles were less effective than smaller ones in reducing pellet density. However, the total volume of incorporated glass was larger for large microparticles. In addition, analysis of MPEC pellets from different times of cultivation indicated that spore agglomeration is decisive for the development of MPEC pellets. The developed 3D morphometric analysis method and the presented results will promote the general understanding and further development of MPEC for industrial application.

Analysis of secondary metabolites and morphology in Streptomyces rimosus microparticle-enhanced cultivation (MPEC) at various initial organic nitrogen concentrations

The influence of talc microparticles on metabolism and morphology of S. rimosus at various initial organic nitrogen concentrations was investigated. The shake flask cultivations were conducted in the media with yeast extract (nitrogen source) concentration equal to 1 g YE L- 1 and 20 g YE L- 1. Two talc microparticle concentrations of 5 g TALC L- 1 and 10 g TALC L- 1 were tested in microparticle-enhanced cultivation (MPEC) runs. A high nitrogen concentration of 20 g YE L- 1 promoted the development of small agglomerates (pellets) of projected area lower than 105 µm2 and dispersed pseudohyphae. A low nitrogen concentration of 1 g YE L- 1 led to the limitation of S. rimosus growth and, in consequence, the development of the smaller number of large pseudohyphal agglomerates (pellets) of projected area higher than 105 µm2 compared to the culture containing a high amount of nitrogen source. In both cases talc microparticles were embedded into pellets and caused the decrease in their sizes. The lower amount of talc (5 g TALC L- 1) usually caused the weaker effect on S. rimosus morphology and metabolite production than the higher one. This correlation between the microparticles effect on morphology and metabolism of S. rimosus was especially noticeable in the biosynthesis of oxytetracycline, 2-acetyl-2-dicarboxamide oxytetracycline (ADOTC) and spinoxazine A. Compared to the control run, in MPEC their levels increased 4-fold, 5-fold and 1.6-fold respectively. The addition of talc also improved the production of 2-methylthio-cis-zeatin, lorneic acid J and milbemycin A3.

Exploring the Potential of Aspergillus oryzae for Sustainable Mycoprotein Production Using Okara and Soy Whey as Cost-Effective Substrates

Mycoprotein is an alternative protein produced through fungal fermentation. However, it typically relies on refined glucose syrup derived from starch, which can be costly and unsustainable. This study investigates the potential of soybean processing by-products (okara and soy whey) as alternative substrates for producing mycoprotein using Aspergillus oryzae. A. oryzae was cultured for 7 days at 30 °C in diluted okara (1:50) and soy whey (1:1) with or without agitation (100 rpm). Soy whey produced higher biomass yields (369.2-408.8 mg dry biomass/g dry substrate), but had a lower biomass concentration (0.783-0.867 g dry weight/L). Conversely, okara produced a higher biomass concentration (2.02 g dry weight/L) with a yield of 114.7 mg dry biomass/g dry substrate. However, biomass formation in okara was only observed in static conditions, as agitation caused biomass to entangle with soy pulp, hampering its production. Additionally, okara tended to release protein into the media, while soy whey accumulated protein within the biomass, reaching up to 53% w/w protein content. The results of this study provide a promising approach to addressing both soybean processing waste reduction and food security concerns.

Morphological responses of filamentous fungi to stressful environmental conditions

The filamentous growth mode of fungi, with its modular design, facilitates fungal adaptation to stresses they encounter in diverse terrestrial and anthropogenic environments. Surface growth conditions elicit diverse morphological responses in filamentous fungi, particularly demonstrating the remarkable adaptability of mycelial systems to metal- and mineral-rich environments. These responses are coupled with fungal biogeochemical activity and can ameliorate hostile conditions. A tessellated agar tile system, mimicking natural environmental heterogeneity, revealed negative chemotropism to toxic metals, distinct extreme growth strategies, such as phalanx and guerrilla movements and transitions between them, and the formation of aggregated re-allocation structures (strands, cords, synnemata). Other systems showed intrahyphal growth, intense biomineralization, and extracellular hair-like structures. Studies on submerged mycelial growth, using the thermophilic fungus Thielavia terrestris as an example, provided mechanistic insights into the morphogenesis of two extreme forms of fungal submerged culture-pelleted and dispersed growth. It was found that the development of fungal pellets was related to fungal adaptation to unfavorable stressful conditions. The two key elements affecting morphogenesis leading to the formation of either pelleted or dispersed growth were found to be (1) a lag phase (or conidia swelling stage) as a specific period of fungal morphogenesis when a certain growth form is programmed in response to morphogenic stressors, and (2) cAMP as a secondary messenger of cell signaling, defining the implementation of the particular growth strategy. These findings can contribute to knowledge of fungal-based biotechnologies, providing a means for controllable industrial processes at both morphological and physiological levels.

Optimization of biotransformation processes of Camarosporium laburnicola to improve production yields of potent telomerase activators

BACKGROUND

Telomerase activators are promising agents for the healthy aging process and the treatment/prevention of short telomere-related and age-related diseases. The discovery of new telomerase activators and later optimizing their activities through chemical and biological transformations are crucial for the pharmaceutical sector. In our previous studies, several potent telomerase activators were discovered via fungal biotransformation, which in turn necessitated optimization of their production. It is practical to improve the production processes by implementing the design of experiment (DoE) strategy, leading to increased yield and productivity. In this study, we focused on optimizing biotransformation conditions utilizing Camarosporium laburnicola, a recently discovered filamentous fungus, to afford the target telomerase activators (E-CG-01, E-AG-01, and E-AG-02).

RESULTS

DoE approaches were used to optimize the microbial biotransformation processes of C. laburnicola. Nine parameters were screened by Plackett-Burman Design, and three significant parameters (biotransformation time, temperature, shaking speed) were optimized using Central Composite Design. After conducting validation experiments, we were able to further enhance the production yield of target metabolites through scale-up studies in shake flasks (55.3-fold for E-AG-01, 13-fold for E-AG-02, and 1.96-fold for E-CG-01).

CONCLUSION

Following a process optimization study using C. laburnicola, a significant increase was achieved in the production yields. Thus, the present study demonstrates a promising methodology to increase the production yield of potent telomerase activators. Furthermore, C. laburnicola is identified as a potential biocatalyst for further industrial utilization.

Morphological Engineering of Filamentous Fungi: Research Progress and Perspectives

Filamentous fungi are important cell factories for the production of high-value enzymes and chemicals for the food, chemical, and pharmaceutical industries. Under submerged fermentation, filamentous fungi exhibit diverse fungal morphologies that are influenced by environmental factors, which in turn affect the rheological properties and mass transfer of the fermentation system, and ultimately the synthesis of products. In this review, we first summarize the mechanisms of mycelial morphogenesis and then provide an overview of current developments in methods and strategies for morphological regulation, including physicochemical and metabolic engineering approaches. We also anticipate that rapid developments in synthetic biology and genetic manipulation tools will accelerate morphological engineering in the future.

Airlift bioreactor-based strategies for prolonged semi-continuous cultivation of edible Agaricomycetes

Submerged cultivation of edible filamentous fungi (Agaricomycetes) in bioreactors enables maximum mass transfer of nutrients and has the potential to increase the volumetric productivity of fungal biomass compared to solid state cultivation. These aspects are paramount if one wants to increase the range of bioactives (e.g. glucans) in convenient time frames. In this study, Trametes versicolor (M9911) outperformed four other Agaricomycetes tested strains (during batch cultivations in an airlift bioreactor). This strain was therefore further tested in semi-continuous cultivation. Continuous and semi-continuous cultivations (driven by the dilution rate, D) are the preferred bioprocess strategies for biomass production. We examined the semi-continuous cultivation of T. versicolor at dilution rates between 0.02 and 0.1 h-1. A maximum volumetric productivity of 0.87 g/L/h was obtained with a D of 0.1 h-1 but with a lower total biomass production (cell dry weight, CDW 8.7 g/L) than the one obtained at lower dilution rates (12.3 g/L at D of 0.04 and vs 13.4 g/L, at a D of 0.02 h-1). However, growth at a D of 0.1 h-1 resulted in a very short fermentation (18 h) which terminated due to washout (the specific D exceeded the maximum growth rate of the fungal biomass). At a D of 0.04 h-1, a CDW of 12.3 g/L was achieved without compromising the total residence time (184 h) of the fermentation. While the D of 0.04 h-1 and 0.07 h-1 achieved comparable volumetric productivities (0.5 g/L/h), the total duration of the fermentation at D of 0.07 h-1 was only 85 h. The highest glucan content of cells (27.8 as percentage of CDW) was obtained at a D of 0.07 h-1, while the lowest glucan content was observed in T. versicolor cells grown at a D of 0.02 h-1. KEY POINTS: • The highest reported volumetric productivity for fungal biomass was 0.87 g/L/h. • Semi-continuous fermentation at D of 0.02 h-1 resulted in 13.4 g/L of fungal biomass. • Semi-continuous fermentation at D of 0.07 h-1 resulted in fungal biomass with 28% of total glucans.

Removal of pharmaceutical compounds and toxicology study in wastewater using Malaysian fungal Ganoderma lucidum

Elevated usage of pharmaceutical products leads to the accumulation of emerging contaminants in sewage. In the current work, Ganoderma lucidum (GL) was used to remove pharmaceutical compounds (PCs), proposed as a tertiary method in sewage treatment plants (STPs). The PCs consisted of a group of painkillers (ketoprofen, diclofenac, and dexamethasone), psychiatrists (carbamazepine, venlafaxine, and citalopram), beta-blockers (atenolol, metoprolol, and propranolol), and anti-hypertensives (losartan and valsartan). The performance of 800 mL of synthetic water, effluent STP, and hospital wastewater (HWW) was evaluated. Parameters, including treatment time, inoculum volume, and mechanical agitation speed, have been tested. The toxicity of the GL after treatment is being studied based on exposure levels to zebrafish embryos (ZFET) and the morphology of the GL has been observed via Field Emission Scanning Electron Microscopy (FESEM). The findings conclude that GL can reduce PCs from <10% to >90%. Diclofenac and valsartan are the highest (>90%) in the synthetic model, while citalopram and propranolol (>80%) are in the real wastewater. GL effectively removed pollutants in 48 h, 1% of the inoculum volume, and 50 rpm. The ZFET showed GL is non-toxic (LC50 is 209.95 mg/mL). In the morphology observation, pellets GL do not show major differences after treatment, showing potential to be used for a longer treatment time and to be re-useable in the system. GL offers advantages to removing PCs in water due to their non-specific extracellular enzymes that allow for the biodegradation of PCs and indicates a good potential in real-world applications as a favourable alternative treatment.

Edible mycelium as proliferation and differentiation support for anchorage-dependent animal cells in cultivated meat production

Cultivated meat production requires bioprocess optimization to achieve cell densities that are multiple orders of magnitude higher compared to conventional cell culture techniques. These processes must maximize resource efficiency and cost-effectiveness by attaining high cell growth productivity per unit of medium. Microcarriers, or carriers, are compatible with large-scale bioreactor use, and offer a large surface-area-to-volume ratio for the adhesion and proliferation of anchorage-dependent animal cells. An ongoing challenge persists in the efficient retrieval of cells from the carriers, with conflicting reports on the effectiveness of trypsinization and the need for additional optimization measures such as carrier sieving. To surmount this issue, edible carriers have been proposed, offering the advantage of integration into the final food product while providing opportunities for texture, flavor, and nutritional incorporation. Recently, a proof of concept (POC) utilizing inactivated mycelium biomass derived from edible filamentous fungus demonstrated its potential as a support structure for myoblasts. However, this POC relied on a model mammalian cell line combination with a single mycelium species, limiting realistic applicability to cultivated meat production. This study aims to advance the POC. We found that the species of fungi composing the carriers impacts C2C12 myoblast cell attachment-with carriers derived from Aspergillus oryzae promoting the best proliferation. C2C12 myoblasts effectively differentiated on mycelium carriers when induced in myogenic differentiation media. Mycelium carriers also supported proliferation and differentiation of bovine satellite cells. These findings demonstrate the potential of edible mycelium carrier technology to be readily adapted in product development within the cultivated meat industry.

Emergence of per- and poly-fluoroalkyl substances (PFAS) and advances in the remediation strategies

A group of fluorinated organic molecules known as per- and poly-fluoroalkyl substances (PFAS) have been commonly produced and circulated in the environment. PFAS, owing to multiple strong CF bonds, exhibit exceptional stability and possess a high level of resistance against biological or chemical degradation. Recently, PFAS have been identified to cause numerous hazardous effects on the biotic ecosystem. As a result, extensive efforts have been made in recent years to develop effective methods to remove PFAS. Adsorption, filtration, heat treatment, chemical oxidation/reduction, and soil washing are a few of the physicochemical techniques that have shown their ability to remove PFAS from contaminated matrixes. However these methods also carry significant drawbacks, including the fact that they are expensive, energy-intensive, unsuitable for in-situ treatment, and requirement to be carried under dormant conditions. The metabolic products released upon PFAS degradation are largely unknown, despite the fact that thermal disintegration methods are widely used. In contrast to physical and chemical methods, biological degradation of PFAS has been regarded as efficient method. However, PFAS are difficult to instantly and completely metabolize through biological methods due to the limitations of biocatalytic mechanisms. Nevertheless, cost, easy-to-operate and environmentally safe are some of the advantages over its counterpart. The present review comprehensively discusses the occurrence of PFAS, the state-of-the science of remediation technologies and approaches applied, and the remediation challenges. The article also focuses on the future research directions toward the development of effective methods for PFAS-contaminated site in-situ treatment.

Real-time monitoring of mycelial growth in liquid culture using hyphal dispersion mutant of Aspergillus fumigatus

Hyphal pellet formation by Aspergillus species in liquid cultures is one of the main obstacles to high-throughput anti-Aspergillus reagent screening. We previously constructed a hyphal dispersion mutant of Aspergillus fumigatus by disrupting the genes encoding the primary cell wall α-1,3-glucan synthase Ags1 and putative galactosaminogalactan synthase Gtb3 (Δags1Δgtb3). Mycelial growth of the mutant in liquid cultures monitored by optical density was reproducible, and the dose-response of hyphal growth to antifungal agents has been quantified by optical density. However, Δags1Δgtb3 still forms hyphal pellets in some rich growth media. Here, we constructed a disruptant lacking all three α-1,3-glucan synthases and galactosaminogalactan synthase (Δags1Δags2Δags3Δgtb3), and confirmed that its hyphae were dispersed in all the media tested. We established an automatic method to monitor hyphal growth of the mutant in a 24-well plate shaken with a real-time plate reader. Dose-dependent growth suppression and unique growth responses to antifungal agents (voriconazole, amphotericin B, and micafungin) were clearly observed. A 96-well plate was also found to be useful for the evaluation of mycelial growth by optical density. Our method is potentially applicable to high-throughput screening for anti-Aspergillus agents.

The serine/threonine protein kinase MpSTE1 directly governs hyphal branching in Monascus spp

Monascus spp. are commercially important fungi due to their ability to produce beneficial secondary metabolites such as the cholesterol-lowering agent lovastatin and natural food colorants azaphilone pigments. Although hyphal branching intensively influenced the production of these secondary metabolites, the pivotal regulators of hyphal development in Monascus spp. remain unclear. To identify these important regulators, we developed an artificial intelligence (AI)-assisted image analysis tool for quantification of hyphae-branching and constructed a random T-DNA insertion library. High-throughput screening revealed that a STE kinase, MpSTE1, was considered as a key regulator of hyphal branching based on the hyphal phenotype. To further validate the role of MpSTE1, we generated an mpSTE1 gene knockout mutant, a complemented mutant, and an overexpression mutant (OE::mpSTE1). Microscopic observations revealed that overexpression of mpSTE1 led to a 63% increase in branch number while deletion of mpSTE1 reduced the hyphal branching by 68% compared to the wild-type strain. In flask cultures, the strain OE::mpSTE1 showed accelerated growth and glucose consumption. More importantly, the strain OE::mpSTE1 produced 9.2 mg/L lovastatin and 17.0 mg/L azaphilone pigments, respectively, 47.0% and 30.1% higher than those of the wild-type strain. Phosphoproteomic analysis revealed that MpSTE1 directly phosphorylated 7 downstream signal proteins involved in cell division, cytoskeletal organization, and signal transduction. To our best knowledge, MpSTE1 is reported as the first characterized regulator for tightly regulating the hyphal branching in Monascus spp. These findings significantly expanded current understanding of the signaling pathway governing the hyphal branching and development in Monascus spp. Furthermore, MpSTE1 and its analogs were demonstrated as promising targets for improving production of valuable secondary metabolites. KEY POINTS: • MpSTE1 is the first characterized regulator for tightly regulating hyphal branching • Overexpression of mpSTE1 significantly improves secondary metabolite production • A high-throughput image analysis tool was developed for counting hyphal branching.

Exploring Culture Media Diversity to Produce Fungal Secondary Metabolites and Cyborg Cells

Fungi are microorganisms of significant biotechnological importance due to their ability to provide food and produce several value-added secondary metabolites and enzymes. Its products move billions of dollars in the pharmaceutical, cosmetics, and additives sectors. These microorganisms also play a notable role in bionanotechnology, leading to the production of hybrid biological-inorganic materials (such as cyborg cells) and the use of their enzyme complex in the biosynthesis of nanoparticles. In this sense, optimizing the fungal growth process is necessary, with selecting the cultivation medium as one of the essential factors for the microorganism to reach its maximum metabolic expression. The culture medium's composition can also impact the nanomaterial's stability and prevent the incorporation of nanoparticles into fungal cells. Therefore, our main objectives are the following: (1) compile and discuss the most commonly employed culture media for the production of fungal secondary metabolites and the formation of cyborg cells, accompanied by preparation methods; (2) provide a six-step guide to investigating the fungal metabolomic profile and (3) discuss the main procedures of microbial cultivation to produce fungal cyborg cells.

Application of sequential design for enhanced L-asparaginase synthesis from Ganoderma australe GPC191

With an increasing demand for L-asparaginase in pharmaceutical and food sectors for its cytostatic and acrylamide-reducing qualities, there's a need to discover novel, highly productive enzyme sources with improved pharmacokinetic profiles. Keeping this in mind, the present study aimed at maximizing the potential of Ganoderma australe GPC191 to produce L-asparaginase by fermentation medium optimization using statistical validation. Of the 11 physicochemical parameters evaluated under submerged fermentation conditions through one-factor-at-a-time approach and Plackett-Burman design, only four parameters (inoculum load, L-asparagine, soybean meal, and initial pH) influenced L-asparaginase production, significantly (p < 0.001). The optimal levels and interaction effects of these on the overall production were further evaluated by the central composite rotatable design of response surface methodology. Post-optimization, 27.34 U/mL was predicted as the maximum activity at pH 7 with 5n inoculum load and 15 g/L each of L-asparagine and soybean meal. Experimental validation yielded an activity of 28.52 U/mL, indicating an overall 18.17-fold increase from the unoptimized stage. To our knowledge, this is the first report signifying the L-asparaginase production aptitude of G. australe with sequential statistical validation using agricultural waste, which can serve as a model to enhance its yields, offering a sustainable and cost-effective solution for industrial application.

Fermentative processes for the upcycling of xylose to xylitol by immobilized cells of Pichia fermentans WC1507

Xylitol is a pentose-polyol widely applied in the food and pharmaceutical industry. It can be produced from lignocellulosic biomass, valorizing second-generation feedstocks. Biotechnological production of xylitol requires scalable solutions suitable for industrial scale processes. Immobilized-cells systems offer numerous advantages. Although fungal pellet carriers have gained attention, their application in xylitol production remains unexplored. In this study, the yeast strain P. fermentans WC 1507 was employed for xylitol production. The optimal conditions were observed with free-cell cultures at pH above 3.5, low oxygenation, and medium containing (NH4)2SO4 and yeast extract as nitrogen sources (xylitol titer 79.4 g/L, YP/S 66.3%, and volumetric productivity 1.3 g/L/h). Yeast cells were immobilized using inactive Aspergillus oryzae pellet mycelial carrier (MC) and alginate beads (AB) and were tested in flasks over three consecutive production runs. Additionally, the effect of a 0.2% w/v alginate layer, coating the outer surface of the carriers (cMC and cAB, respectively), was examined. While YP/S values observed with both immobilized and free cells were similar, the immobilized cells exhibited lower final xylitol titer and volumetric productivity, likely due to mass transfer limitations. AB and cAB outperformed MC and cMC. The uncoated AB carriers were tested in a laboratory-scale airlift bioreactor, which demonstrated a progressive increase in xylitol production in a repeated batch process: in the third run, a xylitol titer of 63.0 g/L, YP/S of 61.5%, and volumetric productivity of 0.52 g/L/h were achieved. This study confirmed P. fermentans WC 1507 as a promising strain for xylitol production in both free- and entrapped-cells systems. Considering the performance of the wild strain, a metabolic engineering intervention aiming at further improving the efficiency of xylitol production could be justified. MC and AB proved to be viable supports for cell immobilization, but additional process development is necessary to identify the optimal bioreactor configuration and fermentation conditions.

Comparative exploration of biological treatment of hydrothermal liquefaction wastewater from sewage sludge: Effects of culture, fermentation conditions, and ammonia stripping

Hydrothermal liquefaction wastewater from sewage sludge (sludge HTLWW) is an emerging waste stream that requires treatment before being discharged into the environment. Biological treatment of sludge HTLWW is an attractive option due to the low cost and operational flexibility. In this study, we investigated and compared the performance of three bacterial strains and four fungal strains for biodegradation of sludge HTLWW. Our screening experiments established pH and mineral supplementation (iron, magnesium, calcium, and phosphorus) conditions that greatly improved COD removal and chemical compound degradation by the microbes. An ammonia stripping pretreatment improved COD removal efficiency of Rhodococci jostii RHA1 by 44%. All tested bacterial strains can tolerate 10× dilution of HTLWW and remove 35-44% of COD in 2-15 days, while all tested fungal strains were able to tolerate 20× dilution and were better at degrading phenolic compounds than bacteria. HTLWW treatment with biomass pellets of fungus Aspergillus niger NRRL 2001 achieved the best COD removal efficiency of 47% in 12 days without the need of nutrient supplementation. Comparisons on chemical compound degradation by the tested microbes suggested that organic acids in HTLWW were highly degradable, followed by phenolic compounds. N-heterocyclic compounds were resistant to biodegradation and were removed by 38%. This study demonstrated pure culture biological treatment of sludge HTLWW with diverse types of microorganisms, which would guide the culture development and bioprocess parameter optimization for treating HTLWW of different compositions.

[Aspergillus Cell Surface Structural Analysis and Its Applications to Industrial and Medical Use]

The hyphal surface of cells of filamentous fungi is covered with cell wall, which is mainly composed of polysaccharides. Since the cell wall is the first structure to come in contact with the infection host, the environment, and the fungus itself, the elucidation of the cell wall structure and biogenesis is essential for understanding fungal ecology. Among filamentous fungi, the genus Aspergillus is an important group in the industrial, food, and medical fields. It is known that Aspergillus species form hyphal pellets in shake liquid culture. The authors previously found the role of α-1,3-glucan in hyphal aggregation in Aspergillus species. In addition, extracellular polysaccharide galactosaminogalactan contributed to hyphal aggregation as well, and dual disruption of biosynthesis genes of α-1,3-glucan and galactosaminogalactan resulted in complete hyphal dispersion in shake liquid culture. The characteristic of mycelia to form pellets under liquid culture conditions was the main reason why the growth measurement methods used for unicellular organisms could not be applied. We reported that hyphal growth of the dual disruption mutant could be measured by optical density. A real-time plate reader could be used to determine the growth curve of the mycelial growth of the dual disruption mutant. This measurement approach not only provides basic microbiological insights in filamentous fungi, but also has the potential to be applied to high-throughput screening of anti-Aspergillus drugs.

Agri-residues and agro-industrial waste substrates bioconversion by fungal cultures to biocatalyst lipase for green chemistry: A review

Huge amounts of agri-residues generated from food crops and processing are discarded in landfills, causing environmental problems. There is an urgent need to manage them with a green technological approach. Agri-residues are rich in nutrients such as proteins, lipids, sugars, minerals etc., and provide an opportunity for bioconversion into value-added products. Considering the importance of lipase as a biocatalyst for various industrial applications and its growing need for economic production, a detailed review of bioconversion of agri-residues and agro-industrial substrate for the production of lipase from fungal species from a technological perspective has been reported for the first time. Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) flow diagram was used for the identification and selection of articles from ScienceDirect, Google Scholar, and Scopus databases from 2010 to 2023 (July), and 108 peer-reviewed journal articles were included based on the scope of the study. The composition of agri-residues/agro-industrial wastes, fungal species, lipase production, industrial/green chemistry applications, and the economic impact of using agri-residues on lipase costs have been discussed. Bioconversion procedure, process developments, and technology gaps required to be addressed before commercialization have also been discussed. This process expects to decrease the environmental pollution from wastes, and low-cost lipase can help in the growth of the bioeconomy.

Enhancing Monascus Pellet Formation for Improved Secondary Metabolite Production

Filamentous fungi are well-known for their ability to form mycelial pellets during submerged cultures, a characteristic that has been extensively studied and applied. However, Monascus, a filamentous saprophytic fungus with a rich history of medicinal and culinary applications, has not been widely documented for pellet formation. This study aimed to investigate the factors influencing pellet formation in Monascus and their impact on citrinin production, a key secondary metabolite. Through systematic exploration, we identified pH and inoculum size as critical factors governing pellet formation. Monascus exhibited optimal pellet growth within the acidic pH range from 5 to 6, resulting in smaller, more homogeneous pellets with lower citrinin content. Additionally, we found that inoculum size played a vital role, with lower spore concentrations favoring the formation of small, uniformly distributed pellets. The choice of carbon and nitrogen sources also influenced pellet stability, with glucose, peptone, and fishmeal supporting stable pellet formation. Notably, citrinin content was closely linked to pellet diameter, with larger pellets exhibiting higher citrinin levels. Our findings shed light on optimizing Monascus pellet formation for enhanced citrinin production and provide valuable insights into the cultivation of this fungus for various industrial applications. Further research is warranted to elucidate the molecular mechanisms underlying these observations.

Growth of fungi and yeasts in food production waste streams: a feasibility study

Food production produces nutrient-rich waste streams which, depending on local legislation, are either sent to wastewater treatment plants or discharged into the environment. In addition to causing environmental harm in the second instance, valuable nutrients are lost. A more circular approach would be to reuse these waste streams. Fungi and yeasts are ideal candidates as they require lots of organic carbon (which is especially high in food production waste streams) for growth, with the potential for producing value-added biomass. Here, we tested the metabolic activity and possible growth of seven fungi and three yeasts in five different food production waste streams. Initial tests were done to find the most promising waste streams for growth and these were chosen for further study. All species were then cultured in these waste streams and oxygen uptake was measured to gauge metabolic activity which we used as a proxy for growth rate. Pelletization's effect on metabolic rates was tested on the most pellet-forming species, by adding agar to inhibit pellet formation. The most promising waste stream for yeast/fungal growth was cheese whey (Whey). Pellet inhibition (i.e., filamentous growth) resulted in increased metabolic activity of cells in the confectionary bakery waste stream with agar but decreased metabolic activity in Whey with agar. The best-growing species, Geotrichum candidum, has potential commercial value as a producer of enzymes, biochemicals and lipids and could provide added value while improving the circularity of water and nutrients in food production.

Synchrotron radiation-based microcomputed tomography for three-dimensional growth analysis of Aspergillus niger pellets

Filamentous fungi produce a wide range of relevant biotechnological compounds. The close relationship between fungal morphology and productivity has led to a variety of analytical methods to quantify their macromorphology. Nevertheless, only a µ-computed tomography (µ-CT) based method allows a detailed analysis of the 3D micromorphology of fungal pellets. However, the low sample throughput of a laboratory µ-CT limits the tracking of the micromorphological evolution of a statistically representative number of submerged cultivated fungal pellets over time. To meet this challenge, we applied synchrotron radiation-based X-ray microtomography at the Deutsches Elektronen-Synchrotron [German Electron Synchrotron Research Center], resulting in 19,940 3D analyzed individual fungal pellets that were obtained from 26 sampling points during a 48 h Aspergillus niger submerged batch cultivation. For each of the pellets, we were able to determine micromorphological properties such as number and density of spores, tips, branching points, and hyphae. The computed data allowed us to monitor the growth of submerged cultivated fungal pellets in highly resolved 3D for the first time. The generated morphological database from synchrotron measurements can be used to understand, describe, and model the growth of filamentous fungal cultivations.

Antifungal Activity of Ageritin, a Ribotoxin-like Protein from Cyclocybe aegerita Edible Mushroom, against Phytopathogenic Fungi

Ageritin from poplar mushrooms is a specific endonuclease that hydrolyzes a single phosphodiester bond located in the sarcin-ricin loop (SRL) of the large rRNA, thereby blocking protein synthesis. Considering the possible biotechnological use of this enzyme, here we report its antifungal activity against virulent fungi affecting crops of economic interest. Our results show that ageritin (200 µg/plug; ~13.5 nmole) inhibits the growth of Botrytis cinerea (57%), Colletotrichum truncatum (42%), and Alternaria alternata (57%), when tested on potato dextrose agar plates. At the same time, no effect was observed against Trichoderma harzianum (a fungus promoting beneficial effects in plants). To verify whether the antifungal action of ageritin against B. cinerea and T. harzianum was due to ribosome damage, we tested ageritin in vitro on partially isolated B. cinerea and T. harzianum ribosomes. Interestingly, ageritin was able to release the Endo's fragment from both tested fungal ribosomes. We therefore decided to test the antifungal effect of ageritin on B. cinerea and T. harzianum using a different growth condition (liquid medium). Differently from the result in solid medium, ageritin can inhibit both B. cinerea and T. harzianum fungal growth in liquid medium in a concentration-dependent manner up to 35.7% and 38.7%, respectively, at the highest concentration tested (~200 µg/mL; 12 µM), and the analysis of RNA isolated from ageritin-treated cells revealed the presence of Endo's fragment, highlighting its ability to cross the fungal cell wall and reach the ribosomes. Overall, these data highlight that the efficacy of antifungal treatment to prevent or treat a potential fungal disease may depend not only on the fungal species but also on the conditions of toxin application.

The Deciphering of Growth-Dependent Strategies for Quorum-Sensing Networks in Pseudomonas aeruginosa

Pseudomonas aeruginosa is recognized as a significant cause of morbidity and mortality among nosocomial pathogens. In respiratory infections, P. aeruginosa acts not only as a single player but also collaborates with the opportunistic fungal pathogen Aspergillus fumigatus. This study introduced a QS molecule portfolio as a potential new biomarker that affects the secretion of virulence factors and biofilm formation. The quantitative levels of QS molecules, including 3-o-C12-HSL, 3-o-C8-HSL, C4-HSL, C6-HSL, HHQ, PQS, and PYO, measured using mass spectrometry in a monoculture, indicated metabolic changes during the transition from planktonic to sessile cells. In the co-cultures with A. fumigatus, the profile of abundant QS molecules was reduced to 3-o-C12-HSL, C4-HSL, PQS, and PYO. A decrease in C4-HSL by 50% to 170.6 ± 11.8 ng/mL and an increase 3-o-C12-HSL by 30% up to 784.4 ± 0.6 ng/mL were detected at the stage of the coverage of the hyphae with bacteria. Using scanning electron microscopy, we showed the morphological stages of the P. aeruginosa biofilm, such as cell aggregates, maturated biofilm, and cell dispersion. qPCR quantification of the genome equivalents of both microorganisms suggested that they exhibited an interplay strategy rather than antagonism. This is the first study demonstrating the quantitative growth-dependent appearance of QS molecule secretion in a monoculture of P. aeruginosa and a co-culture with A. fumigatus.

Quantification and modeling of macroparticle-induced mechanical stress for varying shake flask cultivation conditions

In biotechnological processes, filamentous microorganisms are known for their broad product spectrum and complex cellular morphology. Product formation and cellular morphology are often closely linked, requiring a well-defined level of mechanical stress to achieve high product concentrations. Macroparticles were added to shake flask cultures of the filamentous actinomycete Lentzea aerocolonigenes to find these optimal cultivation conditions. However, there is currently no model concept for the dependence of the strength and frequency of the bead-induced stress on the process parameters. Therefore, shake flask simulations were performed for combinations of bead size, bead concentration, bead density and shaking frequency. Contact analysis showed that the highest shear stresses were caused by bead-bottom contacts. Based on this, a newly generated characteristic parameter, the stress area ratio (SAR), was defined, which relates the bead wall shear and normal stresses to the total shear area. Comparison of the SAR with previous cultivation results revealed an optimum pattern for product concentration and mean product-to-biomass related yield coefficient. Thus, this model is a suitable tool for future optimization, comparison and scaling up of shear-sensitive microorganism cultivation. Finally, the simulation results were validated using high-speed recordings of the bead motion on the bottom of the shake flask.

Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections

Soil-borne pathogens pose a major threat to food production worldwide, particularly under global change and with growing populations. Yet, we still know very little about how the soil microbiome regulates the abundance of soil pathogens and their impact on plant health. Here we combined field surveys with experiments to investigate the relationships of soil properties and the structure and function of the soil microbiome with contrasting plant health outcomes. We find that soil acidification largely impacts bacterial communities and reduces the capacity of soils to combat fungal pathogens. In vitro assays with microbiomes from acidified soils further highlight a declined ability to suppress Fusarium, a globally important plant pathogen. Similarly, when we inoculate healthy plants with an acidified soil microbiome, we show a greatly reduced capacity to prevent pathogen invasion. Finally, metagenome sequencing of the soil microbiome and untargeted metabolomics reveals a down regulation of genes associated with the synthesis of sulfur compounds and reduction of key traits related to sulfur metabolism in acidic soils. Our findings suggest that changes in the soil microbiome and disruption of specific microbial processes induced by soil acidification can play a critical role for plant health.

Beyond Penicillin: The Potential of Filamentous Fungi for Drug Discovery in the Age of Antibiotic Resistance

Antibiotics are a staple in current medicine for the therapy of infectious diseases. However, their extensive use and misuse, combined with the high adaptability of bacteria, has dangerously increased the incidence of multi-drug-resistant (MDR) bacteria. This makes the treatment of infections challenging, especially when MDR bacteria form biofilms. The most recent antibiotics entering the market have very similar modes of action to the existing ones, so bacteria rapidly catch up to those as well. As such, it is very important to adopt effective measures to avoid the development of antibiotic resistance by pathogenic bacteria, but also to perform bioprospecting of new molecules from diverse sources to expand the arsenal of drugs that are available to fight these infectious bacteria. Filamentous fungi have a large and vastly unexplored secondary metabolome and are rich in bioactive molecules that can be potential novel antimicrobial drugs. Their production can be challenging, as the associated biosynthetic pathways may not be active under standard culture conditions. New techniques involving metabolic and genetic engineering can help boost antibiotic production. This study aims to review the bioprospection of fungi to produce new drugs to face the growing problem of MDR bacteria and biofilm-associated infections.

Regression modelling of conditional morphogene expression links and quantifies the impact of growth rate, fitness and macromorphology with protein secretion in Aspergillus niger

BACKGROUND

Filamentous fungi are used as industrial cell factories to produce a diverse portfolio of proteins, organic acids, and secondary metabolites in submerged fermentation. Generating optimized strains for maximum product titres relies on a complex interplay of molecular, cellular, morphological, and macromorphological factors that are not yet fully understood.

RESULTS

In this study, we generate six conditional expression mutants in the protein producing ascomycete Aspergillus niger and use them as tools to reverse engineer factors which impact total secreted protein during submerged growth. By harnessing gene coexpression network data, we bioinformatically predicted six morphology and productivity associated 'morphogenes', and placed them under control of a conditional Tet-on gene switch using CRISPR-Cas genome editing. Strains were phenotypically screened on solid and liquid media following titration of morphogene expression, generating quantitative measurements of growth rate, filamentous morphology, response to various abiotic perturbations, Euclidean parameters of submerged macromorphologies, and total secreted protein. These data were built into a multiple linear regression model, which identified radial growth rate and fitness under heat stress as positively correlated with protein titres. In contrast, diameter of submerged pellets and cell wall integrity were negatively associated with productivity. Remarkably, our model predicts over 60% of variation in A. niger secreted protein titres is dependent on these four variables, suggesting that they play crucial roles in productivity and are high priority processes to be targeted in future engineering programs. Additionally, this study suggests A. niger dlpA and crzA genes are promising new leads for enhancing protein titres during fermentation.

CONCLUSIONS

Taken together this study has identified several potential genetic leads for maximizing protein titres, delivered a suite of chassis strains with user controllable macromorphologies during pilot fermentation studies, and has quantified four crucial factors which impact secreted protein titres in A. niger.