Search Results (1,028)

Background: Developments in biology, genetics, soil science, plant breeding, engineering, and agricultural microbiology are driving advances in soil microbiology and microbial biotechnology. Material and methods: The literature for this review was collected by searching leading scientific databases such as Embase, Medline/PubMed, Scopus, and Web of Science. Results: Recent advances in soil microbiology and biotechnology are discussed, emphasizing the role of microorganisms in sustainable agriculture. It has been shown that soil and plant microbiomes significantly contribute to improving soil fertility and plant and soil health. Microbes promote plant growth through various mechanisms, including potassium, phosphorus, and zinc solubilization, biological nitrogen fixation, production of ammonia, HCN, siderophores, and other secondary metabolites with antagonistic effects. The diversity of microbiomes related to crops, plant protection, and the environment is analyzed, as well as their role in improving food quality, especially under stress conditions. Particular attention was paid to the diversity of microbiomes and their mechanisms supporting plant growth and soil fertility. Conclusions: The key role of soil microorganisms in sustainable agriculture was highlighted. They can support the production of natural substances used as plant protection products, as well as biopesticides, bioregulators, or biofertilizers. Microbial biotechnology also offers potential in the production of sustainable chemicals, such as biofuels or biodegradable plastics (PHA) from plant sugars, and in the production of pharmaceuticals, including antibiotics, hormones, or enzymes. Full article

Sustainability represents a significant global challenge, requiring a balance between environmental impact and the use of natural resources. White biotechnology, which uses microorganisms and enzymes for environmentally friendly products and processes, offers promising solutions to support a growing population. Within this context, the yeast Yarrowia lipolytica stands out, so we investigated the generation of biomass from two wild strains (ATCC 9773 and NRRL Y-50997) using different carbon sources. Additionally, protein content and amino acid profiles were assessed via standardized analytical methods to evaluate their potential as nutritional yeasts. Both strains demonstrated potential as nutritional yeasts, with biomass productivities of up to 35.5 g/L and 42 g/L, respectively. The protein content was high, with 58.8% for ATCC 9773 and 58.2% for NRRL Y-50997. Furthermore, the strains presented essential amino acid contents of 62.6% and 41.5%, with lysine being the most abundant amino acid. These findings underscore the versatility and productivity of Y. lipolytica, highlighting its potential for sustainable biotechnological applications such as single-cell protein production. Full article

Fungal lytic polysaccharide monooxygenases (LPMOs) have revolutionized the field of biomass degradation by introducing an oxidative mechanism that complements traditional hydrolytic enzymes. These copper-dependent enzymes catalyze the cleavage of glycosidic bonds in recalcitrant polysaccharides such as cellulose, hemicellulose, and chitin, through the activation of molecular oxygen (O₂) or hydrogen peroxide (H₂O₂). Their catalytic versatility is intricately modulated by structural features, including the histidine brace active site, surface-binding loops, and, in some cases, appended carbohydrate-binding modules (CBMs). The oxidation pattern, whether at the C1, C4, or both positions, is dictated by subtle variations in loop architecture, amino acid microenvironments, and substrate interactions. LPMOs are embedded in a highly synergistic fungal enzymatic system, working alongside cellulases, hemicellulases, lignin-modifying enzymes, and oxidoreductases to enable efficient lignocellulose decomposition. Industrial applications of fungal LPMOs are rapidly expanding, with key roles in second-generation biofuels, biorefineries, textile processing, food and feed industries, and the development of sustainable biomaterials. Recent advances in genome mining, protein engineering, and heterologous expression are accelerating the discovery of novel LPMOs with improved functionalities. Understanding the balance between O₂- and H₂O₂-driven mechanisms remains critical for optimizing their catalytic efficiency while mitigating oxidative inactivation. As the demand for sustainable biotechnological solutions grows, this narrative review highlights how fungal LPMOs function as indispensable biocatalysts for the future of the Circular Bioeconomy and green industrial processes. Full article

Background: Clinical diagnostics, food industries, and biotechnological processes typically use an enzyme called alpha-amylase to metabolize carbohydrates. Objective: The aim of this study is to investigate how low-level laser irradiation (LLLI) affects alpha-amylase activity towards determining the usability of LLLI in non-invasive enzymatic modulation. Methods: Enzyme solutions were irradiated at 10, 20, 30, and 40 J/cm² utilizing 589 nm and 532 nm diode-pumped solid-state lasers. The iodine–starch colorimetric method was used to quantify post-irradiation enzymatic activity, with inverse correlations found between absorbance and activity levels. Modulation was determined by the wavelength and dosage. Results: Enzymatic activity significantly improved when utilizing 589 nm irradiation at lower doses, maximizing at 120% at 20 J/cm² (p < 0.01). Neutral or inhibitory effects were revealed when higher doses were applied. Enzymatic activity showed progressive inhibition when 532 nm irradiation was applied, declining to 75% at 40 J/cm² (p < 0.01). Conclusions: These outcomes indicate that conformational flexibility and catalytic efficiency occur when applying lower-energy photons at 589 nm, whilst oxidative stress and impaired enzymatic function are induced by higher-energy photons at 532 nm. This is consistent with the biphasic dose–response characteristic of photobiomodulation. Full article

Agricultural and industrial residues are increasingly recognized as valuable resources for sustainable innovation, offering significant potential for biotechnological applications. By integrating waste valorization into production systems, this approach aims to mitigate environmental impacts and enhance economic value across various sectors. The findings underline the critical need for further research and policy support to scale these solutions, advancing global sustainability goals through innovative resource management. In this perspective, this article reviews the utilization of key by-products, including coffee residues, sugarcane bagasse, whey, cassava wastewater (manipueira), and brewery waste, highlighting their transformation into high-value products such as biofuels, bioplastics, enzymes, bioactive compounds, and organic fertilizers. The discussion presented encompasses the challenges and opportunities in leveraging these residues, emphasizing the role of advanced technologies, intellectual property, and circular economy principles. Full article

The majority of studies of fungal utilization of chitosan are associated with the production of a specific enzyme, chitosanase, which catalyzes the hydrolytic cleavage of the macrochain. In our opinion, the development of approaches to obtaining materials with new functional properties based on non-destructive chitosan transformation by living organisms and their enzyme systems is promising. This study was conducted using a wide range of classical and modern methods of microbiology, biochemistry, and physical chemistry. The ability of the ascomycete Fusarium oxysporum Schltdl. to modify films of chitosan with average-viscosity molecular weights of 200, 450, and 530 kDa was discovered. F. oxysporum was shown to use chitosan as the sole source of carbon/energy and actively overgrew films without deformations and signs of integrity loss. Scanning electron microscopy (SEM) recorded an increase in the porosity of film substrates. An analysis of the FTIR spectra revealed the occurrence of oxidation processes and crosslinking of macrochains without breaking β-(1,4)-glycosidic bonds. After F. oxysporum growth, the resistance of the films to mechanical dispersion and the degree of ordering of the polymer structure increased, while their solubility in the acetate buffer with pH 4.4 and sorption capacity for Fe²⁺ and Cu²⁺ decreased. Elemental analysis revealed a decrease in the nitrogen content in chitosan, which may indicate its inclusion into the fungal metabolism. The film transformation was accompanied by the production of extracellular hydrolase (different from chitosanase) and peroxidase, as well as biosurfactants. The results obtained indicate a specific mechanism of aminopolysaccharide transformation by F. oxysporum. Although the biochemical mechanisms of action remain to be analyzed in detail, the results obtained create new ways of using fungi and show the potential for the use of Fusarium and/or its extracellular enzymes for the formation of chitosan-containing materials with the required range of functional properties and qualities for biotechnological applications. Full article

Membrane technology is primarily used for the separation and purification of biotechnological products, which contain proteins and enzymes. Membrane fouling during crossflow filtration remains a significant challenge. This study aims to initially validate crossflow filtration models, particularly related to pore-blocking mechanisms, through a comparative analysis with dead-end filtration models. One crossflow microfiltration (MF) and six consecutive ultrafiltration (UF) stages were implemented to concentrate laccase extracts from Pleurotus ostreatus 202 fungi. The complete pore-blocking mechanism significantly impacts the MF, UF 1000, UF 100 and UF 10 stages, with the highest related filtration constant (Kb_F) estimated at 12.60 × 10⁻⁴ (m⁻¹). Although the intermediate pore-blocking mechanism appears across all filtration stages, UF 100 is the most affected, with an associated filtration constant (Ki_F) of 16.70 (m⁻¹). This trend is supported by the highest purification factor (6.95) and the presence of 65, 62 and 56 kDa laccases in the retentate. Standard pore blocking occurs at the end of filtration, only in the MF and UF 1000 stages, with filtration constants (Ks_F) of 29.83 (s^−0.5m^−0.5) and 31.17 (s^−0.5m^−0.5), respectively. The absence of cake formation and the volume of permeate recovered indicate that neither membrane was exposed to exhaustive fouling that could not be reversed by backwashing. Full article

Fungal communities in high plateau ecosystems remain understudied despite their crucial roles in soil ecosystems, and yeasts inhabiting extreme regions have potential for industrial and biotechnological applications. We studied the fungal diversity in soils across 14 Chilean Altiplano sites using amplicon-based metagenomics and isolation of yeasts to assess their growth under various conditions and hydrolytic enzyme secretion. Using the metagenomic approach, the Ascomycota and Basidiomycota phyla were found to be the most abundant (85% and 8%, respectively). Unclassified families and genera prevailed at six and ten sites, respectively. At the other sites, the most abundant families included Cladosporiaceae, Teratosphaeriaceae, and Sporormiaceae, and the genera Oleoguttula, Coniochaeta, and Peziza. Biodiversity indices did not correlate with the soil’s geographic origin, organic matter content, humidity, or pH. Most isolated yeasts belong to the Naganishia, Holtermanniella, and Vishniacozyma genera, growing at temperatures ranging from 4 °C to 26 °C. Most isolates could use glucose, sucrose, and maltose as carbon sources and exhibited amylase, esterase, pectinase, and protease activities at 30 °C and below. Our results indicate that the evaluated soil physicochemical parameters do not explain the fungal distribution in the Altiplano and highlight the region as a reservoir of unknown fungi, including yeasts with industrially relevant enzymes. Full article

Seaweeds, classified as non-vascular plants, have definite advantages over terrestrial plants as they grow rapidly, can be cultivated in coastal environments, and are dependable and non-endangered sources of biomass. Algal bioproducts, which include a wide range of bioactive compounds, have drawn much interest because of their applications in nutraceuticals, pharmaceuticals, agriculture, and cosmetics. Particularly in the pharmaceutical and nutraceutical fields, algal bioproducts have shown tremendous activity in regulating enzymes involved in human diseases. However, the drawbacks of conventional extraction methods impede the complete exploitation of seaweed biomass. These include low efficiency, high cost, and potential harm to the environment. Enzyme technology developments in recent years present a viable way to overcome these challenges. Enzymatic processes improve product yields and reduce the environmental impact of processing, while facilitating the more effective extraction of valuable bioactive compounds as part of an integrated biorefinery approach. Enzyme-assisted biorefinery techniques can greatly advance the creation of a circular bioeconomy and increase the yield of extracted seaweed bioproducts, thus improving their value. With the potential to scale up to industrial levels, these biotechnological developments in enzymatic extraction are developing rapidly and can advance the sustainable exploitation of seaweed resources. This review emphasises the increasing importance of enzyme technologies in the seaweed biorefinery and their contribution to developing more environmentally friendly, economically feasible, and sustainable methods for valorising products derived from seaweed. In the biorefinery industry, enzyme-assisted methods have enormous potential for large-scale industrial applications with further development, opening the door to a more sustainable, circular bioeconomy. Full article

Cellulose, the most abundant organic polymer in soil, is degraded by the action of microbial communities. Cellulolytic taxa are widespread in soils, enhancing the biodegradation of cellulose by the synergistic action of different cellulase enzymes. β-glucosidases are the last enzymes responsible for the degradation of cellulose by producing glucose from the conversion of the disaccharide cellobiose. Different soils from the states of Delaware, Maryland, New Jersey, and New York were analyzed by direct DNA extraction, PCR analysis, and next generation sequencing of amplicon sequences coding for β-glucosidase genes. To determine the community structure and diversity of microorganisms carrying β-glucosidase genes, amplicon sequence variant analysis was performed. Results showed that the majority of β-glucosidase genes did not match any known phylum or genera with an average of 84% of sequences identified as unclassified. The forest soil sample from New York showed the highest value with 95.62%. When identification was possible, the bacterial phyla Pseudomonadota, Actinomycetota, and Chloroflexota were found to be dominant microorganisms with β-glucosidase genes in soils. The Delaware soil showed the highest diversity with phyla and genera showing the presence of β-glucosidase gene sequences in bacteria, fungi, and plants. However, the Chloroflexota genus Kallotanue was detected in 3 out of the 4 soil locations. When phylogenetic analysis of unclassified β-glucosidase genes was completed, most sequences aligned with the Chloroflexota genus Kallotenue and the Pseudomonadota species Sphingomonas paucimobilis. Since most sequences did not match known phyla, there is tremendous potential to discover new enzymes for possible biotechnological and pharmaceutical applications. Full article

The shikimate pathway is the fundamental metabolic route for aromatic amino acid biosynthesis in bacteria, plants, and fungi, but is absent in mammals. This review explores how multi-enzyme synergy and allosteric regulation coordinate metabolic flux through this pathway by focusing on three key enzymes: 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase, chorismate mutase, and tryptophan synthase. We examine the structural diversity and distribution of these enzymes across evolutionary domains, highlighting conserved catalytic mechanisms alongside species-specific regulatory adaptations. The review covers directed evolution strategies that have transformed naturally regulated enzymes into standalone biocatalysts with enhanced activity and expanded substrate scope, enabling synthesis of non-canonical amino acids and complex organic molecules. Industrial applications demonstrate the pathway’s potential for sustainable production of pharmaceuticals, polymer precursors, and specialty chemicals through engineered microbial platforms. Additionally, we discuss the therapeutic potential of inhibitors targeting pathogenic organisms, particularly their mechanisms of action and antimicrobial efficacy. This comprehensive review establishes the shikimate pathway as a paradigmatic system where understanding allosteric networks enables the rational design of biocatalytic platforms, providing blueprints for biotechnological innovation and demonstrating how evolutionary constraints can be overcome through protein engineering to create superior industrial biocatalysts. Full article

The nitrogen cycle (N-cycle) is a cornerstone of global biogeochemistry, regulating nitrogen availability and affecting atmospheric chemistry, agricultural productivity, and ecological balance. Central to this cycle is the reversible interplay between nitrate (NO₃⁻) and nitrite (NO₂⁻), mediated by molybdenum-dependent enzymes—Nitrate reductases (NARs) and Nitrite oxidoreductases (NXRs). Despite catalyzing opposite reactions, these enzymes exhibit remarkable structural and mechanistic similarities. This review aims to elucidate the molecular underpinnings of nitrate reduction and nitrite oxidation by dissecting their enzymatic architectures, redox mechanisms, and evolutionary relationships. By focusing on recent structural, spectroscopic, and thermodynamic data, we explore how these two enzyme families represent “two sides of the same coin” in microbial nitrogen metabolism. Special emphasis is placed on the role of oxygen atom transfer (OAT) as a unifying mechanistic principle, the influence of environmental redox conditions, and the emerging evidence of bidirectional catalytic potential. Understanding this dynamic enzymatic interconversion provides insight into the flexibility and resilience of nitrogen-transforming pathways, with implications for environmental management, biotechnology, and synthetic biology. Full article

Background: Endophytic fungi are prolific sources of bioactive metabolites with potential in pharmaceutical and biotechnological applications. Methods: Here, the endophytic fungus, Alternaria alstroemeriae S6, was isolated from Veronica acinifolia (speedwell), and conducted its anti-microbial activities, whole-genome sequencing and metabolome analysis. Results: The ethyl acetate extract of this fungus exhibited strong anti-bacterial activity and the inhibition zones, induced by the fungal extract at 20 mg/mL, reached 16.25 ± 0.5 mm and 26.5 ± 0.5 mm against Gram-positive and Gram-negative bacteria. To unravel the biosynthetic potential for anti-bacterial compounds, whole-genome sequencing was conducted on A. alstroemeriae S6, resulting in a high-quality assembly of 42.93 Mb encoding 13,885 protein-coding genes. Comprehensive functional genome annotation analyses, including gene ontology (GO) terms, clusters of orthologous groups (COGs), Kyoto encyclopedia of genes and genomes (KEGG), carbohydrate-active enzymes (CAZymes), and antibiotics and secondary metabolites analysis shell (antiSMASH) analyses, were performed. According to the antiSMASH analysis, 58 biosynthetic gene clusters (BGCs), including 16 non-ribosomal peptide synthetases (NRPSs), 21 terpene synthases, 12 polyketide synthetases (PKSs), and 9 hybrids, were identified. In addition, succinic acid was identified as the major metabolite within the fungal extract, while 20 minor bioactive compounds were identified through LC-MS/MS-based molecular networking on a GNPS database. Conclusions: These findings support the biotechnological potential of A. alstroemeriae S6 as an alternative producer of succinic acid, as well as novel anti-bacterial agents. Full article

The growing demand for efficient sustainable biocatalysts for industrial applications has driven the exploration of extremozymes from extremophiles, particularly those thriving in geothermal environments. This study aimed to isolate and characterize extracellular amylase-producing thermophilic bacteria from the Nelumwewa geothermal spring in Sri Lanka, an underexplored ecosystem. Among the isolated thermophilic bacterial strains, NW2 isolates exhibited a prominent extracellular amylase activity. Molecular characterization by 16S rRNA gene sequencing confirmed the close phylogenetic relationship between NW2 and Thermaerobacillus caldiproteolyticus, which is well-known for thermostable proteases. Biochemical assays revealed optimal amylase activity of NW2 isolate at 60 °C and pH 8.0, with a crude enzyme activity of 0.85 U/mL. The enzyme demonstrated efficient hydrolysis of raw cassava starch, highlighting its potential for industrial applications in food, biofuel, and detergent industries. This study reports the first T. caldiproteolyticus-like strain from Sri Lanka with significant extracellular amylase activity, emphasizing the biotechnological potential of geothermal springs as sources of novel extremozymes. These findings contribute to the growing repository of thermostable enzymes, highlighting the need for further exploration of Sri Lanka’s geothermal microbial diversity for industrial biocatalysts. Full article

Spent coffee grounds (SCG) are a widely available agro-industrial residue rich in carbon and phenolic compounds, presenting significant potential for biotechnological valorization. This study evaluated the use of SCG as a suitable substrate for fungal laccase production and the application of the resulting fermented biomass (RFB), a mixture of fermented SCG and fungal biomass as a biosorbent for textile dye removal. Two fungal strains, namely Lentinus crinitus UCP 1206 and Trametes sp. UCP 1244, were evaluated in both submerged (SmF) and solid-state fermentation (SSF) using SCG. L. crinitus showed superior performance in SSF, reaching 14.62 U/g of laccase activity. Factorial design revealed that a lower SCG amount (5 g) and higher moisture (80%) and temperature (30 °C ± 0.2) favored enzyme production. Fourier transform infrared (FTIR) spectroscopy and scanning electron microscopy (SEM) analyses confirmed significant structural degradation of SCG after fermentation, especially in SSF. Furthermore, SCG and RFB were chemically activated and evaluated as biosorbents. The activated carbon from SCG (ACSCG) and RFB (ACRFB) exhibited high removal efficiencies for Remazol dyes, comparable to commercial activated carbon. These findings highlight the potential of SCG as a low-cost, sustainable resource for enzyme production and wastewater treatment, contributing to circular bioeconomy strategies. Full article