Extremophilic microorganisms live in extreme environmental conditions such as high or low temperature, high or low pH, high concentration of salt and accordingly are classified as thermophilic, psychrophilic, alkaliphilic, acidophilic and halophilic respectively. They adapt themselves to the extreme conditions by producing novel biomolecules like heat shock proteins, cold active enzymes, compatible solutes and exopolysaccharides. Extremophilic microorganisms maintain their cellular integrity with the help of exopolysaccharide (EPS) which constitutes slime or a hydrated matrix that keeps the cells embedded. EPS are composed of carbohydrates and some amino acids. Thermophilic microorganisms namely Thermus, Geobacillus, Bacillus, Thermococcus and halophilic microorganisms namely Halomonas, Halobacillus, Haloferax and Halococcus are reported and well-studied for production of EPS. The EPSs exhibit emulsifying, viscofying and antioxidant properties that find applications in food industry, oil recovery and anticancer agents.
Decaprenoxanthin (DPXT) is an unusual bacterial C50 carotenoid that has historically received limited attention despite its well-defined structure. For decades, carotenoid research and industrial development have been dominated by C40 carotenoids, leaving longer-chain carotenoids largely overlooked. Recent discoveries, particularly from microorganisms inhabiting Antarctic and other extreme environments, have repositioned DPXT as an adaptive pigment shaped by intense environmental pressures. Its extended polyene chain and membrane-associated behavior suggest roles in membrane stabilization and protection against ultraviolet radiation and oxidative stress, features that may hold relevance for food and biotechnological applications. This review integrates historical and recent knowledge on DPXT, covering its structural characteristics, biosynthetic pathways, ecological function, and emerging technological relevance. Special attention is given to microbial sources, particularly Actinomycetota from extreme environments, and to recent advances in microbial genomics, metabolic engineering, and sustainable bioprocess development that enable the production and exploration of C50 carotenoids beyond their native extremophilic context. The analysis highlights DPXT as a representative example of stress-resilient carotenoids, with physicochemical and membrane-interacting properties that may offer advantages for future food and biotechnological systems. Although significant challenges remain in cultivation strategies, yield optimization, and downstream recovery, advances in microbial cell factories and green extraction technologies open new opportunities for valorizing C50 carotenoids. This review bridges extremophile microbiology, carotenoid biochemistry, and sustainable food innovation, positioning DPXT as an emerging molecule that may expand the functional and structural landscape of carotenoids relevant to food science.
Antimicrobial resistance (AMR) is a global threat driven by the interplay between microbial evolution and human activity. Antimicrobial use in human and veterinary medicine, as well as in agriculture, accelerates the selection and dissemination of resistant bacteria and genes across interconnected human, animal, and environmental reservoirs. These dynamic exchanges render single-sector interventions ineffective. A One Health approach integrating human, animal, and environmental health is therefore essential to understand and mitigate the emergence and spread of AMR. This chapter focuses on bacterial antimicrobial resistance, addressing key concepts, major challenges, and emerging technologies within a One Health framework. Advances in next-generation sequencing and omics technologies have transformed our capacity to resolve AMR at unprecedented scale and resolution. These tools enable the tracking of resistance genes and high-risk clones across ecosystems, uncover transmission pathways, and identify key drivers of dissemination. Such insights support real-time epidemiological surveillance, outbreak detection, and targeted interventions. However, translating these advances into routine practice remains a major challenge, requiring harmonized methodologies, data integration, and cross-sector coordination. Addressing AMR demands sustained collaboration across disciplines and stakeholders, including clinicians, veterinarians, farmers, researchers, policymakers, industry, and the public. And framing AMR as a shared ecological and societal responsibility underscores the urgency of coordinated global action. We call for the urgent integration of One Health principles into surveillance, policy, and innovation to preserve antimicrobial effectiveness and safeguard future health.
Mushrooms are considered suitable bioindicators of environmental pollution arising from certain elements, including radionuclides, because of their tendency to bioaccumulate varying levels of these essential and non-essential elements. Different species have different capacities for retaining individual radionuclides, both natural and anthropogenic. Medium and long-lived isotopes generally pose a very significant hazard to human health. Following pollution events, the consumption of mushrooms may pose a risk from exposure to highly radiotoxic emitters. This review focuses on the most common natural and anthropogenic alpha- and beta-emitting radionuclides in wild mushrooms worldwide, but also includes those that are less critical from a radiation-hazard perspective. The activity concentrations of the reported radionuclides accumulated in macrofungi range over nine orders of magnitude.
Bioleaching of metal sulfides (MS) is driven by acidophilic chemolithotrophic microorganisms that oxidize ferrous ions and reduced inorganic sulfur compounds under extremely acidic conditions. These microorganisms form biofilms on mineral surfaces, influencing their metabolism and bioleaching activity. Studying biofilms in bioleaching acidophiles presents unique challenges, such as the dual role of MS surfaces as electron donors that generate reactive oxygen species, provide selective colonization sites, biofilm mineralization, and limited knowledge of inter- and intra-species interactions. This chapter reviews recent advances in bioleaching biofilm research, focusing on cell-to-cell communication through Quorum Sensing (QS), extracellular polymeric substances (EPS) studies using non-invasive cell labeling, as well as high-throughput image analysis for biofilm quantification. We discuss the effects of acyl homoserine lactone (AHLs)-based and diffusible signal factor (DSF)-based QS systems on the metabolic activity and biofilm formation of bioleaching bacteria. Additionally, we examine evidence suggesting that QS influences biofilm formation and MS bioleaching in mixed acidophilic cultures. We also review recent progress in visualizing acidophilic leaching biofilms by fluorescence microscopy techniques (Epifluorescence and Confocal Laser Scanning Microscopy) to study their establishment on mineral surfaces, EPS production, and interspecies interactions. Finally, we present an improved approach using Open-Source Software to overcome limitations in biofilm quantitative analysis, addressing biases caused by the low number of images frequently analyzed and the absence of robust statistical frameworks for cell and microcolony quantification.
The advent of high-throughput DNA sequencing technology has facilitated the rapid and explicit analysis of human microbiome. Microbiome analysis from the crime scene provides definitive evidence of human contacts and/or their body fluids. Besides, personalized microbiome is strongly influenced by the geographic, lifestyle, ethnic and other environmental factors. The role of microbiome analysis in the prediction of post-mortem time interval has been widely established. Forensic Microbiome Database has featured a catalogue of varied group of microorganisms in different parts of the body which might provide a crucial piece of evidence in identification of body-fluids. Though the forensically relevant human microbiome analysis faces significant challenges both from technological and data related issues, this field holds significant promise in generating investigative leads and subsequent identification of an individual in the post-DNA profiling era. The proposed chapter describes the various aspects of human microbiome in forensics use and its challenges in its practical application in various forensic scenarios.
Rapidly growing nontuberculous mycobacteria (NTM) are emerging pathogens that are well-known entities behind pulmonary, extra-pulmonary, cutaneous, subcutaneous, as well as systemic and disseminated infections. Mycobacterium fortuitum is an important human pathogenic NTM. It is a routine nosocomial contaminant capable of forming resilient biofilms that enhance its resistance to antibiotics and disinfectants and contribute to persistent healthcare-associated infections. Moreover, varying symptoms of M. fortuitum infections, long duration therapeutics, and lack of a standardized drug regimen underscores medical significance of the pathogen. Limited knowledge regarding M. fortuitum pathogenesis, however, entices research investigating M. fortuitum planktonic as well as the biofilm phenotype. The review article aims to gather data about the prevalence and clinical significance of NTM in general, with special emphasis on M. fortuitum. It further delves into the biofilm aspect of the pathogen and examines current therapeutic strategies against NTM infections and diseases. Emerging horizons in NTM therapeutics, including repurposing antitubercular drugs, bacteriophage therapy, photodynamic therapy, and advancements in molecular diagnostic techniques are being explored to combat NTM infections. In addition, innovative treatments specifically targeting NTM biofilms, such as combination therapies, liposomal formulations, thiopeptide antibiotics, monoclonal antibodies, and inhibitors of the DosRS system, are under investigation. The concluding section of the article emphasizes the necessity for future research to delve into molecular mechanisms underlying biofilm formation and maintenance, develop targeted therapies, and refine diagnostic tools to effectively manage and treat NTM infections. Collectively, the information will be helpful to the researchers working on strategies and treatments to combat NTM infections.
Monascus spp., as an important model microorganism in food and medical research, has been used in China for thousands of years. Monascus spp. can produce many beneficial secondary metabolites, including pigments (food colorants), monacolins (cholesterollowering agents), γ -amino butyric acid (antihypertensive substance), and dimerumic acid (antioxidant), and some Monascus strains can also produce citrinin, a nephrotoxic metabolite. Currently, the main industrialized production through Monascus is monascus red pigment and monacolin K. The monascus yellow and orange pigments possessing high protein coloring ability and many biological effects have not been industrially produced by fermentation so far. However, to our knowledge, few systematic review related to monascus yellow pigments research have been reported. This paper provides a systematic review the breeding of Monascus strain and its fermentation processes optimization, the identification of monascus yellow pigments and their structures, the pharmacological properties and biosynthesis pathway of monascus yellow pigments. Finally, an academic view on the future of monascus yellow pigments from the perspective of industrialized production is presented.
Microbial pesticides derived from entomopathogenic bacteria occupy the greater share of the global biopesticides market. Since the late 1990s, the exploration of such bacterial species has intensified and expanded beyond the well-described Bacillus thuringiensis to other spore-forming Gram-positive bacteria including Brevibacillus laterosporus and Lysinibacillus sphaericus. Among the non-spore-forming Gram-negative bacteria Chromobacterium spp., Serratia spp., and Pseudomonas spp. are of interest for their insect active properties. Unfortunately, all these bacterial species are susceptible to the effects of some putative antibacterial proteins (ABPs), including bacteria-eating viruses (phages), encapsulins, and phage tail-like bacteriocins (PTLBs). Phage-derived bacteriocins can be either contractile phage tail-like (R-type) or non-contractile tail-like (F-type) structures. Encapsulins, a class of high molecular-weight (HMW) putative ABPs resembling phage capsid or head-like structures have been identified in different bacterial species. These putative ABPs are known to pose a serious threat to the mass production of these useful bacteria by causing a collapse of the culture through lysis of the cells. For instance, B. thuringiensis specific phages can cause production batch failures ranging from 15 to 100%. Recently, the stunted growth of the insect pathogenic B. laterosporus strains 1821L and 1951 from New Zealand has been associated with production of HMW putative ABPs of 31.4 kDa, Linocin M18, and ∼48 kDa, phage-like element PBSX-protein XkdK. This article provides an overview of the biological attributes of the putative ABPs and their implications in harnessing the insecticidal potential of B. thuringienesis and the emerging biocontrol agent B. laterosporus.
Heavy metals are widely used to satiate the demands of growing industrialization and modern life. However, the presence of metal in large quantities in the ecosystem significantly impacts all life forms, particularly microorganisms. Many bacterial strains have developed metal resistance genes (MRG) to survive in extreme conditions through various mechanisms, such as active efflux, sequestration, permeability barriers, or co-resistance with antibiotic resistance genes. Metagenomic analysis is a powerful approach that enables the exploration of the functional repertoire and diversity of microorganisms, providing deeper insights into the mechanisms underlying the development of MRGs, and the active metabolites they produce to adapt to the polluted environments. With the advancement of these techniques, the knowledge can be further applied to environmental applications, such as bioremediation, biomonitoring, and synthetic biology. Bacteria with metal toxicity tolerance can be employed to enhance environmental sustainability and mitigate potential hazards.
Serotonin is a widely distributed monoamine neurotransmitter that plays a critical role in emotion regulation and management in animals. It also serves as a key intermediate in the melatonin biosynthesis pathway. Melatonin is crucial for circadian rhythm regulation, antioxidant defense, and plant growth as well as stress resistance. Both serotonin and melatonin are involved in signaling transduction pathways that modulate various nervous system activities. Currently, serotonin is primarily obtained through natural extraction and chemical synthesis. However, these methods are time-consuming, low-yielding, and environmentally unfriendly. In recent years, environmentally friendly bio-fabrication has garnered significant attention. Microbial synthesis, characterized by short growth cycles and eco-friendly production processes, has emerged as a promising platform for the synthesis of serotonin and melatonin. Nevertheless, the production yield of serotonin and melatonin in microorganisms remains insufficient to meet industrial production demands. This review provides a comprehensive overview of the fundamental properties and physiological functions of serotonin and melatonin with a focus on their biosynthesis. In addition, it examines recent advancements in microbial biosynthesis of serotonin and melatonin, identifies key bottlenecks limiting production efficiency, and proposes metabolic engineering strategies to enhance microbial synthesis efficiency, aiming for scalable industrial applications.
Mycotoxins are secondary metabolites produced by a wide variety of filamentous fungi. These compounds are toxic to humans and animals, and, in several cases, also to invertebrates, plants and microbial cells. Contamination of food and feed with mycotoxins can occur at different stages of the production chain, thus making mycotoxins a very important dietary risk factor. Various methods based on physical and chemical principles can be implemented to mitigate mycotoxin contamination. However, these methods possess two important disadvantages: the generation of toxic residues and the alteration of the nutritional and palatability qualities. Several bacterial and fungal species can detoxify mycotoxins by adsorption and/or biotransformation. Adsorption implies the interaction of the mycotoxin with a cellular component, while biotransformation is the chemical modification of the toxin. There are plenty of examples that demonstrate that detoxification of mycotoxins employing microbial cells or microbial enzymes is an environmentally friendly, efficient, specific and safe method. This chapter focuses on the biological detoxification of structurally different mycotoxins by adsorption to microbial cells or microbial biotransformation. It includes a comprehensive review of the discovery of the most critical mycotoxins, the use of probiotics to remove mycotoxins by surface adsorption, and the microbial biotransformation reactions, products, and mechanisms known to date that result in the detoxification of aflatoxins, fumonisins, zearalenone, ochratoxins, trichothecenes, patulin and fusaric acid.
Deep eutectic solvents (DESs) are new generation green solvents that fulfill most of the principles of green chemistry. A DES is a mixture formed by hydrogen bonds between two or more compounds, of which melting point is much lower than their constituents. They have unique properties such as high solvating capability, low vapor pressure, low toxicity, non-flammability, high thermal stability, easy preparation and being cost-effective. Furthermore, the properties of a DES can be designed for a specific application by proper combinations of their constituents; therefore, they are called "designer solvents" or "tailor-made" solvents. Deep eutectic solvents are successfully used in numerous fields including chemical reactions, biotransformations, bioactive compound extraction, gas absorption, nanoparticles synthesis, drug delivery, electrochemistry, electropolishing and electroanalysis, purification and production of biodiesel, and metal processing. Recently, with the increasing interest on green technologies, deep eutectic solvents have started to be used in applied microbiology. This review covers the applications of DESs in microbial technology as their utilization in fermentations and whole-cell biotransformations, extraction of bioproducts from the cells and cryopreservation of microorganisms.
Comamonas testosteroni TA441 is a model bacterium for aerobic steroid degradation. This review summarizes its steroid degradation pathways, including the genetic organization and enzymatic mechanisms involved in C17-side chain degradation, A,B-ring cleavage, and β-oxidation of B,C,D-rings. Comparative insights from other aerobic steroid-degrading bacteria highlight the evolutionary conservation of key enzymes. Understanding these pathways provides crucial insights into microbial steroid metabolism and its environmental significance.
Edible mushrooms are a valuable source of protein, dietary fiber, vitamins, essential elements, and bioactive compounds with significant nutraceutical benefits for human health. Their popularity has grown in recent years due to their gluten-free nature and essential amino acid profile, making them appealing to vegetarians, vegans, and individuals with celiac disease. The nutritional composition and biological efficiency of mushrooms depend on the species and production system, particularly the substrate used and cultivation conditions. This review explores how different substrates, particularly those containing agribusiness by-products, affect mushrooms' productivity, nutritional, and element content from the Agaricus, Lentinula, and Pleurotus genera. It underscores the importance of these mushrooms in the human diet and highlights how using agro-industrial wastes as substrates offers a sustainable cultivation method. This approach supports a circular bioeconomy, providing an ecologically and economically viable solution while aiding in waste recovery and minimizing environmental impacts associated with improper disposal of agro-industrial wastes.
The understanding of microbial diversity and their metabolic activities inside the oil reservoir is not well understood. The microbial community of the oil reservoir plays diversified roles from souring to microbial enhanced oil recovery. Therefore, studying community dynamics, phylogenetic diversity and ecological roles of the community inside the reservoir is crucial. This chapter discussed different microbial processes taking place in petroleum reservoirs. The study showed the crude oil being the major electron donor inside the reservoir supporting major life forms. The major metabolic reactions taking place are nitrate and nitrite reduction, sulfur and sulfate reduction, iron reduction, fermentation, and methanogenesis. Many of the thermo-tolerant strains that are capable of exploiting numerous energy sources and electron acceptors are among the most often cultured on functional groups, which include sulfate and sulfur reducing bacteria like Desulfacinum infernum, Desulfacinum subterraneum, iron reducing, fermentative such as Thermococcus, Thermotoga, and Thermoanaerobacter species, and methanogenic microorganisms like Methanothermobacter thermautotrophicus. The stimulated growth of microbes could also enhance the oil recovery from the reservoir by 66 percent as proved in some experimental studies. The microbial growth could be increased by injection of nitrate which could also control sulfide production, or nutrients such as sugar molasses that increases fermentative microbial growth, which could improve volumetric sweep efficiency and thus oil recovery. Microbial growth also has the potential for corrosion and souring due to the presence of microbes such as Desulfovibrio¸ Clostridium etc. It could be concluded that the scope of microbial diversity is far more extensive than what is known till date.
Blue-green algae, or cyanobacteria, is a diverse category of prokaryotic photosynthetic organisms. The capacity to extract economically viable compounds from cyanobacteria drives continuous scientific research in this domain. The ability to synthesize fatty acids from cyanobacteria makes them a useful substitute for animal and plant-based sources in the synthesis of oils and fats. Their benefits over other sources include their rapid growth rate, higher biomass production and minimal consumption of land. Since these substances build up inside of the cells, effective procedures for their extraction, recovery, and purification are required. The primary procedures in lipid extraction utilizing cyanobacteria are cultivation, biomass collection, cell disruption and lipid transesterification. Fatty acids are essential components of the metabolic pathways that generate and convert the majority of lipid classes. This chapter outlines the metabolic pathway associated with fatty acid biosynthesis, along with various mechanical and chemical methods that can be employed to extract lipids from cyanobacteria. The composition of fatty acids primarily impacts their characteristics and practical use. This chapter also gives a general overview of the variety of fatty acid profiles found in cyanobacteria, including omega-6 and omega-3 fatty acids, as well as odd-chain, long-chain, short-chain, and medium-chain fatty acids and the different uses of cyanobacterial fatty acids in various industries, such as aquaculture, biofuel, food industry, pharmaceuticals, cosmetics and more. In summary cyanobacterial fatty acids are essential in various fields, offering benefits for both ecosystems and emerging industries.
Mercury occurs in inorganic and organic forms in abiotic and biotic environments, food and humans. Diet is a primary pathway to chronic exposure and the Hg content of food is regulated, including the three most cultivated edible fungi. The reliable determination of total Hg and organo-Hg compounds in fungi is therefore crucial from the regulatory and human exposure viewpoint. So far, no fungal species have been identified that exhibit mercury hyperaccumulation. Chronologically, external fungal biomass decomposition, elementary Hg0 vapour generation and cold vapour-atomic absorption spectroscopy measurement was the first popular instrument technique used to measure Hg in mushrooms. In more recent time, chemical vapour generation - atomic fluorescence spectrometry is getting more popular. Radiochemical analysis, instrumental neutron activation analysis, electrothermal atomic absorption spectrometry and electrochemical techniques (anodic stripping voltammetry, differential pulsed anodic stripping voltammetry and potentiometry) were occasionally used. More recently and going forward, ICP-MS technique that allow precise measurement of multiple elements including Hg simultaneously are likely to most widely used. For speciation studies of Hg in fungal biomass, CV-AAS and a variation of the instrumental couplings of gas- and liquid chromatography (combined with chemical vapor generation) and non-chromatographic separations with various detectors have been used. From the use of L-cysteine as a complexing agent to the quantitative capture and determination of MeHg in various matrices, a number of applications, modifications and updates to the methodology have been introduced since then. L-cysteine has the potential to capture MeHg, EtHg and PhHg or possibly any organo-Hg compound in a sample extract.
Carbon metabolism is an essential process in fungal physiology, balancing energy availability, growth, and survival through the assimilation and breakdown of organic carbon sources. This review focuses on three major families of oxidoreductases that play central roles in fungal carbon metabolism: PF00248, PF00106, and PF00107. These enzymes are not only crucial for energy production but also for the synthesis and breakdown of complex organic molecules. PF00248, the aldo-keto reductase superfamily, is involved in a wide range of redox reactions, while PF00106 includes diverse short-chain reductase/dehydrogenases important for fungal growth and environmental adaptation. PF00107 comprises zinc-binding dehydrogenases with a role in processes such as alcohol metabolism and zinc uptake. These oxidoreductases are evolutionarily conserved with respect to amino acid sequence motifs but show significant genetic diversity across fungal species, reflecting their ecological adaptability and metabolic versatility. Understanding the functions within these enzyme families can enhance the design of efficient fungal cell factories for biotechnological applications, such as biofuel and biochemical production from plant biomass. This review highlights the importance of these enzymes in central carbon metabolism and their potential for industrial applications.
