Properties and Applications of Extremozymes from Deep-Sea Extremophilic Microorganisms: A Mini Review

Cold-active microbial enzymes and their biotechnological applications

Microorganisms known as psychrophiles/psychrotrophs, which survive in cold climates, constitute majority of the biosphere on Earth. Their capability to produce cold-active enzymes along with other distinguishing characteristics allows them to survive in the cold environments. Due to the relative ease of large-scale production compared to enzymes from plants and animals, commercial uses of microbial enzyme are alluring. The ocean depths, polar, and alpine regions, which make up over 85% of the planet, are inhabited to cold ecosystems. Microbes living in these regions are important for their metabolic contribution to the ecosphere as well as for their enzymes, which may have potential industrial applications. Cold-adapted microorganisms are a possible source of cold-active enzymes that have high catalytic efficacy at low and moderate temperatures at which homologous mesophilic enzymes are not active. Cold-active enzymes can be used in a variety of biotechnological processes, including food processing, additives in the detergent and food industries, textile industry, waste-water treatment, biopulping, environmental bioremediation in cold climates, biotransformation, and molecular biology applications with great potential for energy savings. Genetically manipulated strains that are suitable for producing a particular cold-active enzyme would be crucial in a variety of industrial and biotechnological applications. The potential advantage of cold-adapted enzymes will probably lead to a greater annual market than for thermo-stable enzymes in the near future. This review includes latest updates on various microbial source of cold-active enzymes and their biotechnological applications.

Agarose biodegradation by deep-sea bacterium Vibrio natriegens WPAGA4 with the agarases through horizontal gene transfer

This study aimed to reveal the importance of horizontal gene transfer (HGT) for the agarose-degrading ability and the related degradation pathway of a deep-sea bacterium Vibrio natriegens WPAGA4, which was rarely reported in former works. A total of four agarases belonged to the GH50 family, including Aga3418, Aga3419, Aga3420, and Aga3472, were annotated and expressed in Escherichia coli cells. The agarose degradation products of Aga3418, Aga3420, and Aga3472 were neoagarobiose, while those of Aga3419 were neoagarobiose and neoagarotetraose. The RT-qPCR analysis showed that the expression level ratio of Aga3418, Aga3419, Aga3420, and Aga3472 was stable at about 1:1:1.5:2.5 during the degradation, which indicated the optimal expression level ratio of the agarases for agarose degradation by V. natriegens WPAGA4. Based on the genomic information, three of four agarases and other agarose-degrading related genes were in a genome island with a G + C content that was obviously lower than that of the whole genome of V. natriegens WPAGA4, indicating that these agarose-degrading genes were required through HGT. Our results demonstrated that the expression level ratio instead of the expression level itself of agarase genes was crucial for agarose degradation by V. natriegens WPAGA4, and HGT occurred in the deep-sea environment, thereby promoting the deep-sea carbon cycle and providing a reference for studying the evolution and transfer pathways of agar-related genes.

Nocardiopsis synnemataformans NBRM9, an extremophilic actinomycete producing extremozyme cellulase, using lignocellulosic agro-wastes and its biotechnological applications

Actinomycetes are an attractive source of lignocellulose-degrading enzymes. The search for actinomycetes producing extremozyme cellulase using cheap lignocellulosic waste remains a priority goal of enzyme research. In this context, the extremophilic actinomycete NBRM9 showed promising cellulolytic activity in solid and liquid assays. This actinomycete was identified as Nocardiopsis synnemataformans based on its phenotypic characteristics alongside phylogenetic analyses of 16S rRNA gene sequencing (OQ380604.1). Using bean straw as the best agro-waste, the production of cellulase from this strain was statistically optimized using a response surface methodology, with the maximum activity (13.20 U/mL) achieved at an incubation temperature of 40 °C, a pH of 9, an incubation time of 7 days, and a 2% substrate concentration. The partially purified cellulase (PPC) showed promising activity and stability over a wide range of temperatures (20-90 °C), pH values (3-11), and NaCl concentrations (1-19%), with optimal activity at 50 °C, pH 9.0, and 10% salinity. Under these conditions, the enzyme retained >95% of its activity, thus indicating its extremozyme nature. The kinetics of cellulase showed that it has a Vmax of 20.19 ± 1.88 U/mL and a Km of 0.25 ± 0.07 mM. The immobilized PPC had a relative activity of 69.58 ± 0.13%. In the in vitro microtiter assay, the PPC was found to have a concentration-dependent anti-biofilm activity (up to 85.15 ± 1.60%). Additionally, the fermentative conversion of the hydrolyzed bean straw by Saccharomyces cerevisiae (KM504287.1) amounted to 65.80 ± 0.52% of the theoretical ethanol yield. Overall, for the first time, the present work reports the production of extremozymatic (thermo, alkali-, and halo-stable) cellulase from N. synnemataformans NBRM9. Therefore, this strain is recommended for use as a biotool in many lignocellulosic-based applications operating under harsh conditions.

Characterization of Chilean hot spring-origin Staphylococcus sp. BSP3 produced exopolysaccharide as biological additive

A type of high molecular weight bioactive polymers called exopolysaccharides (EPS) are produced by thermophiles, the extremophilic microbes that thrive in acidic environmental conditions of hot springs with excessively warm temperatures. Over time, EPS became important as natural biotechnological additives because of their noncytotoxic, emulsifying, antioxidant, or immunostimulant activities. In this article, we unravelled a new EPS produced by Staphylococcus sp. BSP3 from an acidic (pH 6.03) San Pedro hot spring (38.1 °C) located in the central Andean mountains in Chile. Several physicochemical techniques were performed to characterize the EPS structure including Scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS), Atomic Force Microscopy (AFM), High-Performance Liquid Chromatography (HPLC), Gel permeation chromatography (GPC), Fourier Transform Infrared Spectroscopy (FTIR), 1D Nuclear Magnetic Resonance (NMR), and Thermogravimetric analysis (TGA). It was confirmed that the amorphous surface of the BSP3 EPS, composed of rough pillar-like nanostructures, is evenly distributed. The main EPS monosaccharide constituents were mannose (72%), glucose (24%) and galactose (4%). Also, it is a medium molecular weight (43.7 kDa) heteropolysaccharide. NMR spectroscopy demonstrated the presence of a [→ 6)-⍺-D-Manp-(1 → 6)-⍺-D-Manp-(1 →] backbone 2-O substituted with 1-⍺-D-Manp. A high thermal stability of EPS (287 °C) was confirmed by TGA analysis. Emulsification, antioxidant, flocculation, water-holding (WHC), and oil-holding (OHC) capacities are   also studied for biotechnological industry applications. The results demonstrated that BSP3 EPS could be used as a biodegradable material for different purposes, like flocculation and natural additives in product formulation.

Metagenome-assembled genomes reveal carbohydrate degradation and element metabolism of microorganisms inhabiting Tengchong hot springs, China

A hot spring is a distinctive aquatic environment that provides an excellent system to investigate microorganisms and their function in elemental cycling processes. Previous studies of terrestrial hot springs have been mostly focused on the microbial community, one special phylum or category, or genes involved in a particular metabolic step, while little is known about the overall functional metabolic profiles of microorganisms inhabiting the terrestrial hot springs. Here, we analyzed the microbial community structure and their functional genes based on metagenomic sequencing of six selected hot springs with different temperature and pH conditions. We sequenced a total of 11 samples from six hot springs and constructed 162 metagenome-assembled genomes (MAGs) with completeness above 70% and contamination lower than 10%. Crenarchaeota, Euryarchaeota and Aquificae were found to be the dominant phyla. Functional annotation revealed that bacteria encode versatile carbohydrate-active enzymes (CAZYmes) for the degradation of complex polysaccharides, while archaea tend to assimilate C1 compounds through carbon fixation. Under nitrogen-deficient conditions, there were correspondingly fewer genes involved in nitrogen metabolism, while abundant and diverse set of genes participating in sulfur metabolism, particularly those associated with sulfide oxidation and thiosulfate disproportionation. In summary, archaea and bacteria residing in the hot springs display distinct carbon metabolism fate, while sharing the common energy preference through sulfur metabolism. Overall, this research contributes to a better comprehension of biogeochemistry of terrestrial hot springs.

Insights into Genomic Features and Potential Biotechnological Applications of Bacillus halotolerans Strain HGR5

Algeria is one of the wealthiest countries in terms of hydrothermal sources, with more than two hundred hot springs. However, diverse and little-described microbial communities colonize these habitats, making them an intriguing research subject. This work reports the isolation of bacteria from two hot springs water samples in northeastern Algeria, evaluating their enzymatic activities and effect on plant pathogens. Out of the obtained 72 bacterial isolates and based on the 16S rRNA gene sequence analysis, the strain HGR5 belonging to Bacillus halotolerans had the most interesting activity profile. Interestingly, HGR5 was substantially active against Fusarium graminearum, Phytophthora infestans, and Alternaria alternata. Furthermore, this strain presented a high ability to degrade casein, Tween 80, starch, chitin, cellulose, and xylan. The genome sequence of HGR5 allowed taxonomic validation and screening of specific genetic traits, determining its antagonistic and enzymatic activities. Genome mining revealed that strain HGR5 encloses several secondary metabolite biosynthetic gene clusters (SM-BGCs) involved in metabolite production with antimicrobial properties. Thus, antimicrobial metabolites included bacillaene, fengycin, laterocidine, bacilysin, subtilosin, bacillibactin, surfactin, myxovirescin, dumulmycin, and elansolid A1. HGR5 strain genome was also mined for CAZymes associated with antifungal activity. Finally, the HGR5 strain exhibited the capacity to degrade polycaprolactone (PCL), a model substrate for polyester biodegradation. Overall, these results suggest that this strain may be a promising novel biocontrol agent with interesting plastic-degradation capability, opening the possibilities of its use in various biotechnological applications.

Lignocellulolytic extremozymes and their biotechnological applications

Lignocellulolytic enzymes are used in different industrial and environmental processes. The rigorous operating circumstances of these industries, however, might prevent these enzymes from performing as intended. On the other side, extremozymes are enzymes produced by extremophiles that can function in extremely acidic or basic; hot or cold; under high or low salinity conditions. These severe conditions might denature the normal enzymes that are produced by mesophilic microorganisms. The increased stability of these enzymes has been contributed to a number of conformational modifications in their structures. These modifications may result from a few amino acid substitutions, an improved hydrophobic core, the existence of extra ion pairs and salt bridges, an increase in compactness, or an increase in positively charged amino acids. These enzymes are the best option for industrial and bioremediation activities that must be carried out under difficult conditions due to their improved stability. The review, therefore, discusses lignocellulolytic extremozymes, their structure and mechanisms along with industrial and biotechnological applications.

Release of cell-free enzymes by marine pelagic fungal strains

Fungi are ubiquitous organisms that secrete different enzymes to cleave large molecules into smaller ones so that can then be assimilated. Recent studies suggest that fungi are also present in the oceanic water column harboring the enzymatic repertoire necessary to cleave carbohydrates and proteins. In marine prokaryotes, the cell-free fraction is an important contributor to the oceanic extracellular enzymatic activities (EEAs), but the release of cell-free enzymes by marine fungi remains unknown. Here, to study the cell-free enzymatic activities of marine fungi and the potential influence of salinity on them, five strains of marine fungi that belong to the most abundant pelagic phyla (Ascomycota and Basidiomycota), were grown under non-saline and saline conditions (0 g/L and 35 g/L, respectively). The biomass was separated from the medium by filtration (0.2 μm), and the filtrate was used to perform fluorogenic enzymatic assays with substrate analogues of carbohydrates, lipids, organic phosphorus, sulfur moieties, and proteins. Kinetic parameters such as maximum velocity (Vmax) and half-saturation constant (Km) were obtained. The species studied were able to release cell-free enzymes, and this represented up to 85.1% of the respective total EEA. However, this differed between species and enzymes, with some of the highest contributions being found in those with low total EEA, with some exceptions. This suggests that some of these contributions to the enzymatic pool might be minimal compared to those with higher total EEA. Generally, in the saline medium, the release of cell-free enzymes degrading carbohydrates was reduced compared to the non-saline medium, but those degrading lipids and sulfur moieties were increased. For the remaining substrates, there was not a clear influence of the salinity. Taken together, our results suggest that marine fungi are potential contributors to the oceanic dissolved (i.e., cell-free) enzymatic pool. Our results also suggest that, under salinity changes, a potential effect of global warming, the hydrolysis of organic matter by marine fungal cell-free enzymes might be affected and hence, their potential contribution to the oceanic biogeochemical cycles.

Design of a multi-band Raman tweezers objective for in situ studies of deep-sea microorganisms

The investigation of deep-sea microorganisms holds immense significance and value in advancing the fields of life sciences, biotechnology, and environmental conservation. However, the current lack of specialized underwater objectives specifically designed for in situ studies of deep-sea microorganisms hampers progress in this area. To address this limitation, we present the design of a multi-band Raman tweezer objective tailored for deep-sea environments. The objective is integrated into a high-pressure chamber capable of withstanding depths up to 1.5 km, enabling in situ microscopic imaging, optical tweezer capture, and Raman detection of deep-sea microorganisms. Through meticulous structural optimization, meticulous material selection, and thorough mechanical analysis of the underwater optical window, the objective exhibits remarkable attributes such as multi-band functionality, extended working distance, and high numerical aperture. Our design yields image quality near the diffraction limit, successfully achieving flat-field and apochromatic performance in each respective wavelength bands. Moreover, the tolerance analysis demonstrates that the full-field root mean square (RMS) wave aberration approaches λ/14, effectively meeting the demands of manufacturing and practical applications. This objective lens constitutes a vital tool for the in situ exploration of deep-sea microorganisms.

Enhanced remediation of oil-contaminated intertidal sediment by bacterial consortium of petroleum degraders and biosurfactant producers

Oil pollution in intertidal zones is an important environmental issue that has serious adverse effects on coastal ecosystems. This study investigated the efficacy of a bacterial consortium constructed from petroleum degraders and biosurfactant producers in the bioremediation of oil-polluted sediment. Inoculation of the constructed consortium significantly enhanced the removal of C₈-C₄₀n-alkanes (80.2 ± 2.8% removal efficiency) and aromatic compounds (34.4 ± 10.8% removal efficiency) within 10 weeks. The consortium played dual functions of petroleum degradation and biosurfactant production, greatly improving microbial growth and metabolic activities. Real-time quantitative polymerase chain reaction (PCR) showed that the consortium markedly increased the proportions of indigenous alkane-degrading populations (up to 3.88-times higher than that of the control treatment). Microbial community analysis demonstrated that the exogenous consortium activated the degradation functions of indigenous microflora and promoted synergistic cooperation among microorganisms. Our findings indicated that supplementation of a bacterial consortium of petroleum degraders and biosurfactant producers is a promising bioremediation strategy for oil-polluted sediments.

Exploring Oxidoreductases from Extremophiles for Biosynthesis in a Non-Aqueous System

Organic solvent tolerant oxidoreductases are significant for both scientific research and biomanufacturing. However, it is really challenging to obtain oxidoreductases due to the shortages of natural resources and the difficulty to obtained it via protein modification. This review summarizes the recent advances in gene mining and structure-functional study of oxidoreductases from extremophiles for non-aqueous reaction systems. First, new strategies combining genome mining with bioinformatics provide new insights to the discovery and identification of novel extreme oxidoreductases. Second, analysis from the perspectives of amino acid interaction networks explain the organic solvent tolerant mechanism, which regulate the discrete structure-functional properties of extreme oxidoreductases. Third, further study by conservation and co-evolution analysis of extreme oxidoreductases provides new perspectives and strategies for designing robust enzymes for an organic media reaction system. Furthermore, the challenges and opportunities in designing biocatalysis non-aqueous systems are highlighted.

Marine enzymes: Classification and application in various industries

Oceans are regarded as a plentiful and sustainable source of biological compounds. Enzymes are a group of marine biomaterials that have recently drawn more attention because they are produced in harsh environmental conditions such as high salinity, extensive pH, a wide temperature range, and high pressure. Hence, marine-derived enzymes are capable of exhibiting remarkable properties due to their unique composition. In this review, we overviewed and discussed characteristics of marine enzymes as well as the sources of marine enzymes, ranging from primitive organisms to vertebrates, and presented the importance, advantages, and challenges of using marine enzymes with a summary of their applications in a variety of industries. Current biotechnological advancements need the study of novel marine enzymes that could be applied in a variety of ways. Resources of marine enzyme can benefit greatly for biotechnological applications duo to their biocompatible, ecofriendly and high effectiveness. It is beneficial to use the unique characteristics offered by marine enzymes to either develop new processes and products or improve existing ones. As a result, marine-derived enzymes have promising potential and are an excellent candidate for a variety of biotechnology applications and a future rise in the use of marine enzymes is to be anticipated.

Rio Tinto as a niche for acidophilus enzymes of industrial relevance

Lignocellulosic residues are amongst the most abundant waste products on Earth. Therefore, there is an increasing interest in the utilization of these residues for bioethanol production and for biorefineries to produce compounds of industrial interest. Enzymes that breakdown cellulose and hemicellulose into oligomers and monosaccharides are required in these processes and cellulolytic enzymes with optimum activity at a low pH area are desirable for industrial processes. Here, we explore the fungal biodiversity of Rıo Tinto, the largest acidic ecosystem on Earth, as far as the secretion of cellulolytic enzymes is concerned. Using colorimetric and industrial substrates, we show that a high proportion of the fungi present in this extremophilic environment secrete a wide range of enzymes that are able to hydrolyze cellulose and hemicellulose at acidic pH (4.5-5). Shotgun proteomic analysis of the secretomes of some of these fungi has identified different cellulases and hemicellulolytic enzymes as well as a number of auxiliary enzymes. Supplementation of pre-industrial cocktails from Myceliophtora with Rio Tinto secretomes increased the amount of monosaccharides released from corn stover or sugar cane straw. We conclude that the Rio Tinto fungi display a good variety of hydrolytic enzymes with high industrial potential.

Draft genome sequence of Joostella atrarenae M1-2T with cellulolytic and hemicellulolytic ability

The halophilic genus Joostella is one of the least-studied genera in the family of Flavobacteriaceae. So far, only two species were taxonomically identified with limited genomic analysis in the aspect of application has been reported. Joostella atrarenae M1-2T was previously isolated from a seashore sample and it is the second discovered species of the genus Joostella. In this project, the genome of J. atrarenae M1-2T was sequenced using NovaSeq 6000. The final assembled genome is comprised of 71 contigs, a total of 3,983,942 bp, a GC ratio of 33.2%, and encoded for 3,416 genes. The 16S rRNA gene sequence of J. atrarenae M1-2T shows 97.3% similarity against J. marina DSM 19592T. Genome-genome comparison between the two strains by ANI, dDDH, AAI, and POCP shows values of 80.8%, 23.3%, 83.4%, and 74.1% respectively. Pan-genome analysis shows that strain M1-2T and J. marina DSM 19592T shared a total of 248 core genes. Taken together, strain M-2T and J. marina DSM 19592T belong to the same genus but are two different species. CAZymes analysis revealed that strain M1-2T harbors 109 GHs, 40 GTs, 5 PLs, 9 CEs, and 6 AAs. Among these CAZymes, while 5 genes are related to cellulose degradation, 12 and 24 genes are found to encode for xylanolytic enzymes and other hemicellulases that involve majorly in the side chain removal of the lignocellulose structure, respectively. Furthermore, both the intracellular and extracellular crude extracts of strain M1-2T exhibited enzymatic activities against CMC, xylan, pNPG, and pNPX substrates, which corresponding to endoglucanase, xylanase, β-glucosidase, and β-xylosidase, respectively. Collectively, description of genome coupled with the enzyme assay results demonstrated that J. atrarenae M1-2T has a role in lignocellulosic biomass degradation, and the strain could be useful for lignocellulosic biorefining.

Generation of a high quality library of bioactive filamentous actinomycetes from extreme biomes using a culture-based bioprospecting strategy

Introduction

Filamentous actinomycetes, notably members of the genus Streptomyces, remain a rich source of new specialized metabolites, especially antibiotics. In addition, they are also a valuable source of anticancer and biocontrol agents, biofertilizers, enzymes, immunosuppressive drugs and other biologically active compounds. The new natural products needed for such purposes are now being sought from extreme habitats where harsh environmental conditions select for novel strains with distinctive features, notably an ability to produce specialized metabolites of biotechnological value.

Methods

A culture-based bioprospecting strategy was used to isolate and screen filamentous actinomycetes from three poorly studied extreme biomes. Actinomycetes representing different colony types growing on selective media inoculated with environmental suspensions prepared from high-altitude, hyper-arid Atacama Desert soils, a saline soil from India and from a Polish pine forest soil were assigned to taxonomically predictive groups based on characteristic pigments formed on oatmeal agar. One hundred and fifteen representatives of the colour-groups were identified based on 16S rRNA gene sequences to determine whether they belonged to validly named or to putatively novel species. The antimicrobial activity of these isolates was determined using a standard plate assay. They were also tested for their capacity to produce hydrolytic enzymes and compounds known to promote plant growth while representative strains from the pine forest sites were examined to determine their ability to inhibit the growth of fungal and oomycete plant pathogens.

Results

Comparative 16S rRNA gene sequencing analyses on isolates representing the colour-groups and their immediate phylogenetic neighbours showed that most belonged to either rare or novel species that belong to twelve genera. Representative isolates from the three extreme biomes showed different patterns of taxonomic diversity and characteristic bioactivity profiles. Many of the isolates produced bioactive compounds that inhibited the growth of one or more strains from a panel of nine wild strains in standard antimicrobial assays and are known to promote plant growth. Actinomycetes from the litter and mineral horizons of the pine forest, including acidotolerant and acidophilic strains belonging to the genera Actinacidiphila, Streptacidiphilus and Streptomyces, showed a remarkable ability to inhibit the growth of diverse fungal and oomycete plant pathogens.

Discussion

It can be concluded that selective isolation and characterization of dereplicated filamentous actinomyctes from several extreme biomes is a practical way of generating high quality actinomycete strain libraries for agricultural, industrial and medical biotechnology.

A Review on Psychrophilic β-D-Galactosidases and Their Potential Applications

The majority of the Earth's ecosystem is frigid and frozen, which permits a vast range of microbial life forms to thrive by triggering physiological responses that allow them to survive in cold and frozen settings. The apparent biotechnology value of these cold-adapted enzymes has been targeted. Enzymes' market size was around USD 6.3 billion in 2017 and will witness growth at around 6.8% CAGR up to 2024 owing to shifting consumer preferences towards packaged and processed foods due to the rising awareness pertaining to food safety and security reported by Global Market Insights (Report ID-GMI 743). Various firms are looking for innovative psychrophilic enzymes in order to construct more effective biochemical pathways with shorter reaction times, use less energy, and are ecologically acceptable. D-Galactosidase catalyzes the hydrolysis of the glycosidic oxygen link between the terminal non-reducing D-galactoside unit and the glycoside molecule. At refrigerated temperature, the stable structure of psychrophile enzymes adjusts for the reduced kinetic energy. It may be beneficial in a wide variety of activities such as pasteurization of food, conversion of biomass, biological role of biomolecules, ambient biosensors, and phytoremediation. Recently, psychrophile enzymes are also used in claning the contact lens. β-D-Galactosidases have been identified and extracted from yeasts, fungi, bacteria, and plants. Conventional (hydrolyzing activity) and nonconventional (non-hydrolytic activity) applications are available for these enzymes due to its transgalactosylation activity which produce high value-added oligosaccharides. This review content will offer new perspectives on cold-active β-galactosidases, their source, structure, stability, and application.

Purification and characterization of cold-adapted and salt-tolerant dextranase from Cellulosimicrobium sp. THN1 and its potential application for treatment of dental plaque

The cold-adapted and/or salt-tolerant enzymes from marine microorganisms were confirmed to be meritorious tools to enhance the efficiency of biocatalysis in industrial biotechnology. We purified and characterized a dextranase CeDex from the marine bacterium Cellulosimicrobium sp. THN1. CeDex acted in alkaline pHs (7.5-8.5) and a broad temperature range (10-50°C) with sufficient pH stability and thermostability. Remarkably, CeDex retained approximately 40% of its maximal activities at 4°C and increased its activity to 150% in 4 M NaCl, displaying prominently cold adaptation and salt tolerance. Moreover, CeDex was greatly stimulated by Mg2+, Na+, Ba2+, Ca2+ and Sr2+, and sugarcane juice always contains K+, Ca2+, Mg2+ and Na+, so CeDex will be suitable for removing dextran in the sugar industry. The main hydrolysate of CeDex was isomaltotriose, accompanied by isomaltotetraose, long-chain IOMs, and a small amount of isomaltose. The amino acid sequence of CeDex was identified from the THN1 genomic sequence by Nano LC-MS/MS and classified into the GH49 family. Notably, CeDex could prevent the formation of Streptococcus mutans biofilm and disassemble existing biofilms at 10 U/ml concentration and would have great potential to defeat biofilm-related dental caries.

Improving the Specific Activity and Thermostability of Psychrophilic Xylosidase AX543 by Comparative Mutagenesis

Improving the specific activity and thermostability of psychrophilic xylosidase is important for improving its enzymatic performance and promoting its industrial application. Herein, a psychrophilic xylosidase AX543 exhibited activity in the temperature range between 0 and 35 °C, with optimum activity at 20 °C, which is lower than that of other reported psychrophilic xylosidases. The thermostability, specific activity, and catalytic efficiency of the site-directed variants G110S, Q201R, and L2 were significantly enhanced, without affecting the optimal reaction temperature. Comparative protein structural analysis and molecular dynamics simulation indicated that these improvements might be the result of the increased hydrogen bonds interaction and improved structural rigidity. Furthermore, homologous module substitution with four segments demonstrated that the psychrophilic characteristics of AX543 are the results of the whole protein structure, and the C-terminal segment A4 appears to be more essential in determining psychrophilic characteristics, exhibiting potentiality to produce more psychrophilic xylosidases. This study provides valuable structural information on psychrophilic xylosidases and also offers attractive modification strategies to modify catalytic activity, thermostability, and optimal reaction temperature.

Structural determination of the lipid A from the deep-sea bacterium Zunongwangia profunda SM-A87: a small-scale approach

Zunongwangia profunda SM-A87 is a deep-sea sedimentary bacterium from the phylum Bacteroidetes, representing a new genus of Flavobacteriaceae. It was previously investigated for its capability of yielding high quantities of capsular polysaccharides (CPS) with interesting rheological properties, including high viscosity and tolerance to high salinities and temperatures. However, as a Gram-negative, Z. profunda SM-A87 also expresses lipopolysaccharides (LPS) as the main components of the external leaflet of its outer membrane. Here, we describe the isolation and characterization of the glycolipid part of this LPS, i.e. the lipid A, which was achieved by-passing the extraction procedure of the full LPS and by working on the ethanol precipitation product, which contained both the CPS fraction and bacterial cells. To this aim a dual approach was adopted and all analyses confirmed the isolation of Z. profunda SM-A87 lipid A that turned out to be a blend of species with high levels of heterogeneity both in the acylation and phosphorylation pattern, as well as in the hydrophilic backbone composition. Mono-phosphorylated tetra- and penta-acylated lipid A species were identified and characterized by a high content of branched, odd-numbered, and unsaturated fatty acid chains as well as, for some species, by the presence of a hybrid disaccharide backbone.

A global horizon scan of issues impacting marine and coastal biodiversity conservation

The biodiversity of marine and coastal habitats is experiencing unprecedented change. While there are well-known drivers of these changes, such as overexploitation, climate change and pollution, there are also relatively unknown emerging issues that are poorly understood or recognized that have potentially positive or negative impacts on marine and coastal ecosystems. In this inaugural Marine and Coastal Horizon Scan, we brought together 30 scientists, policymakers and practitioners with transdisciplinary expertise in marine and coastal systems to identify new issues that are likely to have a significant impact on the functioning and conservation of marine and coastal biodiversity over the next 5-10 years. Based on a modified Delphi voting process, the final 15 issues presented were distilled from a list of 75 submitted by participants at the start of the process. These issues are grouped into three categories: ecosystem impacts, for example the impact of wildfires and the effect of poleward migration on equatorial biodiversity; resource exploitation, including an increase in the trade of fish swim bladders and increased exploitation of marine collagens; and new technologies, such as soft robotics and new biodegradable products. Our early identification of these issues and their potential impacts on marine and coastal biodiversity will support scientists, conservationists, resource managers and policymakers to address the challenges facing marine ecosystems.

Sponge–Microbial Symbiosis and Marine Extremozymes: Current Issues and Prospects

Marine microorganisms have great potential for producing extremozymes. They enter useful relationships like many other organisms in the marine habitat. Sponge–microbial symbiosis enables both sponges and microorganisms to mutually benefit each other while performing their activities within the ecosystem. Sponges, because of their nature as marine cosmopolitan benthic epifaunas and filter feeders, serve as a host for many extremophilic marine microorganisms. Potential extremozymes from microbial symbionts are largely dependent on their successful relationship. Extremozymes have found relevance in food processing, bioremediation, detergent, and drug production. Species diversity approach, industrial-scale bioremediation, integrative bioremediation software, government and industrial support are considered. The high cost of sampling, limited research outcomes, low species growth in synthetic media, laborious nature of metagenomics projects, difficulty in the development of synthetic medium, limited number of available experts, and technological knowhow are current challenges. The unique properties of marine extremozymes underpin their application in industry and biotechnological processes. There is therefore an urgent need for the development of cost-effective methods with government and industry support.

Extremophilic lipases for industrial applications: A general review

With industrialization and development in modern science enzymes and their applications increased widely. There is always a hunt for new proficient enzymes with novel properties to meet specific needs of various industrial sectors. Along with the high efficiency, the green and eco-friendly side of enzymes attracts human attention, as they form a true answer to counter the hazardous and toxic conventional industrial catalyst. Lipases have always earned industrial attention due to the broad range of hydrolytic and synthetic reactions they catalyse. When these catalytic properties get accompanied by features like temperature stability, pH stability, and solvent stability lipases becomes an appropriate tool for use in many industrial processes. Extremophilic lipases offer the same, thermostable: hot and cold active thermophilic and psychrophilic lipases, acid and alkali resistant and active acidophilic and alkaliphilic lipases, and salt tolerant halophilic lipases form excellent biocatalyst for detergent formulations, biofuel synthesis, ester synthesis, food processing, pharmaceuticals, leather, and paper industry. An interesting application of these lipases is in the bioremediation of lipid waste in harsh environments. The review gives a brief account on various extremophilic lipases with emphasis on thermophilic, psychrophilic, halophilic, alkaliphilic, and acidophilic lipases, their sources, biochemical properties, and potential applications in recent decades.

A Review on Bioactive Compounds from Marine-Derived Chaetomium Species

Filamentous marine fungi have proven to be a plentiful source of new natural products. Chaetomium, a widely distributed fungal genus in the marine environment, has gained much interest within the scientific community. In the last 20 years, many potential secondary metabolites have been detected from marine-derived Chaetomium. In this review, we attempt to provide a comprehensive summary of the natural products produced by marine-derived Chaetomium species. A total of 122 secondary metabolites that were described from 2001 to 2021 are covered. The structural diversity of the compounds, along with details of the sources and relevant biological properties are also provided, while the relationships between structures and their bioactivities are discussed. It is our expectation that this review will be of benefit to drug development and innovation.

Biomolecules under Pressure: Phase Diagrams, Volume Changes, and High Pressure Spectroscopic Techniques

Pressure is an equally important thermodynamical parameter as temperature. However, its importance is often overlooked in the biophysical and biochemical investigations of biomolecules and biological systems. This review focuses on the application of high pressure (>100 MPa = 1 kbar) in biology. Studies of high pressure can give insight into the volumetric aspects of various biological systems; this information cannot be obtained otherwise. High-pressure treatment is a potentially useful alternative method to heat-treatment in food science. Elevated pressure (up to 120 MPa) is present in the deep sea, which is a considerable part of the biosphere. From a basic scientific point of view, the application of the gamut of modern spectroscopic techniques provides information about the conformational changes of biomolecules, fluctuations, and flexibility. This paper reviews first the thermodynamic aspects of pressure science, the important parameters affecting the volume of a molecule. The technical aspects of high pressure production are briefly mentioned, and the most common high-pressure-compatible spectroscopic techniques are also discussed. The last part of this paper deals with the main biomolecules, lipids, proteins, and nucleic acids: how they are affected by pressure and what information can be gained about them using pressure. I I also briefly mention a few supramolecular structures such as viruses and bacteria. Finally, a subjective view of the most promising directions of high pressure bioscience is outlined.

Optimization of Lipopeptide Biosurfactant Production by Salibacterium sp. 4CTb in Batch Stirred-Tank Bioreactors

Halophilic microorganisms are potentially capable as platforms to produce low-cost biosurfactants. However, the robustness of bioprocesses is still a challenge and, therefore, it is essential to understand the effects of microbiological culture conditions through bioreactor engineering. Based on a design of experiments (DOE) and a response surface methodology (RSM) tailored and taken from the literature, the present work focuses on the evaluation of a composite central design (CCD) under batch cultures in stirred-tank bioreactors with the halophilic bacteria Salibacterium sp. 4CTb in order to determine the operative conditions that favor mass transfer and optimize the production of a lipopeptide. The results obtained showed profiles highlighting the most favorable culture conditions, which lead to an emulsification index (E₂₄%) higher than 70%. Moreover, through the behavior of dissolved oxygen (DO), it was possible to experimentally evaluate the higher volumetric coefficient of mass transfer in the presence of lipopeptide (k_La = 31 1/h) as a key criterion for the synthesis of the biosurfactant on further cell expansion.

Assessing the inhibitory activity of culture supernatants against foodborne pathogens of two psychrotrophic bacteria isolated from river trout

There is a need for new natural products with antimicrobial activity to treat multidrug resistant bacteria that can cause human illness. Some of them are foodborne pathogens. Two different Gram-negative psychrotrophic strains were isolated from healthy trout river samples (Salmotrutta). Based on phenotypic characterization, proteomics, genotyping and phylogenetic analyses of 16 rRNA gene, strains TCPS12 and TCPS13 were identified as Shewanellabaltica and Pseudomonasfragi, respectively. Both of them produced an exopolysaccharide that showed antimicrobial activity against four foodborne pathogens. P. fragi supernatant (AS13) showed higher antimicrobial activity than S. baltica supernatant (AS12) against all tested pathogens. The stability of the antimicrobial activity of AS13 was assessed against Enterococcus faecalis ATCC 29212 under different conditions. This solution was stable when exposed for 30 min to temperatures ranging from 40 to 100 °C. In addition, it retained its activity within a pH range of 2–8 during 2 h of incubation, showing higher activity at pH 6. Serine proteases and α-amylase inactivated significantly the antimicrobial activity of AS13, suggesting that the active molecule could most likely be a glycoprotein. These products are interesting for their possible application as biopreservatives in the food industry.

Industrial Biotechnology Based on Enzymes From Extreme Environments

Biocatalysis is crucial for a green, sustainable, biobased economy, and this has driven major advances in biotechnology and biocatalysis over the past 2 decades. There are numerous benefits to biocatalysis, including increased selectivity and specificity, reduced operating costs and lower toxicity, all of which result in lower environmental impact of industrial processes. Most enzymes available commercially are active and stable under a narrow range of conditions, and quickly lose activity at extremes of ion concentration, temperature, pH, pressure, and solvent concentrations. Extremophilic microorganisms thrive under extreme conditions and produce robust enzymes with higher activity and stability under unconventional circumstances. The number of extremophilic enzymes, or extremozymes, currently available are insufficient to meet growing industrial demand. This is in part due to difficulty in cultivation of extremophiles in a laboratory setting. This review will present an overview of extremozymes and their biotechnological applications. Culture-independent and genomic-based methods for study of extremozymes will be presented.

Evaluation of a Thermophilic, Psychrostable, and Heavy Metal-Resistant Red Sea Brine Pool Esterase

Lipolytic enzymes catalyze the hydrolysis and synthesis of ester compounds. They are valuable in the pulp, food, and textile industries. This study aims to comprehensively evaluate the extreme properties of a hormone-sensitive lipase (EstATII-TM) isolated from the Red Sea Atlantis II brine pool. EstATII-TM was cloned, expressed, and its biochemical activities were assessed under different conditions. EstATII-TM catalytic properties and resistance to different metal ions were compared to commercial thermophilic esterases under different temperatures. Phylogenetically, EstATII-TM was assigned to the GDSAG motif subfamily of hormone-sensitive lipase. The optimal enzyme activity was evident at a temperature of 30 °C and pH 7–8. The enzyme retained 84.9% of its activity at 0.5 M NaCl. EstATII-TM maintained 93% to 97% activity at −40 and −20 °C, respectively. EstATII-TM activity was significantly enhanced, up to 10-fold, at temperatures ranging from 45 to 65 °C in the presence of 1 mM Cu²⁺, Cd²⁺, Ba²⁺, Mn²⁺, and Zn²⁺. EstATII-TM showed superior catalytic activity and resistance-to/enhancement-by metal ions compared to two commercial thermophilic esterases. The Red Sea Atlantis II brine EstATII-TM is characterized by tolerance to high temperatures, stability to hot and cold conditions, as well as toxic heavy metal contamination, making it an ideal candidate for industrial processes.

Identification of BgP, a Cutinase-Like Polyesterase From a Deep-Sea Sponge-Derived Actinobacterium

Many marine bacteria produce extracellular enzymes that degrade complex molecules to facilitate their growth in environmental conditions that are often harsh and low in nutrients. Marine bacteria, including those inhabiting sea sponges, have previously been reported to be a promising source of polyesterase enzymes, which have received recent attention due to their potential ability to degrade polyethylene terephthalate (PET) plastic. During the screening of 51 marine bacterial isolates for hydrolytic activities targeting ester and polyester substrates, a Brachybacterium ginsengisoli B129SM11 isolate from the deep-sea sponge Pheronema sp. was identified as a polyesterase producer. Sequence analysis of genomic DNA from strain B129SM11, coupled with a genome "mining" strategy, allowed the identification of potential polyesterases, using a custom database of enzymes that had previously been reported to hydrolyze PET or other synthetic polyesters. This resulted in the identification of a putative PET hydrolase gene, encoding a polyesterase-type enzyme which we named BgP that shared high overall similarity with three well-characterized PET hydrolases-LCC, TfCut2, and Cut190, all of which are key enzymes currently under investigation for the biological recycling of PET. In silico protein analyses and homology protein modeling offered structural and functional insights into BgP, and a detailed comparison with Cut190 revealed highly conserved features with implications for both catalysis and substrate binding. Polyesterase activity was confirmed using an agar-based polycaprolactone (PCL) clearing assay, following heterologous expression of BgP in Escherichia coli. This is the first report of a polyesterase being identified from a deep-sea sponge bacterium such as Brachybacterium ginsengisoli and provides further insights into marine-derived polyesterases, an important family of enzymes for PET plastic hydrolysis. Microorganisms living in association with sponges are likely to have increased exposure to plastics and microplastics given the wide-scale contamination of marine ecosystems with these plastics, and thus they may represent a worthwhile source of enzymes for use in new plastic waste management systems. This study adds to the growing knowledge of microbial polyesterases and endorses further exploration of marine host-associated microorganisms as a potentially valuable source of this family of enzymes for PET plastic hydrolysis.

Metabolic Potential of Halophilic Filamentous Fungi—Current Perspective

Salty environments are widely known to be inhospitable to most microorganisms. For centuries salt has been used as a food preservative, while highly saline environments were considered uninhabited by organisms, and if habited, only by prokaryotic ones. Nowadays, we know that filamentous fungi are widespread in many saline habitats very often characterized also by other extremes, for example, very low or high temperature, lack of light, high pressure, or low water activity. However, fungi are still the least understood organisms among halophiles, even though they have been shown to counteract these unfavorable conditions by producing multiple secondary metabolites with interesting properties or unique biomolecules as one of their survival strategies. In this review, we focused on biomolecules obtained from halophilic filamentous fungi such as enzymes, pigments, biosurfactants, and osmoprotectants.

Perspectives on the microorganism of extreme environments and their applications

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The applications of extremophiles in various fields like biotechnology, biodegradation, bioremediation, biorefinery and astrobiology along with other industries like pharmaceuticals, food, agricultural, cosmetics, and textile.

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Further research in biodegradation, bioremediation and generation of biofuels using extremophiles is required considering the current climate crisis as it helps in reduction of environmental contamination load.

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The importance of promoting the use of extremophiles in food and agricultural industries and how extremophiles can be the key to achieving the Sustainable Development Goal of global food security.

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Keeping in mind the current global scenario with regards to the Covid-19 pandemic, our paper also focuses on the importance of by-products of extremophiles like biosurfactants in the vaccine production process.

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For advancement of the astrobiology sector, more PFA sites should be located and the extremophiles inhabiting them should be studied.

Extremophiles are organisms that can survive and thrive in conditions termed as “extreme” by human beings. Conventional methods cannot be applied under extreme conditions like temperature and pH fluctuations, high salinity, etc. for a variety of reasons. Extremophiles can function and are adapted to thrive in these environments and are sustainable, cheaper, and efficient, therefore, they serve as better alternatives to the traditional methods. They adapt to these environments with biochemical and physiological changes and produce products like extremolytes, extremozymes, biosurfactants, etc., which are found to be useful in a wide range of industries like sustainable agriculture, food, cosmetics, and pharmaceuticals. These products also play a crucial role in bioremediation, production of biofuels, biorefinery, and astrobiology. This review paper comprehensively lists out the current applications of extremophiles and their products in various industries and explores the prospects of the same. They help us understand the underlying basis of biological mechanisms exploring the boundaries of life and thus help us understand the origin and evolution of life on Earth. This helps us in the research for extra-terrestrial life and space exploration. The structure and biochemical properties of extremophiles along with any possible long-term effects of their applications need to be investigated further.

Ecological and Biotechnological Relevance of Mediterranean Hydrothermal Vent Systems

Marine hydrothermal systems are a special kind of extreme environments associated with submarine volcanic activity and characterized by harsh chemo-physical conditions, in terms of hot temperature, high concentrations of CO2 and H2S, and low pH. Such conditions strongly impact the living organisms, which have to develop adaptation strategies to survive. Hydrothermal systems have attracted the interest of researchers due to their enormous ecological and biotechnological relevance. From ecological perspective, these acidified habitats are useful natural laboratories to predict the effects of global environmental changes, such as ocean acidification at ecosystem level, through the observation of the marine organism responses to environmental extremes. In addition, hydrothermal vents are known as optimal sources for isolation of thermophilic and hyperthermophilic microbes, with biotechnological potential. This double aspect is the focus of this review, which aims at providing a picture of the ecological features of the main Mediterranean hydrothermal vents. The physiological responses, abundance, and distribution of biotic components are elucidated, by focusing on the necto-benthic fauna and prokaryotic communities recognized to possess pivotal role in the marine ecosystem dynamics and as indicator species. The scientific interest in hydrothermal vents will be also reviewed by pointing out their relevance as source of bioactive molecules.

Structural and functional adaptation in extremophilic microbial α-amylases

Maintaining stable native conformation of a protein under a given ecological condition is the prerequisite for survival of organisms. Extremophilic bacteria and archaea have evolved to adapt under extreme conditions of temperature, pH, salt, and pressure. Molecular adaptations of proteins under these conditions are essential for their survival. These organisms have the capability to maintain stable, native conformations of proteins under extreme conditions. The enzymes produced by the extremophiles are also known as extremozyme, which are used in several industries. Stability and functionality of extremozymes under varying temperature, pH, and solvent conditions are the most desirable requirement of industry. α-Amylase is one of the most important enzymes used in food, pharmaceutical, textile, and detergent industries. This enzyme is produced by diverse microorganisms including various extremophiles. Therefore, understanding its stability is important from fundamental as well as an applied point of view. Each class of extremophiles has a distinctive set of dominant non-covalent interactions which are important for their stability. Static information obtained by comparative analysis of amino acid sequence and atomic resolution structure provides information on the prevalence of particular amino acids or a group of non-covalent interactions. Protein folding studies give the information about thermodynamic and kinetic stability in order to understand dynamic aspect of molecular adaptations. In this review, we have summarized information on amino acid sequence, structure, stability, and adaptability of α-amylases from different classes of extremophiles.

Polyextremophilic Chitinolytic Activity by a Marine Strain (IG119) of Clonostachys rosea

The investigation for novel unique extremozymes is a valuable business for which the marine environment has been overlooked. The marine fungus Clonostachys rosea IG119 was tested for growth and chitinolytic enzyme production at different combinations of salinity and pH using response surface methodology. RSM modelling predicted best growth in-between pH 3.0 and 9.0 and at salinity of 0-40‱, and maximum enzyme activity (411.137 IU/L) at pH 6.4 and salinity 0‱; however, quite high production (>390 IU/L) was still predicted at pH 4.5-8.5. The highest growth and activity were obtained, respectively, at pH 4.0 and 8.0, in absence of salt. The crude enzyme was tested at different salinities (0-120‱) and pHs (2.0-13.0). The best activity was achieved at pH 4.0, but it was still high (in-between 3.0 and 12.0) at pH 2.0 and 13.0. Salinity did not affect the activity in all tested conditions. Overall, C. rosea IG119 was able to grow and produce chitinolytic enzymes under polyextremophilic conditions, and its crude enzyme solution showed more evident polyextremophilic features. The promising chitinolytic activity of IG119 and the peculiar characteristics of its chitinolytic enzymes could be suitable for several biotechnological applications (i.e., degradation of salty chitin-rich materials and biocontrol of spoiling organisms, possibly solving some relevant environmental issues).

Cloning, expression, purification and characterization of chitin deacetylase extremozyme from halophilic Bacillus aryabhattai B8W22

Chitin deacetylase (CDA) (EC 3.5.1.41) is a hydrolytic enzyme that belongs to carbohydrate esterase family 4 as per the CAZY database. The CDA enzyme deacetylates chitin into chitosan. As the marine ecosystem is a rich source of chitin, it would also hold the unexplored extremophiles. In this study, an organism was isolated from 40 m sea sediment under halophilic condition and identified as Bacillus aryabhattai B8W22 by 16S rRNA sequencing. The CDA gene from the isolate was cloned and overexpressed in E. coli Rosetta pLysS and purified using a Ni-NTA affinity chromatography. The enzyme was found active on both ethylene glycol chitin (EGC) and chitooligosaccharides (COS). The enzyme characterization study revealed, maximum enzyme velocity at one hour, optimum pH at 7 with 50 mM Tris-HCl buffer, optimum reaction temperature of 30 ºC in standard assay conditions. The co-factor screening affirmed enhancement in the enzyme activity by 142.43 ± 7.13% and 146.88 ± 4.09% with substrate EGC and COS, respectively, in the presence of 2 mM Mg2+. This activity was decreased with the inclusion of EDTA and acetate in the assay solutions. The enzyme was found to be halotolerant; the relative activity increased to 116.98 ± 3.87% and 118.70 ± 0.98% with EGC and COS as substrates in the presence of 1 M NaCl. The enzyme also demonstrated thermo-stability, retaining 87.27 ± 2.85% and 94.08 ± 0.92% activity with substrate EGC and COS, respectively, upon treatment at 50 ºC for 24 h. The kinetic parameters K m, V max, and K cat were 3.06E-05 µg mL-1, 3.06E + 01 µM mg-1 min-1 and 3.27E + 04 s-1, respectively, with EGC as the substrate and 7.14E-07 µg mL-1, 7.14E + 01 µM mg-1 min-1 and 1.40E + 06 s-1, respectively, with COS as the substrate. The enzyme was found to be following Michaelis-Menten kinetics with both the polymeric and oligomeric substrates. In recent years, enzymatic conversion of chitosan is gaining importance due to its known pattern of deacetylation and reproducibility. Thus, this BaCDA extremozyme could be used for industrial production of chitosan polymer as well as chitosan oligosaccharides for biomedical application.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03073-3.

Novel Enzymes From the Red Sea Brine Pools: Current State and Potential

The Red Sea is a marine environment with unique chemical characteristics and physical topographies. Among the various habitats offered by the Red Sea, the deep-sea brine pools are the most extreme in terms of salinity, temperature and metal contents. Nonetheless, the brine pools host rich polyextremophilic bacterial and archaeal communities. These microbial communities are promising sources for various classes of enzymes adapted to harsh environments - extremozymes. Extremozymes are emerging as novel biocatalysts for biotechnological applications due to their ability to perform catalytic reactions under harsh biophysical conditions, such as those used in many industrial processes. In this review, we provide an overview of the extremozymes from different Red Sea brine pools and discuss the overall biotechnological potential of the Red Sea proteome.

Screening and isolation of microbes from a Mud Community of Ischia Island Thermal Springs: preliminary analysis of a bioactive compound

Introduction

Balneotherapy centers of Ischia island (Italy) offer treatments for different dermatological diseases (psoriasis, acne, atopic dermatitis) and upper respiratory tract infections. In this study, we integrated morphological and molecular approaches to give a focus on isolation and screening of extremophile bacteria from Ischia thermal mud for potential antimicrobial applications.

Methods

Samples were collected during 2019 at four sites. Some bacterial strains ATCC for antibacterial and antibiofilm activity were tested. After morphological characterization, screening for antagonistic isolates was made. The colonies isolated from thermal mud samples were submitted to molecular characterization. Susceptibility testing by dilution spotting was carried out and antibacterial efficacies of most active isolate were evaluated with a Minimal inhibition concentration assay. Biofilm formation, inhibition, eradication were examined. Statistical analyses were carried out utilizing Microsoft^® Excel 2016/XLSTAT^©-Pro.

Results

We isolated a natural compound with antimicrobial and antibiofilm activities.

Conclusions

The results obtained in this study are discussed in the context of how hydrothermal systems are important environmental source of uncharted antimicrobial and antibiofilm compounds. In conclusion, to the most effective of our knowledge, this work presents the primary report on the preliminary investigation of thermophile microbial diversity and their antimicrobial and antibiofilm activities for future biotechnological interest.

Technological Prospecting: Mapping Patents on L-asparaginases from Extremophilic Microorganisms

BACKGROUND

L-asparaginase (L-ASNase, L-asparagine amidohydrolase, E.C.3.5.1.1) is an enzyme with wide therapeutic applicability. Currently, the commercialized L-ASNase comes from mesophilic organisms, presenting low specificity to the substrate and limitations regarding thermostability and active pH range. Such factors prevent the maximum performance of the enzyme in different applications. Therefore, extremophilic organisms may represent important candidates for obtaining amidohydrolases with particular characteristics desired by the biotechnological market.

OBJECTIVES

The present study aims to carry out a technological prospecting of patents related to the L-asparaginases derived from extremophilic organisms, contributing to pave the way for further rational investigation and application of such enzymes.

METHODS

This patent literature review used six patents databases: The LENS, WIPO, EPO, USPTO, Patent Inspiration, and INPI.

RESULTS

It was analyzed 2860 patents, and 14 were selected according to combinations of descriptors and study criteria. Approximately 57.14% of the patents refer to enzymes obtained from archaea, especially from the speciesPyrococcus yayanosii (35.71% of the totality).

CONCLUSION

The present prospective study has singular relevance since there are no recent patent reviews for L-asparaginases, especially produced by extremophilic microorganisms. Although such enzymes have well-defined applications, corroborated by the patents compiled in this review, the most recent studies allude to new uses, such as the treatment of infections. The characterization of the catalytic profiles allows us to infer that there are potential sources still unexplored. Hence, the search for new L-ASNases with different characteristics will continue to grow in the coming years and, possibly, ramifications of the technological routes will be witnessed.

Carbohydrate-Binding Module and Linker Allow Cold Adaptation and Salt Tolerance of Maltopentaose-Forming Amylase From Marine Bacterium Saccharophagus degradans 2-40 T

Marine extremophiles produce cold-adapted and/or salt-tolerant enzymes to survive in harsh conditions. These enzymes are naturally evolved with unique structural features that confer a high level of flexibility, solubility and substrate-binding ability compared to mesophilic and thermostable homologs. Here, we identified and characterized an amylase, SdG5A, from the marine bacterium Saccharophagus degradans 2-40 T . We expressed the protein in Bacillus subtilis and found that the purified SdG5A enabled highly specific production of maltopentaose, an important health-promoting food and nutrition component. Notably, SdG5A exhibited outstanding cold adaptation and salt tolerance, retaining approximately 30 and 70% of its maximum activity at 4°C and in 3 M NaCl, respectively. It converted 68 and 83% of starch into maltooligosaccharides at 4 and 25°C, respectively, within 24 h, with 79% of the yield being the maltopentaose. By analyzing the structure of SdG5A, we found that the C-terminal carbohydrate-binding module (CBM) coupled with an extended linker, displayed a relatively high negative charge density and superior conformational flexibility compared to the whole protein and the catalytic domain. Consistent with our bioinformatics analysis, truncation of the linker-CBM region resulted in a significant loss in activities at low temperature and high salt concentration. This highlights the linker-CBM acting as the critical component for the protein to carry out its activity in biologically unfavorable condition. Together, our study indicated that these unique properties of SdG5A have great potential for both basic research and industrial applications in food, biology, and medical and pharmaceutical fields.

Going to extremes - a metagenomic journey into the dark matter of life

The Virus-X-Viral Metagenomics for Innovation Value-project was a scientific expedition to explore and exploit uncharted territory of genetic diversity in extreme natural environments such as geothermal hot springs and deep-sea ocean ecosystems. Specifically, the project was set to analyse and exploit viral metagenomes with the ultimate goal of developing new gene products with high innovation value for applications in biotechnology, pharmaceutical, medical, and the life science sectors. Viral gene pool analysis is also essential to obtain fundamental insight into ecosystem dynamics and to investigate how viruses influence the evolution of microbes and multicellular organisms. The Virus-X Consortium, established in 2016, included experts from eight European countries. The unique approach based on high throughput bioinformatics technologies combined with structural and functional studies resulted in the development of a biodiscovery pipeline of significant capacity and scale. The activities within the Virus-X consortium cover the entire range from bioprospecting and methods development in bioinformatics to protein production and characterisation, with the final goal of translating our results into new products for the bioeconomy. The significant impact the consortium made in all of these areas was possible due to the successful cooperation between expert teams that worked together to solve a complex scientific problem using state-of-the-art technologies as well as developing novel tools to explore the virosphere, widely considered as the last great frontier of life.

Characterization and Transcriptome Analysis of a Long-Chain n-Alkane-Degrading Strain Acinetobacter pittii SW-1

Strain sw-1, isolated from 7619-m seawater of the Mariana Trench, was identified as Acinetobacter pittii by 16S rRNA gene and whole-genome sequencing. A. pittii sw-1 was able to efficiently utilize long-chain n-alkanes (C₁₈–C₃₆), but not short- and medium-chain n-alkanes (C₈–C₁₆). The degradation rate of C₂₀ was 91.25%, followed by C₁₈, C₂₂, C₂₄, C₃₂, and C₃₆ with the degradation rates of 89.30%, 84.03%, 80.29%, 30.29%, and 13.37%, respectively. To investigate the degradation mechanisms of n-alkanes for this strain, the genome and the transcriptome analyses were performed. Four key alkane hydroxylase genes (alkB, almA, ladA1, and ladA2) were identified in the genome. Transcriptomes of strain sw-1 grown in C₂₀ or CH₃COONa (NaAc) as the sole carbon source were compared. The transcriptional levels of alkB and almA, respectively, increased 78.28- and 3.51-fold in C₂₀ compared with NaAc, while ladA1 and ladA2 did not show obvious change. The expression levels of other genes involved in the synthesis of unsaturated fatty acids, permeases, membrane proteins, and sulfur metabolism were also upregulated, and they might be involved in n-alkane uptake. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) confirmed that alkB expression was significantly induced by C₂₀, C₂₄, and C₃₂, and almA induction extent by C₂₄ and C₃₂ was higher than that with C_20. Furthermore, ladA2 expression was only induced by C₃₂, and ladA1 expression was not induced by any of n-alkanes. In addition, A. pittii sw-1 could grow with 0%–3% NaCl or 8 out of 10 kinds of the tested heavy metals and degrade n-alkanes at 15 °C. Taken together, these results provide comprehensive insights into the degradation of long-chain n-alkanes by Acinetobacter isolated from the deep ocean environment.

An integrated overview of bacterial carboxylesterase: Structure, function and biocatalytic applications

Carboxylesterases (CEs) are members of prominent esterase, and as their name imply, they catalyze the cleavage of ester linkages. By far, a considerable number of novel CEs have been identified to investigate their exquisite physiological and biochemical properties. They are abundant enzymes in nature, widely distributed in relatively broad temperature range and in various sources; both macroorganisms and microorganisms. Given the importance of these enzymes in broad industries, interest in the study of their mechanisms and structural-based engineering are greatly increasing. This review presents the current state of knowledge and understanding about the structure and functions of this ester-metabolizing enzyme, primarily from bacterial sources. In addition, the potential biotechnological applications of bacterial CEs are also encompassed. This review will be useful in understanding the molecular basis and structural protein of bacterial CEs that are significant for the advancement of enzymology field in industries.

Diversity, Ecological Role and Biotechnological Potential of Antarctic Marine Fungi

The Antarctic Ocean is one of the most remote and inaccessible environments on our planet and hosts potentially high biodiversity, being largely unexplored and undescribed. Fungi have key functions and unique physiological and morphological adaptations even in extreme conditions, from shallow habitats to deep-sea sediments. Here, we summarized information on diversity, the ecological role, and biotechnological potential of marine fungi in the coldest biome on Earth. This review also discloses the importance of boosting research on Antarctic fungi as hidden treasures of biodiversity and bioactive molecules to better understand their role in marine ecosystem functioning and their applications in different biotechnological fields.

From Enzyme Stability to Enzymatic Bioelectrode Stabilization Processes

Bioelectrocatalysis using redox enzymes appears as a sustainable way for biosensing, electricity production, or biosynthesis of fine products. Despite advances in the knowledge of parameters that drive the efficiency of enzymatic electrocatalysis, the weak stability of bioelectrodes prevents large scale development of bioelectrocatalysis. In this review, starting from the understanding of the parameters that drive protein instability, we will discuss the main strategies available to improve all enzyme stability, including use of chemicals, protein engineering and immobilization. Considering in a second step the additional requirements for use of redox enzymes, we will evaluate how far these general strategies can be applied to bioelectrocatalysis.

The Use of Electroactive Halophilic Bacteria for Improvements and Advancements in Environmental High Saline Biosensing

Halophilic bacteria are remarkable organisms that have evolved strategies to survive in high saline concentrations. These bacteria offer many advances for microbial-based biotechnologies and are commonly used for industrial processes such as compatible solute synthesis, biofuel production, and other microbial processes that occur in high saline environments. Using halophilic bacteria in electrochemical systems offers enhanced stability and applications in extreme environments where common electroactive microorganisms would not survive. Incorporating halophilic bacteria into microbial fuel cells has become of particular interest for renewable energy generation and self-powered biosensing since many wastewaters can contain fluctuating and high saline concentrations. In this perspective, we highlight the evolutionary mechanisms of halophilic microorganisms, review their application in microbial electrochemical sensing, and offer future perspectives and directions in using halophilic electroactive microorganisms for high saline biosensing.

Bioprospecting of Novel Extremozymes From Prokaryotes-The Advent of Culture-Independent Methods

Extremophiles are remarkable organisms that thrive in the harshest environments on Earth, such as hydrothermal vents, hypersaline lakes and pools, alkaline soda lakes, deserts, cold oceans, and volcanic areas. These organisms have developed several strategies to overcome environmental stress and nutrient limitations. Thus, they are among the best model organisms to study adaptive mechanisms that lead to stress tolerance. Genetic and structural information derived from extremophiles and extremozymes can be used for bioengineering other nontolerant enzymes. Furthermore, extremophiles can be a valuable resource for novel biotechnological and biomedical products due to their biosynthetic properties. However, understanding life under extreme conditions is challenging due to the difficulties of in vitro cultivation and observation since > 99% of organisms cannot be cultivated. Consequently, only a minor percentage of the potential extremophiles on Earth have been discovered and characterized. Herein, we present a review of culture-independent methods, sequence-based metagenomics (SBM), and single amplified genomes (SAGs) for studying enzymes from extremophiles, with a focus on prokaryotic (archaea and bacteria) microorganisms. Additionally, we provide a comprehensive list of extremozymes discovered via metagenomics and SAGs.

An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.

Bioactive Molecules from Extreme Environments

Marine organisms inhabiting extreme habitats are a promising reservoir of bioactive compounds for drug discovery. Extreme environments, i.e., polar and hot regions, deep sea, hydrothermal vents, marine areas of high pressure or high salinity, experience conditions close to the limit of life. In these marine ecosystems, “hot spots” of biodiversity, organisms have adopted a huge variety of strategies to cope with such harsh conditions, such as the production of bioactive molecules potentially valuable for biotechnological applications and for pharmaceutical, nutraceutical and cosmeceutical sectors. Many enzymes isolated from extreme environments may be of great interest in the detergent, textile, paper and food industries. Marine natural products produced by organisms evolved under hostile conditions exhibit a wide structural diversity and biological activities. In fact, they exert antimicrobial, anticancer, antioxidant and anti-inflammatory activities. The aim of this Special Issue “Bioactive Molecules from Extreme Environments” was to provide the most recent findings on bioactive molecules as well as enzymes isolated from extreme environments, to be used in biotechnological discovery pipelines and pharmaceutical applications, in an effort to encourage further research in these extreme habitats.