Extremophiles, a Nifty Tool to Face Environmental Pollution: From Exploitation of Metabolism to Genome Engineering

Recent perspectives on biotechnological production, modulation and applications of glycerophosphoryl diester phosphodiesterases

Organophosphate (OP) compounds have been extensively employed as pesticides, insecticides and nerve agents. Stockpiles of chemical warfare agents must be destroyed as recommended by Chemical Weapon Convention (CWC). Toxicity of OP compounds to insects and mammals is due to their ability to inhibit the activity of acetylcholinesterase. Accumulation of acetylcholine leads to overstimulation of nerves, leading to convulsion, paralysis or even death. There is a dire need to decontaminate OP contaminated sites by using inexpensive and eco-friendly agents. Recently, OP hydrolyzing enzymes such as glycerophosphoryl diester phosphodiesterases (GDPDs) emerged as appealing agents to clean-up OP contaminated environmental sites. GDPDs are well known for enzymatic generation of glycerol 3-phosphate and corresponding alcoholic moiety from glycerophosphodiesters. Additionally, they are also involved in hydrolysis of OP compounds and degradative products of nerve agents. In the current review, structural and functional characteristics of GDPDs have been elaborated. Production of GDPDs from natural sources is quiet low so the current study aims at recombinant production of GDPDs from various sources. Comparative analysis of biochemical characteristics of various GDPDs indicated that thermostable GDPDs are active over broad temperature and pH range. In addition, thermostable GDPDs are resistant to high concentrations of organic solvents as well as metal ions. In order to enhance their practical utility, different engineering approaches (directed evolution, rational design and site-saturation mutagenesis) as well as immobilization strategies can be utilized to improve catalytic properties of GDPDs. Thus, the current review highlights the utilization of recombinant engineered free or immobilized GDPDs as tools in OP bioremediation.

Metagenomic approaches and opportunities in arid soil research

Arid soils present unique challenges and opportunities for studying microbial diversity and bioactive potential due to the extreme environmental conditions they bear. This review article investigates soil metagenomics as an emerging tool to explore complex microbial dynamics and unexplored bioactive potential in harsh environments. Utilizing advanced metagenomic techniques, diverse microbial populations that grow under extreme conditions such as high temperatures, salinity, high pH levels, and exposure to metals and radiation can be studied. The use of extremophiles to discover novel natural products and biocatalysts emphasizes the role of functional metagenomics in identifying enzymes and secondary metabolites for industrial and pharmaceutical purposes. Metagenomic sequencing uncovers a complex network of microbial diversity, offering significant potential for discovering new bioactive compounds. Functional metagenomics, connecting taxonomic diversity to genetic capabilities, provides a pathway to identify microbes' mechanisms to synthesize valuable secondary metabolites and other bioactive substances. Contrary to the common perception of desert soil as barren land, the metagenomic analysis reveals a rich diversity of life forms adept at extreme survival. It provides valuable findings into their resilience and potential applications in biotechnology. Moreover, the challenges associated with metagenomics in arid soils, such as low microbial biomass, high DNA degradation rates, and DNA extraction inhibitors and strategies to overcome these issues, outline the latest advancements in extraction methods, high-throughput sequencing, and bioinformatics. The importance of metagenomics for investigating diverse environments opens the way for future research to develop sustainable solutions in agriculture, industry, and medicine. Extensive studies are necessary to utilize the full potential of these powerful microbial communities. This research will significantly improve our understanding of microbial ecology and biotechnology in arid environments.

Genomic mining of Geobacillus stearothermophilus GF16 for xylose production from hemicellulose-rich biomasses using secreted enzymes

The valorization of lignocellulosic biomass, derived from various bio-waste materials, has received considerable attention as a sustainable approach to improve production chains while reducing environmental impact. Microbial enzymes have emerged as key players in the degradation of polysaccharides, offering versatile applications in biotechnology and industry. Among these enzymes, glycoside hydrolases (GHs) play a central role. Xylanases, in particular, are used in a wide range of applications and are essential for the production of xylose, which can be fermented into bioethanol or find use in many other industries. Currently, fungal secretomes dominate as the main reservoir of lignocellulolytic enzymes, but thermophilic microorganisms offer notable advantages in terms of enzyme stability and production efficiency. Here we present the genomic characterization of Geobacillus stearothermophilus GF16 to identify genes encoding putative enzymes involved in lignocellulose degradation. Thermostable GHs secreted by G. stearothermophilus GF16 were investigated and found to be active on different natural polysaccharides and synthetic substrates, revealing an array of inducible GH activities. In particular, the concentrated secretome possesses significant thermostable xylanase and β-xylosidase activities (5 ×103 U/L and 1.7 ×105 U/L, respectively), highlighting its potential for application in biomass valorization. We assessed the hemicellulose hydrolysis capabilities of various agri-food wastes using the concentrated secretome of the strain cultivated on xylan. An impressive 300-fold increase in xylose release compared to a commercially available cocktail was obtained with the secretome, underscoring the remarkable efficacy of this approach.

The Undeniable Potential of Thermophiles in Industrial Processes

Extremophilic microorganisms play a key role in understanding how life on Earth originated and evolved over centuries. Their ability to thrive in harsh environments relies on a plethora of mechanisms developed to survive at extreme temperatures, pressures, salinity, and pH values. From a biotechnological point of view, thermophiles are considered a robust tool for synthetic biology as well as a reliable starting material for the development of sustainable bioprocesses. This review discusses the current progress in the biomanufacturing of high-added bioproducts from thermophilic microorganisms and their industrial applications.

From waste management to circular economy: Leveraging thermophiles for sustainable growth and global resource optimization

Waste of any origin is one of the most serious global and man-made concerns of our day. It causes climate change, environmental degradation, and human health problems. Proper waste management practices, including waste reduction, safe handling, and appropriate treatment, are essential to mitigate these consequences. It is thus essential to implement effective waste management strategies that reduce waste at the source, promote recycling and reuse, and safely dispose of waste. Transitioning to a circular economy with policies involving governments, industries, and individuals is essential for sustainable growth and waste management. The review focuses on diverse kinds of environmental waste sources around the world, such as residential, industrial, commercial, municipal services, electronic wastes, wastewater sewerage, and agricultural wastes, and their challenges in efficiently valorizing them into useful products. It highlights the need for rational waste management, circularity, and sustainable growth, and the potential of a circular economy to address these challenges. The article has explored the role of thermophilic microbes in the bioremediation of waste. Thermophiles known for their thermostability and thermostable enzymes, have emerged to have diverse applications in biotechnology and various industrial processes. Several approaches have been explored to unlock the potential of thermophiles in achieving the objective of establishing a zero-carbon sustainable bio-economy and minimizing waste generation. Various thermophiles have demonstrated substantial potential in addressing different waste challenges. The review findings affirm that thermophilic microbes have emerged as pivotal and indispensable candidates for harnessing and valorizing a range of environmental wastes into valuable products, thereby fostering the bio-circular economy.

Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation

BACKGROUND

Hot spring biofilms provide a window into the survival strategies of microbial communities in extreme environments and offer potential for biotechnological applications. This study focused on green and brown biofilms thriving on submerged plant litter within the Sungai Klah hot spring in Malaysia, characterised by temperatures of 58-74 °C. Using Illumina shotgun metagenomics and Nanopore ligation sequencing, we investigated the microbial diversity and functional potential of metagenome-assembled genomes (MAGs) with specific focus on biofilm formation, heat stress response, and carbohydrate catabolism.

RESULTS

Leveraging the power of both Illumina short-reads and Nanopore long-reads, we employed an Illumina-Nanopore hybrid assembly approach to construct MAGs with enhanced quality. The dereplication process, facilitated by the dRep tool, validated the efficiency of the hybrid assembly, yielding MAGs that reflected the intricate microbial diversity of these extreme ecosystems. The comprehensive analysis of these MAGs uncovered intriguing insights into the survival strategies of thermophilic taxa in the hot spring biofilms. Moreover, we examined the plant litter degradation potential within the biofilms, shedding light on the participation of diverse microbial taxa in the breakdown of starch, cellulose, and hemicellulose. We highlight that Chloroflexota and Armatimonadota MAGs exhibited a wide array of glycosyl hydrolases targeting various carbohydrate substrates, underscoring their metabolic versatility in utilisation of carbohydrates at elevated temperatures.

CONCLUSIONS

This study advances understanding of microbial ecology on plant litter under elevated temperature by revealing the functional adaptation of MAGs from hot spring biofilms. In addition, our findings highlight potential for biotechnology application through identification of thermophilic lignocellulose-degrading enzymes. By demonstrating the efficiency of hybrid assembly utilising Illumina-Nanopore reads, we highlight the value of combining multiple sequencing methods for a more thorough exploration of complex microbial communities.

Extremozyme-Based Biosensors for Environmental Pollution Monitoring: Recent Developments

Extremozymes combine high specificity and sensitivity with the ability to withstand extreme operational conditions. This work presents an overview of extremozymes that show potential for environmental monitoring devices and outlines the latest advances in biosensors utilizing these unique molecules. The characteristics of various extremozymes described so far are presented, underlining their stability and operational conditions that make them attractive for biosensing. The biosensor design is discussed based on the detection of photosynthesis-inhibiting herbicides as a case study. Several biosensors for the detection of pesticides, heavy metals, and phenols are presented in more detail to highlight interesting substrate specificity, applications or immobilization methods. Compared to mesophilic enzymes, the integration of extremozymes in biosensors faces additional challenges related to lower availability and high production costs. The use of extremozymes in biosensing does not parallel their success in industrial applications. In recent years, the "collection" of recognition elements was enriched by extremozymes with interesting selectivity and by thermostable chimeras. The perspectives for biosensor development are exciting, considering also the progress in genetic editing for the oriented immobilization of enzymes, efficient folding, and better electron transport. Stability, production costs and immobilization at sensing interfaces must be improved to encourage wider applications of extremozymes in biosensors.

Halo-alkaliphilic microbes as an effective tool for heavy metal pollution abatement and resource recovery: challenges and future prospects

The current study presents an overview of heavy metals bioremediation from halo-alkaline conditions by using extremophilic microorganisms. Heavy metal remediation from the extreme environment with high pH and elevated salt concentration is a challenge as mesophilic microorganisms are unable to thrive under these polyextremophilic conditions. Thus, for effective bioremediation of extreme systems, specialized microbes (extremophiles) are projected as potential bioremediating agents, that not only thrive under such extreme conditions but are also capable of remediating heavy metals from these environments. The physiological versatility of extremophiles especially halophiles and alkaliphiles and their enzymes (extremozymes) could conveniently be harnessed to remediate and detoxify heavy metals from the high alkaline saline environment. Bibliometric analysis has shown that research in this direction has found pace in recent years and thus this review is a timely attempt to highlight the importance of halo-alkaliphiles for effective contaminant removal in extreme conditions. Also, this review systematically presents insights on adaptive measures utilized by extremophiles to cope with harsh environments and outlines the role of extremophilic microbes in industrial wastewater treatment and recovery of metals from waste with relevant examples. Further, the major challenges and way forward for the effective applicability of halo-alkaliphilic microbes in heavy metals bioremediation from extremophilic conditions are also highlighted.

Investigating Bio-Inspired Degradation of Toxic Dyes Using Potential Multi-Enzyme Producing Extremophiles

Biological treatment methods overcome many of the drawbacks of physicochemical strategies and play a significant role in removing dye contamination for environmental sustainability. Numerous microorganisms have been investigated as promising dye-degrading candidates because of their high metabolic potential. However, few can be applied on a large scale because of the extremely harsh conditions in effluents polluted with multiple dyes, such as alkaline pH, high salinity/heavy metals/dye concentration, high temperature, and oxidative stress. Therefore, extremophilic microorganisms offer enormous opportunities for practical biodegradation processes as they are naturally adapted to multi-stress conditions due to the special structure of their cell wall, capsule, S-layer proteins, extracellular polymer substances (EPS), and siderophores structural and functional properties such as poly-enzymes produced. This review provides scientific information for a broader understanding of general dyes, their toxicity, and their harmful effects. The advantages and disadvantages of physicochemical methods are also highlighted and compared to those of microbial strategies. New techniques and methodologies used in recent studies are briefly summarized and discussed. In particular, this study addresses the key adaptation mechanisms, whole-cell, enzymatic degradation, and non-enzymatic pathways in aerobic, anaerobic, and combination conditions of extremophiles in dye degradation and decolorization. Furthermore, they have special metabolic pathways and protein frameworks that contribute significantly to the complete mineralization and decolorization of the dye when all functions are turned on. The high potential efficiency of microbial degradation by unculturable and multi-enzyme-producing extremophiles remains a question that needs to be answered in practical research.

Genetically engineered microorganisms for environmental remediation

In the recent era, the increasing persistence of hazardous contaminants is badly affecting the globe in many ways. Due to high environmental contamination, almost every second species on earth facing the worst issue in their survival. Advances in newer remediation approaches may help enhance bioremediation's quality, while conventional procedures have failed to remove hazardous compounds from the environment. Chemical and physical waste cleanup approaches have been used in current circumstances; however, these methods are costly and harmful to the environment. Thus, there has been a rise in the use of bioremediation due to an increase in environmental contamination, which led to the development of genetically engineered microbes (GEMs). It is safer and more cost-effective to use engineered microorganisms rather than alternative methods. GEMs are created by introducing a stronger protein into bacteria through biotechnology or genetic engineering to enhance the desired trait. Biodegradation of oil spills, halobenzoates naphthalenes, toluenes, trichloroethylene, octanes, xylenes etc. has been accomplished using GEMs such bacteria, fungus, and algae. Biotechnologically induced microorganisms are more powerful than naturally occurring ones and may degrade contaminants faster because they can quickly adapt to new pollutants they encounter or co-metabolize. Genetic engineering is a worthy process that will benefit the environment and ultimately the health of our people.

Insight into CAZymes of Alicyclobacillus mali FL18: Characterization of a New Multifunctional GH9 Enzyme

In the bio-based era, cellulolytic and hemicellulolytic enzymes are biocatalysts used in many industrial processes, playing a key role in the conversion of recalcitrant lignocellulosic waste biomasses. In this context, many thermophilic microorganisms are considered as convenient sources of carbohydrate-active enzymes (CAZymes). In this work, a functional genomic annotation of Alicyclobacillus mali FL18, a recently discovered thermo-acidophilic microorganism, showed a wide reservoir of putative CAZymes. Among them, a novel enzyme belonging to the family 9 of glycosyl hydrolases (GHs), named AmCel9, was identified; in-depth in silico analyses highlighted that AmCel9 shares general features with other GH9 members. The synthetic gene was expressed in Escherichia coli and the recombinant protein was purified and characterized. The monomeric enzyme has an optimal catalytic activity at pH 6.0 and has comparable activity at temperatures ranging from 40 °C to 70 °C. It also has a broad substrate specificity, a typical behavior of multifunctional cellulases; the best activity is displayed on β-1,4 linked glucans. Very interestingly, AmCel9 also hydrolyses filter paper and microcrystalline cellulose. This work gives new insights into the properties of a new thermophilic multifunctional GH9 enzyme, that looks a promising biocatalyst for the deconstruction of lignocellulose.

Adaptive Response of Thermophiles to Redox Stress and Their Role in the Process of dye Degradation From Textile Industry Wastewater

Release of dye-containing textile wastewater into the environment causes severe pollution with serious consequences on aquatic life. Bioremediation of dyes using thermophilic microorganisms has recently attracted attention over conventional treatment techniques. Thermophiles have the natural ability to survive under extreme environmental conditions, including high dye concentration, because they possess stress response adaptation and regulation mechanisms. Therefore, dye detoxification by thermophiles could offer enormous opportunities for bioremediation at elevated temperatures. In addition, the processes of degradation generate reactive oxygen species (ROS) and subject cells to oxidative stress. However, thermophiles exhibit better adaptation to resist the effects of oxidative stress. Some of the major adaptation mechanisms of thermophiles include macromolecule repair system; enzymes such as superoxide dismutase, catalase, and glutathione peroxidase; and non-enzymatic antioxidants like extracellular polymeric substance (EPSs), polyhydroxyalkanoates (PHAs), etc. In addition, different bacteria also possess enzymes that are directly involved in dye degradation such as azoreductase, laccase, and peroxidase. Therefore, through these processes, dyes are first degraded into smaller intermediate products finally releasing products that are non-toxic or of low toxicity. In this review, we discuss the sources of oxidative stress in thermophiles, the adaptive response of thermophiles to redox stress and their roles in dye removal, and the regulation and crosstalk between responses to oxidative stress.

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.

A New Strategy for As(V) Biosensing Based on the Inhibition of the Phosphatase Activity of the Arsenate Reductase from Thermus thermophilus

Arsenic (As) pollution is a widespread problem worldwide. In recent years, biosensors based on enzymatic inhibition have been developed for arsenic detection, making the study of the effect of inhibitors on the selected enzymatic activity crucial for their setup. The arsenate reductase of Thermus thermophilus HB27, TtArsC, reduces As(V) into As(III), but is also endowed with phosphatase activity. This work investigates the inhibitory effects of As(V) and As(III) on phosphatase activity by taking advantage of a simple colorimetric assay; the results show that both of them are non-competitive inhibitors affecting the Vmax but not the K_M of the reaction. However, their Ki values are different from each other (15.2 ± 1.6 μM for As(V) and 394.4 ± 40.3 µm with As(III)), indicating a higher inhibitory effect by As(V). Moreover, the inhibition-based biosystem results to be selective for As(V) since several other metal ions and salts do not affect TtArsC phosphatase activity; it exhibits a sensitivity of 0.53 ± 0.03 mU/mg/μM and a limit of detection (LOD) of 0.28 ± 0.02 μM. The good sensitivity and specificity for As(V) point to consider inhibition of TtArsC phosphatase activity for the setup of a novel biosensor for the detection of As(V).

Bioremediation of soil contaminated with toxic mixed reactive azo dyes by co-cultured cells of Enterobacter cloacae and Bacillus subtilis

Azo dyes, known for its toxicity and mutagenicity, are used by textile industries. Bioremediation serves the best alternative treatment process due to its eco-friendly nature and cost-effectiveness. Degradation using individual bacteria promotes azo dye removal, while the degradation is enhanced using the immobilization method. Bio-carrier promotes the attachment of the bacterial strains and increases azo dye degradation. The present study focuses on the biodegradation of Reactive Red (RR), Reactive Brown (RB), Reactive Black dye (RBL), and mixed dyes in a soil slurry bioreactor containing free cells, co-culture, and immobilized cells. The physico-chemical analysis and soil characteristics were determined. The free cells of Bacillus cereus showed degradation of azo dyes - 79.42 ± 0.03% RR, 78.78 ± 0.02% RBL; 70.76 ± 0.03% RB, and 84.89 ± 0.05% of mixed dyes respectively. Enterobacter cloacae free cells resulted in degradation of 72.87 ± 0.01% RR, 75.21 ± 0.01% RBL, 74.50 ± 0.02% RB, and 73.39 ± 0.04% mixed dyes respectively. Co-cultured bacterial strains resulted in 77.18 ± 0.03% RR, 80.27 ± 0.02% RBL, 76.97 ± 0.02% RB and 86.29 ± 0.05% mixed dyes respectively. The immobilization of Bacillus cereus and Enterobacter cloacae on 2% corn starch resulted in 98.4 ± 0.01% degradation of RR, 89.8 ± 0.09% degradation of RB, 99.4 ± 0.05% of RBL, and 98.1 ± 0.08% of mixed reactive dyes respectively.

A Hyperthermoactive-Cas9 Editing Tool Reveals the Role of a Unique Arsenite Methyltransferase in the Arsenic Resistance System of Thermus thermophilus HB27

Arsenic detoxification systems can be found in a wide range of organisms, from bacteria to humans. In a previous study, we discovered an arsenic-responsive transcriptional regulator in the thermophilic bacterium Thermus thermophilus HB27 (TtSmtB). Here, we characterize the arsenic resistance system of T. thermophilus in more detail. We employed TtSmtB-based pulldown assays with protein extracts from cultures treated with arsenate and arsenite to obtain an S-adenosyl-l-methionine (SAM)-dependent arsenite methyltransferase (TtArsM). In vivo and in vitro analyses were performed to shed light on this new component of the arsenic resistance network and its peculiar catalytic mechanism. Heterologous expression of TtarsM in Escherichia coli resulted in arsenite detoxification at mesophilic temperatures. Although TtArsM does not contain a canonical arsenite binding site, the purified protein does catalyze SAM-dependent arsenite methylation with formation of monomethylarsenites (MMAs) and dimethylarsenites (DMAs). In addition, in vitro analyses confirmed the unique interaction between TtArsM and TtSmtB. Next, a highly efficient ThermoCas9-based genome-editing tool was developed to delete the TtArsM-encoding gene on the T. thermophilus genome and to confirm its involvement in the arsenite detoxification system. Finally, the TtarsX efflux pump gene in the T. thermophilus ΔTtarsM genome was substituted by a gene encoding a stabilized yellow fluorescent protein (sYFP) to create a sensitive genome-based bioreporter system for the detection of arsenic ions.

Steroid Metabolism in Thermophilic Actinobacterium Saccharopolyspora hirsuta VKM Ac-666T

The application of thermophilic microorganisms opens new prospects in steroid biotechnology, but little is known to date on steroid catabolism by thermophilic strains. The thermophilic strain Saccharopolyspora hirsuta VKM Ac-666^T has been shown to convert various steroids and to fully degrade cholesterol. Cholest-4-en-3-one, cholesta-1,4-dien-3-one, 26-hydroxycholest-4-en-3-one, 3-oxo-cholest-4-en-26-oic acid, 3-oxo-cholesta-1,4-dien-26-oic acid, 26-hydroxycholesterol, 3β-hydroxy-cholest-5-en-26-oic acid were identified as intermediates in cholesterol oxidation. The structures were confirmed by ¹H and ¹³C-NMR analyses. Aliphatic side chain hydroxylation at C26 and the A-ring modification at C3, which are putatively catalyzed by cytochrome P450 monooxygenase CYP125 and cholesterol oxidase, respectively, occur simultaneously in the strain and are followed by cascade reactions of aliphatic sidechain degradation and steroid core destruction via the known 9(10)-seco-pathway. The genes putatively related to the sterol and bile acid degradation pathways form three major clusters in the S. hirsuta genome. The sets of the genes include the orthologs of those involved in steroid catabolism in Mycobacterium tuberculosis H37Rv and Rhodococcus jostii RHA1 and related actinobacteria. Bioinformatics analysis of 52 publicly available genomes of thermophilic bacteria revealed only seven candidate strains that possess the key genes related to the 9(10)-seco pathway of steroid degradation, thus demonstrating that the ability to degrade steroids is not widespread among thermophilic bacteria.