Applications of Marine-Derived Microorganisms and Their Enzymes in Biocatalysis and Biotransformation, the Underexplored Potentials

Investigating the nutritional viability of marine-derived protein for sustainable future development

Marine-derived proteins are emerging as a pivotal resource with diverse applications in food, pharmaceuticals, and biotechnological industries. The marine environment offers many protein sources, including fish, shellfish, algae, and microbes, which garnered attention due to their nutritional composition. Evaluating their protein and amino acid profiles is essential in assessing their viability as substitutes for conventional protein sources. Continuously exploiting marine ecosystems for protein extraction has led to significant environmental impacts. The optimization of aquacultural practices and implementation of innovative practices are imperative for the sustainable production of marine-based protein. This review will discuss the different sources of marine proteins, their nutritional profile, and their associated environmental impact. It also reviews the relationship between aquaculture advancements and regulatory frameworks toward attaining sustainable practices, alongside exploring the challenges and potentials in utilizing marine sources for protein production.

Polyphasic Investigation of Aliiroseovarius salicola sp. nov., Isolated from Seawater

A novel Gram-stain-negative, strictly aerobic, short-rod-shaped, and chemo-organoheterotrophic bacterium, designated KMU-50T, was isolated from seawater gathered from Dadaepo Harbor in South Korea. The microorganism grew at 0-4.0% NaCl concentrations (w/v), pH 6.0-8.0, and 4-37 °C. The 16S rRNA gene sequence-based phylogenetic tree demonstrated that the strain KMU-50T is a novel member of the family Roseobacteraceae and were greatly related to Aliiroseovarius crassostreae CV919-312T with sequence similarity of 98.3%. C18:1 ω7c was the main fatty acid and ubiquinone-10 was the only isoprenoid quinone. The dominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified phospholipids, an unidentified aminolipid, and an unidentified lipid. The genome size of strain KMU-50T was 3.60 Mbp with a DNA G+C content of 56.0%. The average nucleotide identity (ANI) and average amino acid identity (AAI) values between the genomes of strain KMU-50T and its closely related species were 76.0-81.2% and 62.2-81.5%, respectively. The digital DNA-DNA hybridization (dDDH) value of strain KMU-50T with the strain of A. crassostreae CV919-312T was 25.1%. The genome of the strain KMU-50T showed that it encoded many genes involved in the breakdown of bio-macromolecules, thus showing a high potential as a producer of industrially useful enzymes. Consequently, the strain is described as a new species in the genus Aliiroseovarius, for which the name Aliiroseovarius salicola sp. nov., is proposed with the type strain KMU-50T (= KCCM 90480T = NBRC 115482T).

Late-stage diversification of bacterial natural products through biocatalysis

Bacterial natural products (BNPs) are very important sources of leads for drug development and chemical novelty. The possibility to perform late-stage diversification of BNPs using biocatalysis is an attractive alternative route other than total chemical synthesis or metal complexation reactions. Although biocatalysis is gaining popularity as a green chemistry methodology, a vast majority of orphan sequenced genomic data related to metabolic pathways for BNP biosynthesis and its tailoring enzymes are underexplored. In this review, we report a systematic overview of biotransformations of 21 molecules, which include derivatization by halogenation, esterification, reduction, oxidation, alkylation and nitration reactions, as well as degradation products as their sub-derivatives. These BNPs were grouped based on their biological activities into antibacterial (5), antifungal (5), anticancer (5), immunosuppressive (2) and quorum sensing modulating (4) compounds. This study summarized 73 derivatives and 16 degradation sub-derivatives originating from 12 BNPs. The highest number of biocatalytic reactions was observed for drugs that are already in clinical use: 28 reactions for the antibacterial drug vancomycin, followed by 18 reactions reported for the immunosuppressive drug rapamycin. The most common biocatalysts include oxidoreductases, transferases, lipases, isomerases and haloperoxidases. This review highlights biocatalytic routes for the late-stage diversification reactions of BNPs, which potentially help to recognize the structural optimizations of bioactive scaffolds for the generation of new biomolecules, eventually leading to drug development.

Blue Biotechnology: Marine Bacteria Bioproducts

The ocean is the habitat of a great number of organisms with different characteristics. Compared to terrestrial microorganisms, marine microorganisms also represent a vast and largely unexplored reservoir of bioactive compounds with diverse industrial applications like terrestrial microorganisms. This review examines the properties and potential applications of products derived from marine microorganisms, including bacteriocins, enzymes, exopolysaccharides, and pigments, juxtaposing them in some cases against their terrestrial counterparts. We discuss the distinct characteristics that set marine-derived products apart, including enhanced stability and unique structural features such as the amount of uronic acid and sulfate groups in exopolysaccharides. Further, we explore the uses of these marine-derived compounds across various industries, ranging from food and pharmaceuticals to cosmetics and biotechnology. This review also presents a broad description of biotechnologically important compounds produced by bacteria isolated from marine environments, some of them with different qualities compared to their terrestrial counterparts.

Bioremediation for the recovery of oil polluted marine environment, opportunities and challenges approaching the Blue Growth

The Blue Growth strategy promises a sustainable use of marine resources for the benefit of the society. However, oil pollution in the marine environment is still a serious issue for human, animal, and environmental health; in addition, it deprives citizens of the potential economic and recreational advantages in the affected areas. Bioremediation, that is the use of bio-resources for the degradation of pollutants, is one of the focal themes on which the Blue Growth aims to. A repertoire of marine-derived bio-products, biomaterials, processes, and services useful for efficient, economic, low impact, treatments for the recovery of oil-polluted areas has been demonstrated in many years of research around the world. Nonetheless, although bioremediation technology is routinely applied in soil, this is not still standardized in the marine environment and the potential market is almost underexploited. This review provides a summary of opportunities for the exploiting and addition of value to research products already validated. Moreover, the review discusses challenges that limit bioremediation in marine environment and actions that can facilitate the conveying of valuable products/processes towards the market.

A novel soluble di-iron monooxygenase from the soil bacterium Solimonas soli

Soluble di-iron monooxygenase (SDIMO) enzymes enable insertion of oxygen into diverse substrates and play significant roles in biogeochemistry, bioremediation and biocatalysis. An unusual SDIMO was detected in an earlier study in the genome of the soil organism Solimonas soli, but was not characterized. Here, we show that the S. soli SDIMO is part of a new clade, which we define as 'Group 7'; these share a conserved gene organization with alkene monooxygenases but have only low amino acid identity. The S. soli genes (named zmoABCD) could be functionally expressed in Pseudomonas putida KT2440 but not in Escherichia coli TOP10. The recombinants made epoxides from C2 C8 alkenes, preferring small linear alkenes (e.g. propene), but also epoxidating branched, carboxylated and chlorinated substrates. Enzymatic epoxidation of acrylic acid was observed for the first time. ZmoABCD oxidised the organochlorine pollutants vinyl chloride (VC) and cis-1,2-dichloroethene (cDCE), with the release of inorganic chloride from VC but not cDCE. The original host bacterium S. soli could not grow on any alkenes tested but grew well on phenol and n-octane. Further work is needed to link ZmoABCD and the other Group 7 SDIMOs to specific physiological and ecological roles.

Marine Bioprospecting: Enzymes and Stress Proteins from the Sea Anemones Anthopleura dowii and Lebrunia neglecta

The bioprospecting of sea anemone tissues and secretions has revealed that they are natural libraries of polypeptides with diverse biological activities that can be utilized to develop of biotechnological tools with potential medical and industrial applications. This study conducted a proteomic analysis of crude venom extracts from Anthopleura dowii Verrill, 1869, and Lebrunia neglecta Duchassaing & Michelotti, 1860. The obtained data allowed us to identify 201 polypeptides, of which 39% were present in both extracts. Among the obtained sequences, hydrolase-type enzymes, oxidoreductases, transferases, heat shock proteins, adhesion proteins, and protease inhibitors, among others, were identified. Interaction analysis and functional annotation indicated that these proteins are primarily involved in endoplasmic reticulum metabolic processes such as carbon metabolism and protein processing. In addition, several proteins related to oxidative stress were identified, including superoxide dismutase, peroxiredoxins, thioredoxin, and glutathione oxidase. Our results provide novel information on the polypeptide composition of the crude venom extract from sea anemones, which can be utilized to develop molecules for therapeutic tools and industrial applications.

Microbial degradation as a powerful weapon in the removal of sulfonylurea herbicides

Sulfonylurea herbicides have been widely used worldwide and play a significant role in modern agricultural production. However, these herbicides have adverse biological effects that can damage the ecosystems and harm human health. As such, rapid and effective techniques that remove sulfonylurea residues from the environment are urgently required. Attempts have been made to remove sulfonylurea residues from environment using various techniques such as incineration, adsorption, photolysis, ozonation, and microbial degradation. Among them, biodegradation is regarded as a practical and environmentally responsible way to eliminate pesticide residues. Microbial strains such as Talaromyces flavus LZM1, Methylopila sp. SD-1, Ochrobactrum sp. ZWS16, Staphylococcus cohnii ZWS13, Enterobacter ludwigii sp. CE-1, Phlebia sp. 606, and Bacillus subtilis LXL-7 can almost completely degrade sulfonylureas. The degradation mechanism of the strains is such that sulfonylureas can be catalyzed by bridge hydrolysis to produce sulfonamides and heterocyclic compounds, which deactivate sulfonylureas. The molecular mechanisms associated with microbial degradation of sulfonylureas are relatively poorly studied, with hydrolase, oxidase, dehydrogenase and esterase currently known to play a pivotal role in the catabolic pathways of sulfonylureas. Till date, there are no reports specifically on the microbial degrading species and biochemical mechanisms of sulfonylureas. Hence, in this article, the degradation strains, metabolic pathways, and biochemical mechanisms of sulfonylurea biodegradation, along with its toxic effects on aquatic and terrestrial animals, are discussed in depth in order to provide new ideas for remediation of soil and sediments polluted by sulfonylurea herbicides.

Current insights into the microbial degradation of nicosulfuron: Strains, metabolic pathways, and molecular mechanisms

Nicosulfuron is among the sulfonylurea herbicides that are widely used to control annual and perennial grass weeds in cornfields. However, nicosulfuron residues in the environment are likely to cause long-lasting harmful environmental and biological effects. Nicosulfuron degrades via photo-degradation, chemical hydrolysis, and microbial degradation. The latter is crucial for pesticide degradation and has become an essential strategy to remove nicosulfuron residues from the environment. Most previous studies have focused on the screening, degradation characteristics, and degradation pathways of biodegrader microorganisms. The isolated nicosulfuron-degrading strains include Bacillus, Pseudomonas, Klebsiella, Alcaligenes, Rhodopseudomonas, Ochrobactrum, Micrococcus, Serratia, Penicillium, Aspergillus, among others, all of which have good degradation efficiency. Two main intermediates, 2-amino-4,6-dimethoxypyrimidine (ADMP) and 2-aminosulfonyl-N,N-dimethylnicotinamide (ASDM), are produced during microbial degradation and are derived from the C-N, C-S, and S-N bond breaks on the sulfonylurea bridge, covering almost every bacterial degradation pathway. In addition, enzymes related to the degradation of nicosulfuron have been identified successively, including the manganese ABC transporter (hydrolase), Flavin-containing monooxygenase (oxidase), and E3 (esterase). Further in-depth studies based on molecular biology and genetics are needed to elaborate on their role in the evolution of novel catabolic pathways and the microbial degradation of nicosulfuron. To date, few reviews have focused on the microbial degradation and degradation mechanisms of nicosulfuron. This review summarizes recent advances in nicosulfuron degradation and comprehensively discusses the potential of nicosulfuron-degrading microorganisms for bioremediating contaminated environments, providing a reference for further research development on nicosulfuron biodegradation in the future.

Purification and biochemical characterization of SM14est, a PET-hydrolyzing enzyme from the marine sponge-derived Streptomyces sp. SM14

The successful enzymatic degradation of polyester substrates has fueled worldwide investigation into the treatment of plastic waste using bio-based processes. Within this realm, marine-associated microorganisms have emerged as a promising source of polyester-degrading enzymes. In this work, we describe the hydrolysis of the synthetic polymer PET by SM14est, a polyesterase which was previously identified from Streptomyces sp. SM14, an isolate of the marine sponge Haliclona simulans. The PET hydrolase activity of purified SM14est was assessed using a suspension-based assay and subsequent analysis of reaction products by UV-spectrophotometry and RP-HPLC. SM14est displayed a preference for high salt conditions, with activity significantly increasing at sodium chloride concentrations from 100 mM up to 1,000 mM. The initial rate of PET hydrolysis by SM14est was determined to be 0.004 s^-1 at 45°C, which was increased by 5-fold to 0.02 s^-1 upon addition of 500 mM sodium chloride. Sequence alignment and structural comparison with known PET hydrolases, including the marine halophile PET6, and the highly efficient, thermophilic PHL7, revealed conserved features of interest. Based on this work, SM14est emerges as a useful enzyme that is more similar to key players in the area of PET hydrolysis, like PHL7 and IsPETase, than it is to its marine counterparts. Salt-tolerant polyesterases such as SM14est are potentially valuable in the biological degradation of plastic particles that readily contaminate marine ecosystems and industrial wastewaters.

Thetidibacter halocola gen. nov., sp. nov., a novel member within the family Roseobacteraceae isolated from seawater

A Gram-staining-negative, strictly aerobic, dark beige-colored, rod-shaped, chemoorganoheterotrophic, and catalase- and oxidase-positive bacterium, designated as KMU-90^T, was isolated from coastal seawater in the Republic of Korea, and subjected to a polyphasic study. The novel isolate was able to grow at 0-6.0% NaCl concentrations (w/v), pH 6.5-9.5, and 4-45 °C. The 16S rRNA gene sequences-based phylogeny revealed that the novel marine isolate belongs to the family Roseobacteraceae of class Alphaproteobacteria and that it shared the greatest sequence similarity (97.3%) with Aestuariicoccus marinus NAP41^T. The novel strain could be distinguished phenotypically from related representatives of the family Roseobacteraceae. The major (> 10%) fatty acids of strain KMU-90^T were C_18:1 ω7c and C_18:1 ω7c 11-methyl and the only respiratory quinone was ubiquinone-10 (Q-10). Strain KMU-90^T contained phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, two unidentified aminolipids, an unidentified phospholipid, and three unidentified glycolipids as polar lipids. The assembled draft genome size of strain KMU-90^T was 4.84 Mbp with a DNA G + C content of 66.5%. The average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values between the genomes of strain KMU-90^T and its closely related representatives were 77.0-79.0%, 14.6-20.0%, and 60.0-69.9%, respectively. From the polyphasic taxonomic results obtained, the strain is considered to represent a novel genus and a new species of the family Roseobacteraceae, for which the name Thetidibacter halocola gen. nov., sp. nov. is proposed. The type species is T. halocola, with the type strain KMU-90^T (= KCCM 90287^T = NBRC 113375^T).

Esfenvalerate biodegradation by marine fungi is affected by seawater and emulsifier formulation

Pesticides already were detected in the oceans, and their fates require evaluation in these environmental conditions. Therefore, marine-derived fungi were assessed for Esfenvalerate biodegradation, approaching the effects of seawater and use of commercial emulsifiable formulation. Residual pesticide and four metabolites were quantified. Furthermore, kinetics were determined for the three tested strains (Microsphaeropsis sp. CBMAI 1675, Acremonium sp. CBMAI 1676, and Westerdykella sp. CBMAI 1679). These facultative marine fungi biodegraded up to 87 ± 2% of 100 mg L^-1 Esfenvalerate in liquid media. However, Esfenvalerate biodegradation was faster in low salinity conditions than in artificial seawater. Moreover, rates of consumption were higher for Esfenvalerate in the pure form than for the commercial emulsifiable formulation. These results suggest that half-life of Esfenvalerate formulated with inert ingredients in seawater can have a double prolongation effect that can contribute to health and environmental issues.

Environmental occurrence, toxicity concerns, and biodegradation of neonicotinoid insecticides

Neonicotinoids (NEOs) are fourth generation pesticides, which emerged after organophosphates, pyrethroids, and carbamates and they are widely used in vegetables, fruits, cotton, rice, and other industrial crops to control insect pests. NEOs are considered ideal substitutes for highly toxic pesticides. Multiple studies have reported NEOs have harmful impacts on non-target biological targets, such as bees, aquatic animals, birds, and mammals. Thus, the remediation of neonicotinoid-sullied environments has gradually become a concern. Microbial degradation is a key natural method for eliminating neonicotinoid insecticides, as biodegradation is an effective, practical, and environmentally friendly strategy for the removal of pesticide residues. To date, several neonicotinoid-degrading strains have been isolated from the environment, including Stenotrophomonas maltophilia, Bacillus thuringiensis, Ensifer meliloti, Pseudomonas stutzeri, Variovorax boronicumulans, and Fusarium sp., and their degradation properties have been investigated. Furthermore, the metabolism and degradation pathways of neonicotinoids have been broadly detailed. Imidacloprid can form 6-chloronicotinic acid via the oxidative cleavage of guanidine residues, and it is then finally converted to non-toxic carbon dioxide. Acetamiprid can also be demethylated to remove cyanoimine (=N-CN) to form a less toxic intermediate metabolite. A few studies have discussed the neonicotinoid toxicity and microbial degradation in contaminated environments. This review is focused on providing an in-depth understanding of neonicotinoid toxicity, microbial degradation, catabolic pathways, and information related to the remediation process of NEOs. Future research directions are also proposed to provide a scientific basis for the risk assessment and removal of these pesticides.

Marine-derived fungi as biocatalysts

Marine microorganisms account for over 90% of ocean biomass and their diversity is believed to be the result of their ability to adapt to extreme conditions of the marine environment. Biotransformations are used to produce a wide range of high-added value materials, and marine-derived fungi have proven to be a source of new enzymes, even for activities not previously discovered. This review focuses on biotransformations by fungi from marine environments, including bioremediation, from the standpoint of the chemical structure of the substrate, and covers up to September 2022.

Bioprospecting for Novel Bacterial Sources of Hydrolytic Enzymes and Antimicrobials in the Romanian Littoral Zone of the Black Sea

Marine microorganisms have evolved a large variety of metabolites and biochemical processes, providing great opportunities for biotechnologies. In the search for new hydrolytic enzymes and antimicrobial compounds with enhanced characteristics, the current study explored the diversity of cultured and uncultured marine bacteria in Black Sea water from two locations along the Romanian coastline. Microbial cell density in the investigated samples varied between 65 and 12.7 × 10³ CFU·mL^-1. The total bacterial community identified by Illumina sequencing of 16S rRNA gene comprised 185 genera belonging to 46 classes, mainly Gammaproteobacteria, Alphaproteobacteria, Flavobacteriia, and 24 phyla. The 66 bacterial strains isolated on seawater-based culture media belonged to 33 genera and showed variable growth temperatures, growth rates, and salt tolerance. A great fraction of these strains, including Pseudoalteromonas and Flavobacterium species, produced extracellular proteases, lipases, and carbohydrases, while two strains belonging to the genera Aquimarina and Streptomyces exhibited antimicrobial activity against human pathogenic bacteria. This study led to a broader view on the diversity of microbial communities in the Black Sea, and provided new marine strains with hydrolytic and antimicrobial capabilities that may be exploited in industrial and pharmaceutical applications.

Insights into the microbial degradation and resistance mechanisms of glyphosate

Glyphosate, as one of the broad-spectrum herbicides for controlling annual and perennial weeds, is widely distributed in various environments and seriously threatens the safety of human beings and ecology. Glyphosate is currently degraded by abiotic and biotic methods, such as adsorption, photolysis, ozone oxidation, and microbial degradation. Of these, microbial degradation has become the most promising method to treat glyphosate because of its high efficiency and environmental protection. Microorganisms are capable of using glyphosate as a phosphorus, nitrogen, or carbon source and subsequently degrade glyphosate into harmless products by cleaving C-N and C-P bonds, in which enzymes and functional genes related to glyphosate degradation play an indispensable role. There have been many studies on the abiotic and biotic treatment technologies, microbial degradation pathways and intermediate products of glyphosate, but the related enzymes and functional genes involved in the glyphosate degradation pathways have not been further discussed. There is little information on the resistance mechanisms of bacteria and fungi to glyphosate, and previous investigations of resistance mechanisms have mainly focused on how bacteria resist glyphosate damage. Therefore, this review explores the microorganisms, enzymes and functional genes related to the microbial degradation of glyphosate and discusses the pathways of microbial degradation and the resistance mechanisms of microorganisms to glyphosate. This review is expected to provide reference for the application and improvement of the microbial degradation of glyphosate in microbial remediation.

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.

Cloning, Expression, and Characterization of a GHF 11 Xylanase from Alteromonas macleodii HY35 in Escherichia coli

A xylanase gene xynZT-1 from Alteromonas macleodii HY35 was cloned and expressed in Escherichia coli (E. coli). The sequencing results showed that the ORF of xynZT-1 was 831 bp. The xylanase DNA sequence encoded a 29 amino acids (aa) signal peptide and a 247-aa mature peptide. The XynZT-1 has been a calculated molecular weight (MW) of 27.93 kDa, isoelectric point (pI) of 5.11 and the formula C₁₂₆₆H₁₈₂₉N₃₂₇O₃₈₄S₅. The amino acid sequence of the xynZT-1 had a high similarity with that of glycosyl hydrolase family 11 (GHF11) reported from other microorganisms. The DNA sequence encoding mature peptide was subcloned into pET-28a(+) expression vector. The resulted plasmid pET-28a-xynZT-1 was transformed into E. coli BL21(DE3), and the recombinant strain BL21(DE3)/xynZT-1 was obtained. The optimum temperature and pH of the recombinant XynZT-1 were 45 ℃ and 5.0, respectively.

From Organic Wastes and Hydrocarbons Pollutants to Polyhydroxyalkanoates: Bioconversion by Terrestrial and Marine Bacteria

The use of fossil-based plastics has become unsustainable because of the polluting production processes, difficulties for waste management sectors, and high environmental impact. Polyhydroxyalkanoates (PHA) are bio-based biodegradable polymers derived from renewable resources and synthesized by bacteria as intracellular energy and carbon storage materials under nutrients or oxygen limitation and through the optimization of cultivation conditions with both pure and mixed culture systems. The PHA properties are affected by the same principles of oil-derived polyolefins, with a broad range of compositions, due to the incorporation of different monomers into the polymer matrix. As a consequence, the properties of such materials are represented by a broad range depending on tunable PHA composition. Producing waste-derived PHA is technically feasible with mixed microbial cultures (MMC), since no sterilization is required; this technology may represent a solution for waste treatment and valorization, and it has recently been developed at the pilot scale level with different process configurations where aerobic microorganisms are usually subjected to a dynamic feeding regime for their selection and to a high organic load for the intracellular accumulation of PHA. In this review, we report on studies on terrestrial and marine bacteria PHA-producers. The available knowledge on PHA production from the use of different kinds of organic wastes, and otherwise, petroleum-polluted natural matrices coupling bioremediation treatment has been explored. The advancements in these areas have been significant; they generally concern the terrestrial environment, where pilot and industrial processes are already established. Recently, marine bacteria have also offered interesting perspectives due to their advantageous effects on production practices, which they can relieve several constraints. Studies on the use of hydrocarbons as carbon sources offer evidence for the feasibility of the bioconversion of fossil-derived plastics into bioplastics.

Characterization of a novel glyphosate-degrading bacterial species, Chryseobacterium sp. Y16C, and evaluation of its effects on microbial communities in glyphosate-contaminated soil

Widespread use of the herbicide glyphosate in agriculture has resulted in serious environmental problems. Thus, environment-friendly technological solutions are urgently needed for the removal of residual glyphosate from soil. Here, we successfully isolated a novel bacterial strain, Chryseobacterium sp. Y16C, which efficiently degrades glyphosate and its main metabolite aminomethylphosphonic acid (AMPA). Strain Y16C was found to completely degrade glyphosate at 400 mg·L-1 concentration within four days. Kinetics analysis indicated that glyphosate biodegradation was concentration-dependent, with a maximum specific degradation rate, half-saturation constant, and inhibition constant of 0.91459 d-1, 15.79796 mg·L-1, and 290.28133 mg·L-1, respectively. AMPA was identified as the major degradation product of glyphosate degradation, suggesting that glyphosate was first degraded via cleavage of its C-N bond prior to subsequent metabolic degradation. Strain Y16C was also found to tolerate and degrade AMPA at concentrations up to 800 mg·L-1. Moreover, strain Y16C accelerated glyphosate degradation in soil indirectly by inducing a slight alteration in the diversity and composition of soil microbial community. Taken together, our results suggest that strain Y16C may be a potential microbial agent for bioremediation of glyphosate-contaminated soil.

Oxygen Measurement in Microdevices

Oxygen plays a fundamental role in respiration and metabolism, and quantifying oxygen levels is essential in many environmental, industrial, and research settings. Microdevices facilitate the study of dynamic, oxygen-dependent effects in real time. This review is organized around the key needs for oxygen measurement in microdevices, including integrability into microfabricated systems; sensor dynamic range and sensitivity; spatially resolved measurements to map oxygen over two- or three-dimensional regions of interest; and compatibility with multimodal and multianalyte measurements. After a brief overview of biological readouts of oxygen, followed by oxygen sensor types that have been implemented in microscale devices and sensing mechanisms, this review presents select recent applications in organs-on-chip in vitro models and new sensor capabilities enabling oxygen microscopy, bioprocess manufacturing, and pharmaceutical industries. With the advancement of multiplexed, interconnected sensors and instruments and integration with industry workflows, intelligent microdevice-sensor systems including oxygen sensors will have further impact in environmental science, manufacturing, and medicine.

Microbial Degradation of Aldrin and Dieldrin: Mechanisms and Biochemical Pathways

As members of the organochlorine group of insecticides, aldrin and dieldrin are effective at protecting agriculture from insect pests. However, because of excessive use and a long half-life, they have contributed to the major pollution of the water/soil environments. Aldrin and dieldrin have been reported to be highly toxic to humans and other non-target organisms, and so their use has gradually been banned worldwide. Various methods have been tried to remove them from the environment, including xenon lamps, combustion, ion conversion, and microbial degradation. Microbial degradation is considered the most promising treatment method because of its advantages of economy, environmental protection, and convenience. To date, a few aldrin/dieldrin-degrading microorganisms have been isolated and identified, including Pseudomonas fluorescens, Trichoderma viride, Pleurotus ostreatus, Mucor racemosus, Burkholderia sp., Cupriavidus sp., Pseudonocardia sp., and a community of anaerobic microorganisms. Many aldrin/dieldrin resistance genes have been identified from insects and microorganisms, such as Rdl, bph, HCo-LGC-38, S2-RDL^A302S, CSRDL1A, CSRDL2S, HaRdl-1, and HaRdl-2. Aldrin degradation includes three pathways: the oxidation pathway, the reduction pathway, and the hydroxylation pathway, with dieldrin as a major metabolite. Degradation of dieldrin includes four pathways: oxidation, reduction, hydroxylation, and hydrolysis, with 9-hydroxydieldrin and dihydroxydieldrin as major products. Many studies have investigated the toxicity and degradation of aldrin/dieldrin. However, few reviews have focused on the microbial degradation and biochemical mechanisms of aldrin/dieldrin. In this review paper, the microbial degradation and degradation mechanisms of aldrin/dieldrin are summarized in order to provide a theoretical and practical basis for the bioremediation of aldrin/dieldrin-polluted environment.

Novel pathway of acephate degradation by the microbial consortium ZQ01 and its potential for environmental bioremediation

The microbial degradation of acephate in pure cultures has been thoroughly explored, but synergistic metabolism at the community level has rarely been investigated. Here, we report a novel microbial consortium, ZQ01, capable of effectively degrading acephate and its toxic product methamidophos, which can use acephate as a source of carbon, phosphorus and nitrogen. The degradation conditions with consortium ZQ01 were optimized using response surface methodology at a temperature of 34.1 °C, a pH of 8.9, and an inoculum size of 2.4 × 10⁸ CFU·mL^-1, with 89.5% of 200 mg L^-1 acephate degradation observed within 32 h. According to the main products methamidophos, acetamide and acetic acid, a novel degradation pathway for acephate was proposed to include hydrolysis and oxidation as the main pathways of acephate degradation. Moreover, the bioaugmentation of acephate-contaminated soils with consortium ZQ01 significantly enhanced the removal rate of acephate. The results of the present work demonstrate the potential of microbial consortium ZQ01 to degrade acephate in water and soil environments, with a different and complementary acephate degradation pathway.

The Family Keeps on Growing: Four Novel Fungal OYEs Characterized

Aiming at expanding the portfolio of Old Yellow Enzymes (OYEs), which have been systematically studied to be employed in the chemical and pharmaceutical industries as useful biocatalysts, we decided to explore the immense reservoir of filamentous fungi. We drew from the genome of the two Ascomycetes Aspergillus niger and Botryotinia fuckeliana four new members of the OYE superfamily belonging to the classical and thermophilic-like subfamilies. The two BfOYEs show wider substrate spectra than the AnOYE homologues, which appear as more specialized biocatalysts. According to their mesophilic origins, the new enzymes neither show high thermostability nor extreme pH optimums. The crystal structures of BfOYE4 and AnOYE8 have been determined, revealing the conserved features of the thermophilic-like subclass as well as unique properties, such as a peculiar N-terminal loop involved in dimer surface interactions. For the classical representatives BfOYE1 and AnOYE2, model structures were built and analyzed, showing surprisingly wide open access to the active site cavities due to a shorter β6-loop and a disordered capping subdomain.

Immobilization of Baeyer-Villiger monooxygenase from acetone grown Fusarium sp

OBJECTIVE

A novel biocatalyst for Baeyer-Villiger oxidations is necessary for pharmaceutical and chemical industries, so this study aims to find a Baeyer-Villiger monooxygenase (BVMO) and to improve its stability by immobilization.

RESULTS

Acetone, the simplest ketone, was selected as the only carbon source for the screening of microorganisms with a BVMO. A eukaryote, Fusarium sp. NBRC 109816, with a BVMO (FBVMO), was isolated from a soil sample. FBVMO was overexpressed in E. coli and successfully immobilized by the organic-inorganic nanocrystal formation method. The immobilization improved the thermostability of FBVMO. Substrate specificity investigation revealed that both free and immobilized FBVMO were found to show catalytic activities not only for Baeyer-Villiger oxidation of ketones to esters but also for oxidation of sulfides to sulfoxides. Furthermore, a preparative scale reaction using immobilized FBVMO was successfully conducted.

CONCLUSIONS

FBVMO was discovered from an environmental sample, overexpressed in E. coli, and immobilized by the organic-inorganic nanocrystal formation method. The immobilization successfully improved its thermostability.

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).

Environmental Occurrence, Toxicity Concerns, and Degradation of Diazinon Using a Microbial System

Diazinon is an organophosphorus pesticide widely used to control cabbage insects, cotton aphids and underground pests. The continuous application of diazinon in agricultural activities has caused both ecological risk and biological hazards in the environment. Diazinon can be degraded via physical and chemical methods such as photocatalysis, adsorption and advanced oxidation. The microbial degradation of diazinon is found to be more effective than physicochemical methods for its complete clean-up from contaminated soil and water environments. The microbial strains belonging to Ochrobactrum sp., Stenotrophomonas sp., Lactobacillus brevis, Serratia marcescens, Aspergillus niger, Rhodotorula glutinis, and Rhodotorula rubra were found to be very promising for the ecofriendly removal of diazinon. The degradation pathways of diazinon and the fate of several metabolites were investigated. In addition, a variety of diazinon-degrading enzymes, such as hydrolase, acid phosphatase, laccase, cytochrome P450, and flavin monooxygenase were also discovered to play a crucial role in the biodegradation of diazinon. However, many unanswered questions still exist regarding the environmental fate and degradation mechanisms of this pesticide. The catalytic mechanisms responsible for enzymatic degradation remain unexplained, and ecotechnological techniques need to be applied to gain a comprehensive understanding of these issues. Hence, this review article provides in-depth information about the impact and toxicity of diazinon in living systems and discusses the developed ecotechnological remedial methods used for the effective biodegradation of diazinon in a contaminated environment.

Characterizations of novel pesticide-degrading bacterial strains from industrial wastes found in the industrial cities of Pakistan and their biodegradation potential

Background

Lack of infrastructure for disposal of effluents in industries leads to severe pollution of natural resources in developing countries. These pollutants accompanied by solid waste are equally hazardous to biological growth. Natural attenuation of these pollutants was evidenced that involved degradation by native microbial communities. The current study encompasses the isolation of pesticide-degrading bacteria from the vicinity of pesticide manufacturing industries.

Methods

The isolation and identification of biodegrading microbes was done. An enrichment culture technique was used to isolate the selected pesticide-degrading bacteria from industrial waste.

Results

Around 20 different strains were isolated, among which six isolates showed significant pesticide biodegrading activity. After 16S rRNA analysis, two isolated bacteria were identified as Acinetobacter baumannii (5B) and Acidothiobacillus ferroxidans, and the remaining four were identified as different strains of Pseudomonas aeruginosa (1A, 2B, 3C, 4D). Phylogenetic analysis confirmed their evolution from a common ancestor. All strains showed distinctive degradation ability up to 36 hours. The Pseudomonas aeruginosa strains 1A and 4D showed highest degradation percentage of about 80% for DDT, and P. aeruginosa strain 3C showed highest degradation percentage, i.e., 78% for aldrin whilst in the case of malathion, A. baumannii and A. ferroxidans have shown considerable degradation percentages of 53% and 54%, respectively. Overall, the degradation trend showed that all the selected strains can utilize the given pesticides as sole carbon energy sources even at a concentration of 50 mg/mL.

Conclusion

This study provided strong evidence for utilizing these strains to remove persistent residual pesticide; thus, it gives potential for soil treatment and restoration.

Molecular signatures of Janthinobacterium lividum from Trinidad support high potential for crude oil metabolism

Background

Janthinobacterium lividum is considered to be a psychrotrophic bacterial species. For the first time in the literature, J. lividum strains were isolated from Trinidad presenting with atypical features - hydrocarbonoclastic and able to survive in a tropical environment.

Methods

Identification of the Trinidad strains was carried out through 16S rRNA phylogenetic analysis. Gene-specific primers were designed to target the VioA which encodes violacein pigment and the EstA/B gene which encodes secreted extracellular lipase. Bioinformatics analyses were carried out on the nucleotide and amino acid sequences of VioA and EstA/B genes of the Trinidad Janthinobacterium strains to assess functionality and phylogenetic relatedness to other Janthinobacterium sequences specifically and more broadly, to other members of the Oxalobacteraceae family of betaproteobacteria.

Results

16S rRNA confirmed the identity of the Trinidad strains as J. lividum and resolved three of the Trinidad strains at the intra-specific level. Typical motility patterns of this species were recorded. VioAp sequences were highly conserved, however, synonymous substitutions located outside of the critical sites for enzyme function were detected for the Trinidad strains. Comparisons with PDB 6g2p model from aa231 to aa406 further indicated no functional disruption of the VioA gene of the Trinidad strains. Phylogeny of the VioA protein sequences inferred placement of all J. lividum taxa into a highly supported species-specific clade (bs = 98%). EstA/Bp sequences were highly conserved, however, synonymous substitutions were detected that were unique to the Trinidad strains. Phylogenetic inference positioned the Trinidad consensus VioA and EstA protein sequences in a clearly distinct branch.

Conclusions

The findings showed that the primary sequence of VioAp and EstA/Bp were unique to the Trinidad strains and these molecular signatures were reflected in phylogenetic inference. Our results supported chemotaxis, possible elective inactivation of VioA gene expression and secreted lipase activity as survival mechanisms of the Trinidad strains in petrogenic conditions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02346-4.

Biodegradation of fipronil: current state of mechanisms of biodegradation and future perspectives

Fipronil is a broad-spectrum phenyl-pyrazole insecticide that is widely used in agriculture. However, in the environment, its residues are toxic to aquatic animals, crustaceans, bees, termites, rabbits, lizards, and humans, and it has been classified as a C carcinogen. Due to its residual environmental hazards, various effective approaches, such as adsorption, ozone oxidation, catalyst coupling, inorganic plasma degradation, and microbial degradation, have been developed. Biodegradation is deemed to be the most effective and environmentally friendly method, and several pure cultures of bacteria and fungi capable of degrading fipronil have been isolated and identified, including Streptomyces rochei, Paracoccus sp., Bacillus firmus, Bacillus thuringiensis, Bacillus spp., Stenotrophomonas acidaminiphila, and Aspergillus glaucus. The metabolic reactions of fipronil degradation appear to be the same in different bacteria and are mainly oxidation, reduction, photolysis, and hydrolysis. However, the enzymes and genes responsible for the degradation are somewhat different. The ligninolytic enzyme MnP, the cytochrome P450 enzyme, and esterase play key roles in different strains of bacteria and fungal. Many unanswered questions exist regarding the environmental fate and degradation mechanisms of this pesticide. The genes and enzymes responsible for biodegradation remain largely unexplained, and biomolecular techniques need to be applied in order to gain a comprehensive understanding of these issues. In this review, we summarize the literature on the degradation of fipronil, focusing on biodegradation pathways and identifying the main knowledge gaps that currently exist in order to inform future research. KEY POINTS: • Biodegradation is a powerful tool for the removal of fipronil. • Oxidation, reduction, photolysis, and hydrolysis play key roles in the degradation of fipronil. • Possible biochemical pathways of fipronil in the environment are described.

Characterization of a Novel Shewanella algae Arginine Decarboxylase Expressed in Escherichia coli

Arginine decarboxylase (ADC) catalyzes the decarboxylation of arginine to form agmatine, an important physiological and pharmacological amine, and attracts attention to the enzymatic production of agmatine. In this study, we for the first time overexpressed and characterized the marine Shewanella algae ADC (SaADC) in Escherichia coli. The recombinant SaADC showed the maximum activity at pH 7.5 and 40 °C. The SaADC displayed previously unreported substrate inhibition when the substrate concentration was higher than 50 mM, which was the upper limit of testing condition in other reports. In the range of 1-80 mM L-arginine, the SaADC showed the K_m, k_cat, K_i, and k_cat/K_m values of 72.99 ± 6.45 mM, 42.88 ± 2.63 s^-1, 20.56 ± 2.18 mM, and 0.59 s/mM, respectively, which were much higher than the K_m (14.55 ± 1.45 mM) and k_cat (12.62 ± 0.68 s^-1) value obtained by assaying at 1-50 mM L-arginine without considering substrate inhibition. Both the k_cat values of SaADC with and without substrate inhibition are the highest ones to the best of our knowledge. This provides a reference for the study of substrate inhibition of ADCs.

Novel Mechanism and Kinetics of Tetramethrin Degradation Using an Indigenous Gordonia cholesterolivorans A16

Tetramethrin is a pyrethroid insecticide that is commonly used worldwide. The toxicity of this insecticide into the living system is an important concern. In this study, a novel tetramethrin-degrading bacterial strain named A16 was isolated from the activated sludge and identified as Gordonia cholesterolivorans. Strain A16 exhibited superior tetramethrin degradation activity, and utilized tetramethrin as the sole carbon source for growth in a mineral salt medium (MSM). High-performance liquid chromatography (HPLC) analysis revealed that the A16 strain was able to completely degrade 25 mg·L⁻¹ of tetramethrin after 9 days of incubation. Strain A16 effectively degraded tetramethrin at temperature 20–40 °C, pH 5–9, and initial tetramethrin 25–800 mg·L⁻¹. The maximum specific degradation rate (q_max), half-saturation constant (K_s), and inhibition constant (K_i) were determined to be 0.4561 day⁻¹, 7.3 mg·L⁻¹, and 75.2 mg·L⁻¹, respectively. The Box–Behnken design was used to optimize degradation conditions, and maximum degradation was observed at pH 8.5 and a temperature of 38 °C. Five intermediate metabolites were identified after analyzing the degradation products through gas chromatography–mass spectrometry (GC-MS), which suggested that tetramethrin could be degraded first by cleavage of its carboxylester bond, followed by degradation of the five-carbon ring and its subsequent metabolism. This is the first report of a metabolic pathway of tetramethrin in a microorganism. Furthermore, bioaugmentation of tetramethrin-contaminated soils (50 mg·kg⁻¹) with strain A16 (1.0 × 10⁷ cells g⁻¹ of soil) significantly accelerated the degradation rate of tetramethrin, and 74.1% and 82.9% of tetramethrin was removed from sterile and non-sterile soils within 11 days, respectively. The strain A16 was also capable of efficiently degrading a broad spectrum of synthetic pyrethroids including D-cyphenothrin, chlorempenthrin, prallethrin, and allethrin, with a degradation efficiency of 68.3%, 60.7%, 91.6%, and 94.7%, respectively, after being cultured under the same conditions for 11 days. The results of the present study confirmed the bioremediation potential of strain A16 from a contaminated environment.

Emerging Strategies for the Bioremediation of the Phenylurea Herbicide Diuron

Diuron (DUR) is a phenylurea herbicide widely used for the effective control of most annual and perennial weeds in farming areas. The extensive use of DUR has led to its widespread presence in soil, sediment, and aquatic environments, which poses a threat to non-target crops, animals, humans, and ecosystems. Therefore, the removal of DUR from contaminated environments has been a hot topic for researchers in recent decades. Bioremediation seldom leaves harmful intermediate metabolites and is emerging as the most effective and eco-friendly strategy for removing DUR from the environment. Microorganisms, such as bacteria, fungi, and actinomycetes, can use DUR as their sole source of carbon. Some of them have been isolated, including organisms from the bacterial genera Arthrobacter, Bacillus, Vagococcus, Burkholderia, Micrococcus, Stenotrophomonas, and Pseudomonas and fungal genera Aspergillus, Pycnoporus, Pluteus, Trametes, Neurospora, Cunninghamella, and Mortierella. A number of studies have investigated the toxicity and fate of DUR, its degradation pathways and metabolites, and DUR-degrading hydrolases and related genes. However, few reviews have focused on the microbial degradation and biochemical mechanisms of DUR. The common microbial degradation pathway for DUR is via transformation to 3,4-dichloroaniline, which is then metabolized through two different metabolic pathways: dehalogenation and hydroxylation, the products of which are further degraded via cooperative metabolism. Microbial degradation hydrolases, including PuhA, PuhB, LibA, HylA, Phh, Mhh, and LahB, provide new knowledge about the underlying pathways governing DUR metabolism. The present review summarizes the state-of-the-art knowledge regarding (1) the environmental occurrence and toxicity of DUR, (2) newly isolated and identified DUR-degrading microbes and their enzymes/genes, and (3) the bioremediation of DUR in soil and water environments. This review further updates the recent knowledge on bioremediation strategies with a focus on the metabolic pathways and molecular mechanisms involved in the bioremediation of DUR.

Identification and classification of Croceivirga thetidis sp. nov., a marine Flavobacteriaceae isolated from the hard coral Acropora

A taxonomic investigation using a polyphasic method was conducted to identify a novel marine flavobacterium, designated as DJ-13^T, isolated from the hard coral Acropora sp. collected at Okinawa, Japan. Bacterial cells were Gram-stain-negative, yellow-colored, strictly aerobic, rod-shaped, catalase- and oxidase-positive, non-motile, and chemoorganoheterotrophic. The novel isolate grew at NaCl concentrations of 0.5-7%, pH 6.5-9.0, and 15-37 °C. A phylogenetic study on the basis of the 16S rRNA gene sequence revealed that strain DJ-13^T belongs to the family Flavobacteriaceae and that it shared the greatest sequence similarity (95.9%) with Croceivirga lutea CSW06^T. Strain DJ-13^T comprised iso-C17:0 3-OH, iso-C15:0, and iso-C15:1 G as the main (> 10%) cellular fatty acids. Menaquinone-6 (MK-6) was the only respiratory quinone. The assembled draft genome size of strain DJ-13^T was 3.71 Mbp with G + C content of 38.7 mol%. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values of DJ-13^T and the species of the genus Croceivirga were found to be 74.9-75.5%, 13.4-14.7%, and 68.2-72.4%, respectively. Strain DJ-13^T contained phosphatidylethanolamine, two unidentified aminolipids, and five unidentified lipids as polar lipids. From the polyphasic taxonomic results presented, the strain is considered to represent a novel species of the genus Croceivirga for which the name Croceivirga thetidis sp. nov. is proposed. The type strain of C. thetidis sp. nov. is DJ-13^T (= KCTC 72790^T = NBRC 114252^T).

Machine Learning Approach Reveals the Assembly of Activated Sludge Microbiome with Different Carbon Sources during Microcosm Startup

Activated sludge (AS) microcosm experiments usually begin with inoculating a bioreactor with an AS mixed culture. During the bioreactor startup, AS communities undergo, to some extent, a distortion in their characteristics (e.g., loss of diversity). This work aimed to provide a predictive understanding of the dynamic changes in the community structure and diversity occurring during aerobic AS microcosm startups. AS microcosms were developed using three frequently used carbon sources: acetate (A), glucose (G), and starch (S), respectively. A mathematical modeling approach quantitatively determined that 1.7–2.4 times the solid retention time (SRT) was minimally required for the microcosm startups, during which substantial divergences in the community biomass and diversity (33–45% reduction in species richness and diversity) were observed. A machine learning modeling application using AS microbiome data could successfully (>95% accuracy) predict the assembly pattern of aerobic AS microcosm communities responsive to each carbon source. A feature importance analysis pinpointed specific taxa that were highly indicative of a microcosm feed source (A, G, or S) and significantly contributed for the ML-based predictive classification. The results of this study have important implications on the interpretation and validity of microcosm experiments using AS.

Emerging Technologies for Degradation of Dichlorvos: A Review

Dichlorvos (O,O-dimethyl O-(2,2-dichlorovinyl)phosphate, DDVP) is a widely acknowledged broad-spectrum organophosphorus insecticide and acaracide. This pesticide has been used for more than four decades and is still in strong demand in many developing countries. Extensive application of DDVP in agriculture has caused severe hazardous impacts on living systems. The International Agency for Research on Cancer of the World Health Organization considered DDVP among the list of 2B carcinogens, which means a certain extent of cancer risk. Hence, removing DDVP from the environment has attracted worldwide attention. Many studies have tested the removal of DDVP using different kinds of physicochemical methods including gas phase surface discharge plasma, physical adsorption, hydrodynamic cavitation, and nanoparticles. Compared to physicochemical methods, microbial degradation is regarded as an environmentally friendly approach to solve several environmental issues caused by pesticides. Till now, several DDVP-degrading microbes have been isolated and reported, including but not limited to Cunninghamella, Fusarium, Talaromyces, Aspergillus, Penicillium, Ochrobium, Pseudomonas, Bacillus, and Trichoderma. Moreover, the possible degradation pathways of DDVP and the transformation of several metabolites have been fully explored. In addition, there are a few studies on DDVP-degrading enzymes and the corresponding genes in microorganisms. However, further research relevant to molecular biology and genetics are still needed to explore the bioremediation of DDVP. This review summarizes the latest development in DDVP degradation and provides reasonable and scientific advice for pesticide removal in contaminated environments.

Biodegradation pathway of the organophosphate pesticides chlorpyrifos, methyl parathion and profenofos by the marine-derived fungus Aspergillus sydowii CBMAI 935 and its potential for methylation reactions of phenolic compounds

The indiscriminate use of organophosphate pesticides causes serious environmental and human health problems. This study aims the biodegradation of chlorpyrifos, methyl parathion and profenofos with the proposal of new biodegradation pathways employing marine-derived fungi as biocatalysts. Firstly, a growth screening was carried out with seven fungi strains and Aspergillus sydowii CBMAI 935 was selected. For chlorpyrifos, 32% biodegradation was observed and the metabolites tetraethyl dithiodiphosphate, 3,5,6-trichloropyridin-2-ol, 2,3,5-trichloro-6-methoxypyridine, and 3,5,6-trichloro-1-methylpyridin-2(1H)-one were identified. Whereas 80% methyl parathion was biodegraded with the identification of isoparathion, methyl paraoxon, trimethyl phosphate, O,O,O-trimethyl phosphorothioate, O,O,S-trimethyl phosphorothioate, 1-methoxy-4-nitrobenzene, and 4-nitrophenol. For profenofos, 52% biodegradation was determined and the identified metabolites were 4-bromo-2-chlorophenol, 4-bromo-2-chloro-1-methoxybenzene and O,O-diethyl S-propylphosphorothioate. Moreover, A. sydowii CBMAI 935 methylated different phenolic substrates (phenol, 2-chlorophenol, 6-chloropyridin-3-ol, and pentachlorophenol). Therefore, the knowledge about the fate of these compounds in the sea was expanded, and the marine-derived fungus A. sydowii CBMAI 935 showed potential for biotransformation reactions.

New Role for a Commercially Available Bioinsecticide: Bacillus thuringiensis Berliner Biodegrades the Pyrethroid Cypermethrin

The microbial diversity of several environments has been explored by researchers for the biodegradation of pyrethroids. In this study, a new approach was employed aiming at the use of Bacillus thuringiensis Berliner, a strain commercially available as bioinsecticide, for Cypermethrin (Cyp) biodegradation. This bacterial strain grew in the presence of Cyp and biodegraded this xenobiotic in a liquid medium. A central composite design for surface response methodology was employed for biodegradation. Under optimized conditions (50 mg·L^-1 of Cyp, pH 8.5, 37 °C), 83.5% biodegradation was determined with the production of 12.0 ± 0.6 mg·L^-1 3-phenoxybenzoic acid after 5 days. Moreover, a biodegradation pathway with the 18 compounds identified by GC-MS and LC-MS/MS was proposed. Experiments in soil for 28 days at 30 °C were performed, and 16.7% Cyp degradation was determined under abiotic conditions, whereas 36.6 ± 1.9% biodegradation was observed for B. thuringiensis Berliner with the native microbiome, indicating that bioaugmentation with this strain promoted a significant increase in the Cyp decontamination. Therefore, B. thuringiensis Berliner can act as biodegrader agent and insecticide at the same time, promoting decontamination of chemicals as Cyp while maintaining the protection of crops against insects. Moreover, B. thuringiensis species can produce bacteriocins with antifungal activity, which may increase agricultural productivity.

A potential type-II L-asparaginase from marine isolate Bacillus australimaris NJB19: Statistical optimization, in silico analysis and structural modeling

L-asparaginase is a cardinal biotherapeutic drug for treating acute lymphoblastic leukemia, which is highly prevalent in children worldwide. In the current investigation, L-asparaginase producing marine bacterial isolate, Bacillus australimaris NJB19 (MG734654), was observed to be producing extracellular glutaminase free L-asparaginase (13.27 ± 0.4 IU mL^-1). Production of L-asparaginase was enhanced by the Box-Behnken design approach that enumerated the significant variables affecting the enzyme production. The optimum levels of the derived variables resulted in 2.8-fold higher levels of the enzyme production (37.93 ± 1.06 IU mL^-1). An 1146 bp L-asparaginase biosynthetic gene of Bacillus australimaris NJB19 was identified and cloned in E. coli DH5α, fused with a histidine tag. The in silico analysis of the protein sequence revealed the presence of a signal peptide and classified it as a type II L-asparaginase. Toxic peptide prediction disclosed no toxin domain in the protein sequence, hence suggesting it as a non-toxic protein. The secondary structure analysis of the enzyme displayed a comparable percentage of alpha-helical and random coil structure, while 14.39% and 6.57% of amino acid residues were composed of extended strands and beta-turns, respectively. The functional sites in the three-dimensional structural model of the protein were predicted and interestingly had a few less conserved residues. Bacillus australimaris NJB19 identified in this study produces type-II L-asparaginase, known for its high affinity for asparagine and effectiveness against leukemic cells. Hence, these observations indicate the L-asparaginase, thus obtained, as a potentially significant and novel therapeutic drug.

Impact of redox-mediators in the degradation of olsalazine by marine-derived fungus, Aspergillus aculeatus strain bpo2: Response surface methodology, laccase stability and kinetics

The indiscriminate disposal of olsalazine in the environment poses a threat to human health and natural ecosystems because of its cytotoxic and genotoxic nature. In the present study, degradation efficiency of olsalazine by the marine-derived fungus, Aspergillus aculeatus (MT492456) was investigated. Optimization of physicochemical parameters (pH. Temperature, Dry weight) and redox mediators {(2,20-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS), p-Coumaric acid and 1-hydroxybenzotriazole (HOBT)} was achieved with Response Surface Methodology (RSM)-Box-Behnken Design (BBD) resulting in 89.43% removal of olsalazine on 7^th day. The second-order polynomial regression model was found to be statistically significant, adequate and fit with p < 0.0001, F value=41.87 and correlation coefficient (R²=0.9826). Biotransformation was enhanced in the redox mediator-laccase systems resulting in 99.5% degradation of olsalazine. The efficiency of ABTS in the removal of olsalazine was more pronounced than HOBT and p-Coumaric acid in the laccase-mediator system. This is attributed to the potent nature of the electron transfer mechanism deployed during oxidation of olsalazine. The pseudo-second-order kinetics revealed that the average half-life (t_1/2) and removal rates (k₁) increases with increasing concentrations of olsalazine. Michaelis-Menten kinetics affirmed the interaction between laccase and olsalazine under optimized conditions with maximum removal rate, V_max=111.11 hr^-1 and half-saturation constant, K_m=1537 mg L^-1. At the highest drug concentration (2 mM); 98%, 95% and 93% laccase was remarkably stabilized in the enzyme-drug degradation system by HOBT, ABTS and p-Coumaric acid respectively. This study further revealed that the deactivation of laccase by the redox mediators is adequately compensated with enhanced removal of olsalazine.

Marine Bacterial Esterases: Emerging Biocatalysts for Industrial Applications

The marine ecosystem has been known to be a significant source of novel enzymes. Esterase enzymes (EC 3.1.1.1) represent a diverse group of hydrolases that catalyze the cleavage and formation of ester bonds. Although esterases are widely distributed among marine organisms, only microbial esterases are of paramount industrial importance. This article discusses the importance of marine microbial esterases, their biochemical and kinetic properties, and their stability under extreme conditions. Since culture-dependent techniques provide limited insights into microbial diversity of the marine ecosystem, therefore, genomics and metagenomics approaches have widely been adopted in search of novel esterases. Additionally, the article also explains industrial applications of marine bacterial esterases particularly for the synthesis of optically pure substances, the preparation of enantiomerically pure drugs, the degradation of human-made plastics and organophosphorus compounds, degradation of the lipophilic components of the ink, and production of short-chain flavor esters.

The Callus of Phaseolus coccineus and Glycine max Biotransform Flavanones into the Corresponding Flavones

In vitro plant cultures are gaining in industrial importance, especially as biocatalysts and as sources of secondary metabolites used in pharmacy. The idea that guided us in our research was to evaluate the biocatalytic potential of newly obtained callus tissue towards flavonoid compounds. In this publication, we describe new ways of using callus cultures in the biotransformations. In the first method, the callus cultures grown on a solid medium are transferred to the water, the reaction medium into which the substrate is introduced. In the second method, biotransformation is carried out on a solid medium by growing callus cultures. In the course of the research, we have shown that the callus obtained from Phaseolus coccineus and Glycine max is capable of converting flavanone, 5-methoxyflavanone and 6-methoxyflavanone into the corresponding flavones.

Binding interaction of allethrin with esterase: Bioremediation potential and mechanism

The main aim of this work was to study the allethrin binding interactions with esterase and its bioremediation potential using an isolated bacterial strain CW7, identified as Pseudomonas nitroreducens. The degradation conditions with strain CW7 were optimized using response surface methodology at pH 7.0, a temperature of 32 °C, and an inocula concentration of 150 mg·L^-1, with 96% allethrin degradation observed over 7 days. The kinetic parameters q_max, K_s, and K_i were calculated to be 0.512 day^-1, 4.97 mg·L^-1, and 317.13 mg·L^-1, respectively. Nine intermediate metabolites were identified after analysing the degradation products by gas chromatography-mass spectrometry. Strain CW7 effectively degraded a wide variety of pyrethroids as a carbon source. Molecular modeling, docking, and enzyme kinetics were used to investigate the binding pocket of the esterase containing amino acids such as alanine, arginine, valine, proline, cysteine, glycine, isoleucine, phenylalanine, serine, asparagine, and threonine, which play active roles in allethrin degradation.

Microbial Modifications of Androstane and Androstene Steroids by Penicillium vinaceum

The biotransformation of steroid compounds is a promising, environmentally friendly route to new pharmaceuticals and hormones. One of the reaction types common in the metabolic fate of steroids is Baeyer-Villiger oxidation, which in the case of cyclic ketones, such as steroids, leads to lactones. Fungal enzymes catalyzing this reaction, Baeyer-Villiger monooxygenases (BVMOs), have been shown to possess broad substrate scope, selectivity, and catalytic performance competitive to chemical oxidation, being far more environmentally green. This study covers the biotransformation of a series of androstane steroids (epiandrosterone and androsterone) and androstene steroids (progesterone, pregnenolone, dehydroepiandrosterone, androstenedione, 19-OH-androstenedione, testosterone, and 19-nortestosterone) by the cultures of filamentous fungus Penicillium vinaceum AM110. The transformation was monitored by GC and the resulting products were identified on the basis of chromatographic and spectral data. The investigated fungus carries out effective Baeyer-Villiger oxidation of the substrates. Interestingly, introduction of the 19-OH group into androstenedione skeleton has significant inhibitory effect on the BVMO activity, as the 10-day transformation leaves half of the 19-OH-androstenedione unreacted. The metabolic fate of epiandrosterone and androsterone, the only 5α-saturated substrates among the investigated compounds, is more complicated. The transformation of these two substrates combined with time course monitoring revealed that each substrate is converted into three products, corresponding to oxidation at C-3 and C-17, with different time profiles and yields.

Annular oxygenation and rearrangement products of cryptotanshinone by biotransformation with marine-derived fungi Cochliobolus lunatus and Aspergillus terreus

Structural modification of natural products by biotransformation with fungi is an attractive tool to obtain novel bioactive derivatives. In the present study, cryptotanshinone (1), a quinoid abietane diterpene from traditional Chinese medicine Salvia miltiorrhiza (Danshen), was transformed by two marine-derived fungi. By using Cochliobolus lunatus TA26-46, one new oxygenated and rearranged product (2), containing a 5,6-dihydropyrano[4,3-b]chromene moiety, together with one known metabolite (10), were obtained from the converted broth of cryptotanshinone (1) with the isolated yields of 1.0% and 2.1%, respectively. While, under the action of Aspergillus terreus RA2905, seven new transformation products (3-9) as well as 10 with the fragments of 2-methylpropan-1-ol and oxygenated p-benzoquinone were produced and obtained with the isolated yields of 0.1%-1.3%. The structures of the new compounds were elucidated by comprehensive spectroscopic analysis including High Resolution Electrospray Ionization Mass Spectroscopy (HRESIMS), Nuclear Magnetic Resonance (NMR) and Electronic Circular Dichroism (ECD). The metabolic pathways of cryptotanshinone by these two fungi were presumed to be the opening and rearrangement of furan ring, and/or oxygenation of cyclohexane ring. Cryptotanshinone (1) and its metabolites displayed anti-inflammatory activities against NO production in LPS-stimulated BV-2 cells and antibacterial activities towards methicillin-resistant Staphylococcus aureus. These findings revealed the potential of marine fungi to transform the structures of natural products by biotransformation.

Harnessing the sponge microbiome for industrial biocatalysts

Within the marine sphere, host-associated microbiomes are receiving growing attention as prolific sources of novel biocatalysts. Given the known biocatalytic potential of poriferan microbial inhabitants, this review focuses on enzymes from the sponge microbiome, with special attention on their relevant properties and the wide range of their potential biotechnological applications within various industries. Cultivable bacterial and filamentous fungal isolates account for the majority of the enzymatic sources. Hydrolases, mainly glycoside hydrolases and carboxylesterases, are the predominant reported group of enzymes, with varying degrees of tolerance to alkaline pH and growing salt concentrations being common. Prospective areas for the application of these microbial enzymes include biorefinery, detergent, food and effluent treatment industries. Finally, alternative strategies to identify novel biocatalysts from the sponge microbiome are addressed, with an emphasis on modern -omics-based approaches that are currently available in the enzyme research arena. By providing this current overview of the field, we hope to not only increase the appetite of researchers to instigate forthcoming studies but also to stress how basic and applied research can pave the way for new biocatalysts from these symbiotic microbial communities in a productive fashion. KEY POINTS: • The sponge microbiome is a burgeoning source of industrial biocatalysts. • Sponge microbial enzymes have useful habitat-related traits for several industries. • Strategies are provided for the future discovery of microbial enzymes from sponges.

Degradation of Acephate and Its Intermediate Methamidophos: Mechanisms and Biochemical Pathways

Acephate is an organophosphate pesticide that has been widely used to control insect pests in agricultural fields for decades. However, its use has been partially restricted in many countries due to its toxic intermediate product methamidophos. Long term exposure to acephate and methamidophos in non-target organisms results in severe poisonous effects, which has raised public concern and demand for the removal of these pollutants from the environment. In this paper, the toxicological effects of acephate and/or methamidophos on aquatic and land animals, including humans are reviewed, as these effects promote the necessity of removing acephate from the environment. Physicochemical degradation mechanisms of acephate and/or methamidophos are explored and explained, such as photo-Fenton, ultraviolet/titanium dioxide (UV/TiO₂) photocatalysis, and ultrasonic ozonation. Compared with physicochemical methods, the microbial degradation of acephate and methamidophos is emerging as an eco-friendly method that can be used for large-scale treatment. In recent years, microorganisms capable of degrading methamidophos or acephate have been isolated, including Hyphomicrobium sp., Penicillium oxalicum, Luteibacter jiangsuensis, Pseudomonas aeruginosa, and Bacillus subtilis. Enzymes related to acephate and/or methamidophos biodegradation include phosphotriesterase, paraoxonase 1, and carboxylesterase. Furthermore, several genes encoding organophosphorus degrading enzymes have been identified, such as opd, mpd, and ophc2. However, few reviews have focused on the biochemical pathways and molecular mechanisms of acephate and methamidophos. In this review, the mechanisms and degradation pathways of acephate and methamidophos are summarized in order to provide a new way of thinking for the study of the degradation of acephate and methamidophos.

Engineering marine fungi for conversion of D-galacturonic acid to mucic acid

BACKGROUND

Two marine fungi, a Trichoderma sp. and a Coniochaeta sp., which can grow on D-galacturonic acid and pectin, were selected as hosts to engineer for mucic acid production, assessing the suitability of marine fungi for production of platform chemicals. The pathway for biotechnologcial production of mucic (galactaric) acid from D-galacturonic acid is simple and requires minimal modification of the genome, optimally one deletion and one insertion. D-Galacturonic acid, the main component of pectin, is a potential substrate for bioconversion, since pectin-rich waste is abundant.

RESULTS

Trichoderma sp. LF328 and Coniochaeta sp. MF729 were engineered using CRISPR-Cas9 to oxidize D-galacturonic acid to mucic acid, disrupting the endogenous pathway for D-galacturonic acid catabolism when inserting a gene encoding bacterial uronate dehydrogenase. The uronate dehydrogenase was expressed under control of a synthetic expression system, which fucntioned in both marine strains. The marine Trichoderma transformants produced 25 g L-1 mucic acid from D-galacturonic acid in equimolar amounts: the yield was 1.0 to 1.1 g mucic acid [g D-galacturonic acid utilized]-1. D-Xylose and lactose were the preferred co-substrates. The engineered marine Trichoderma sp. was more productive than the best Trichoderma reesei strain (D-161646) described in the literature to date, that had been engineered to produce mucic acid. With marine Coniochaeta transformants, D-glucose was the preferred co-substrate, but the highest yield was 0.82 g g-1: a portion of D-galacturonic acid was still metabolized. Coniochaeta sp. transformants produced adequate pectinases to produce mucic acid from pectin, but Trichoderma sp. transformants did not.

CONCLUSIONS

Both marine species were successfully engineered using CRISPR-Cas9 and the synthetic expression system was functional in both species. Although Coniochaeta sp. transformants produced mucic acid directly from pectin, the metabolism of D-galacturonic acid was not completely disrupted and mucic acid amounts were low. The D-galacturonic pathway was completely disrupted in the transformants of the marine Trichoderma sp., which produced more mucic acid than a previously constructed T. reesei mucic acid producing strain, when grown under similar conditions. This demonstrated that marine fungi may be useful as production organisms, not only for native enzymes or bioactive compounds, but also for other compounds.