Exploring the role of microbial proteins in controlling environmental pollutants based on molecular simulation

Molecular simulation has been widely used to study microbial proteins' structural composition and dynamic properties, such as volatility, flexibility, and stability at the microscopic scale. Herein, this review describes the key elements of molecular docking and molecular dynamics (MD) simulations in molecular simulation; reviews the techniques combined with molecular simulation, such as crystallography, spectroscopy, molecular biology, and machine learning, to validate simulation results and bridge information gaps in the structure, microenvironmental changes, expression mechanisms, and intensity quantification; illustrates the application of molecular simulation, in characterizing the molecular mechanisms of interaction of microbial proteins with four different types of contaminants, namely heavy metals (HMs), pesticides, dyes and emerging contaminants (ECs). Finally, the review outlines the important role of molecular simulations in the study of microbial proteins for controlling environmental contamination and provides ideas for the application of molecular simulation in screening microbial proteins and incorporating targeted mutagenesis to obtain more effective contaminant control proteins.

Application of Nanomaterials in the Production of Biomolecules in Microalgae: A Review

Nanomaterials (NMs) are becoming more commonly used in microalgal biotechnology to empower the production of algal biomass and valuable metabolites, such as lipids, proteins, and exopolysaccharides. It provides an effective and promising supplement to the existing algal biotechnology. In this review, the potential for NMs to enhance microalgal growth by improving photosynthetic utilization efficiency and removing reactive oxygen species is first summarized. Then, their positive roles in accumulation, bioactivity modification, and extraction of valuable microalgal metabolites are presented. After the application of NMs in microalgae cultivation, the extracted metabolites, particularly exopolysaccharides, contain trace amounts of NM residues, and thus, the impact of these residues on the functional properties of the metabolites is also evaluated. Finally, the methods for removing NM residues from the extracted metabolites are summarized. This review provides insights into the application of nanotechnology for sustainable production of valuable metabolites in microalgae and will contribute useful information for ongoing and future practice.

Designing advanced S-scheme CdS QDs/La-Bi2WO6 photocatalysts for efficient degradation of RhB

Finding effective strategies to design efficient photocatalysts and decompose refractory organic compounds in wastewater is a challenging problem. Herein, by coupling element doping and constructing heterostructures, S-scheme CdS QDs/La-Bi2WO6 (CS/LBWO) photocatalysts are designed and synthesized by a simple hydrothermal method. As a result, the RhB degradation efficiency of the optimized 5% CS/LBWO reached 99% within 70 min of illumination with excellent stability and recyclability. CS/LBWO shows improvement in the adsorption range of visible light and promotes electron-hole pair generation/migration/separation, attributing the superior degradation performance. The degradation RhB mechanism is proposed by a free radical capture experiment, electron paramagnetic resonance, and high-performance liquid chromatography-mass spectrometry results, indicating that h+ and •O2 - play a significant role during four degradation processes: de-ethylation, chromophore cleavage, ring opening, and mineralization. Based on in situ irradiated X-ray photoelectron spectroscopy, Mulliken electronegativity theory, and the work function results, the S-scheme heterojunction of CS/LBWO promotes the transfer of photogenerated electron-hole pairs and promotes the generation of reactive radicals. This work not only reports that 5% CS/LBWO is a promising photocatalyst for degradation experiments but also provides an approach to design advanced photocatalysts by coupling element doping and constructing heterostructures.

Effect of Tube Diameters and Functional Groups on Adsorption and Suspension Behaviors of Carbon Nanotubes in Presence of Humic Acid

The adsorption and suspension behaviors of carbon nanotubes (CNTs) in the water environment determine the geochemical cycle and ecological risk of CNTs and the compounds attached to them. In this study, CNTs were selected as the research object, and the effect of tube diameters and functional groups (multiwall CNTs (MWNTs) and hydroxylated MWNTs (HMWNTs)) on the adsorption and suspension behaviors of the CNTs in the presence of humic acid (HA) was systematically analyzed. The results indicate that HA adsorption decreased with the increase in the solution pH, and the adsorption amount and rate were negatively correlated with the tube diameter of the CNTs. The surface hydroxylation of the CNTs prevented the adsorption of HA, and the maximum adsorption amounts on the MWNTs and HMWNTs were 195.95 and 74.74 mg g-1, respectively. HA had an important effect on the suspension of the CNTs, especially for the surface hydroxylation, and the suspension of the CNTs increased with the increase in the tube diameter. The characteristics of the CNTs prior to and after adsorbing HA were characterized by transmission electron microscopy, fluorescence spectroscopy, Fourier-transform infrared spectroscopy and Raman spectroscopy. The results indicate that surface hydroxylation of the CNTs increased the adsorption of aromatic compounds, and that the CNTs with a smaller diameter and a larger specific surface area had a disordered carbon accumulation microstructure and many defects, where the adsorption of part of the HA would cover the defects on the CNTs' surface. Density functional theory (DFT) calculations demonstrated that HA was more easily adsorbed on the CNTs without surface hydroxylation. This investigation is helpful in providing a theoretical basis for the scientific management of the production and application of CNTs, and the scientific assessment of their geochemical cycle and ecological risk.

Wastewater treatment nexus: Carbon nanomaterials towards potential aquatic ecotoxicity

Carbon nanomaterials (CNMs) provide an effective solution and a novel advancement for wastewater treatment. In this review, a total of 3823 bibliographic records derived from recent 10 years are visualized based on scientometric analysis. The results indicate metal-free CNMs-mediated advanced oxidation processes (AOPs) might be a motive force to develop CNMs application for wastewater treatment; however, corresponding evaluations of aquatic toxicity still lack sufficient attention. Therefore, recent breakthroughs and topical innovations related to prevalent wastewater treatment technologies (i.e., adsorption, catalysis and membrane separation) using three typical dimensional CNMs (nanodiamonds, carbon nanotubes, and graphene-based nanomaterials) are comprehensively summarized in-depth, along with a compendious introduction to some novel techniques (e.g., computational simulation) for identifying reaction mechanisms. Then, current research focusing on CNMs-associated aquatic toxicity is discussed thoroughly, mainly demonstrating: (1) the adverse effects on aquatic organisms should not be overlooked prior to large-scale CNMs application; (2) divergent consequences can be further reduced if the ecological niche of aquatic organisms is emphasized; and (3) further investigations on joint toxicity can provide greater beneficial insight into realistic exposure scenarios. Finally, ongoing challenges and developmental directions of CNMs-based wastewater treatment and evaluation of its aquatic toxicity are pinpointed and shaped in terms of future research.

Environment-Friendly Removal Methods for Endocrine Disrupting Chemicals

In the past few decades, many emerging pollutants have been detected and monitored in different water sources because of their universal consumption and improper disposal. Among these, endocrine-disrupting chemicals (EDCs), a group of organic chemicals, have received global attention due to their estrogen effect, toxicity, persistence and bioaccumulation. For the removal of EDCs, conventional wastewater treatment methods include flocculation, precipitation, adsorption, etc. However, there are some limitations on these common methods. Herein, in order to enhance the public’s understanding of environmental EDCs, the definition of EDCs and the characteristics of several typical EDCs (physical and chemical properties, sources, usage, concentrations in the environment) are reviewed and summarized in this paper. In particular, the methods of EDC removal are reviewed, including the traditional methods of EDC removal, photocatalysis, biodegradation of EDCs and the latest research results of EDC removal. It is proposed that photocatalysis and biodegradation could be used as an environmentally friendly and efficient EDC removal technology. Photocatalytic technology could be one of the water treatment methods with the most potential, with great development prospects due to its high catalytic efficiency and low energy consumption. Biodegradation is expected to replace traditional water treatment methods and is also considered to be a highly promising method for efficient removal of EDCs. Besides, we summarize several photocatalysts with high catalytic activity and some fungi, bacteria and algae with strong biodegradability.

Advances in the application, toxicity and degradation of carbon nanomaterials in environment: A review

Carbon nanomaterials (CNMs) are novel nanomaterials with excellent physicochemical properties, which are widely used in biomedicine, energy and sensing. Besides, CNMs also play an important role in environmental pollution control, which can absorb heavy metals, antibiotics and harmful gases. However, CNMs are inevitably entering the environment while they are rapidly developing. They are harmful to living organisms in the environment and are difficult to degrade under natural conditions. Here, we systematically describe the toxicity of carbon nanotubes (CNTs), graphene (GRA) and C₆₀ to cells, animals, humans, and microorganisms. According to the current research results, the toxicity mechanism is summarized, including oxidative stress response, mechanical damage and effects on biological enzymes. In addition, according to the latest research progress, we focus on the two major degradation methods of chemical degradation and biodegradation of CNTs, GRA and C₆₀. Meanwhile, the reaction conditions and degradation mechanisms of degradation are respectively stated. Moreover, we have prospects for the limitations of CNM degradation under non-experimental conditions and their potential application.

How do proteins 'response' to common carbon nanomaterials?

Carbon nanomaterials are widely produced and applied in biological and environmental fields because of their outstanding physical and chemical properties, which pose a threat to the safety of living organisms and the ecological environment. Therefore, understanding how carbon nanomaterials and their derivatives work on organisms is becoming important. In recent years, more and more researchers have explored the damage of carbon nanomaterials to organisms at the molecular level. This review pays special emphasis on how proteins response to the main carbon nanomaterials (fullerene, carbon nanotubes, graphene and their derivatives). In addition, how to use the interaction between carbon nanomaterials and proteins to do some beneficial things for human and the development of safe nanomaterials is simply discussed. Finally, some suggestions have been made to lay a theoretical foundation for future research.

Understanding the influence of carbon nanomaterials on microbial communities

Carbon nanomaterials (CNMs) are widely used because of their unique advantages in recent years. At the same time, the influence of CNMs on the environment is becoming increasingly prominent. This review mainly introduces the research progress in the effects of fullerenes, multi-walled carbon nanotubes (MWCNTs), single-walled carbon nanotubes (SWCNTs) and graphene on microorganisms and their toxicity mechanisms. On this basis, we have analyzed beneficial and adverse effects of fullerenes, graphene, MWCNTs and SWCNTs to microorganisms, and discussed the similarities of the toxicity mechanisms of different CNMs on microorganisms. This review helps provide ideas on how to protect microorganisms from the impacts of carbon nanomaterials, and it will be conductive to providing a strong theoretical basis for better application of carbon nanomaterials.

Nanomaterials and plants: Positive effects, toxicity and the remediation of metal and metalloid pollution in soil

Currently, the pollution of metals and metalloids in the soil has attracted considerable attention. Phytoremediation is considered an environmentally friendly means of remediating pollution, but often takes a long time to perform. Therefore, the combination of plants and nanomaterials in environmental management has attracted the attention of many researchers because some nanomaterials can promote the germination of plant seeds and the growth of whole plants. However, when the concentration of nanomaterials is not controlled properly, certain toxicity will be produced. This paper reviews research on the combination of plant and nanomaterials for the remediation of contaminated environments, as well as on the effects of nanomaterials on plants.

Toxicity of carbon nanomaterials to plants, animals and microbes: Recent progress from 2015-present

Nanotechnology has gained significant development over the past decades, which led to the revolution in the fields of information, medicine, industry, food security and aerospace aviation. Nanotechnology has become a new research hot spot in the world. However, we cannot only pay attention to its benefit to the society and economy, because its wide use has been bringing potential environmental and health effects that should be noticed. This paper reviews the recent progress from 2015-present in the toxicity of various carbon nanomaterials to plants, animals and microbes, and lays the foundation for further study on the environmental and ecological risks of carbon nanomaterials.

Interactions of carbon nanotubes and/or graphene with manganese peroxidase during biodegradation of endocrine disruptors and triclosan

Molecular-level biodegradation processes of bisphenol A (BPA), nonylphenol (NP) and triclosan (TCS) mediated by manganese peroxidase (MnP) were investigated with and without single-walled carbon nanotube (SWCNT) and/or graphene (GRA). Although the incorporation of SWCNT, GRA or their combination (SWCNT+GRA) did not break up the complexes composed of manganese peroxidase (MnP) and these substrates, they had different effects on the native contacts between the substrates and MnP. GRA tended to decrease the overall stability of the binding between MnP and its substrates. SWCNT or SWCNT+GRA generally had a minor impact on the mean binding energy between MnP and its substrates. We detected some sensitive residues from MnP that were dramatically disturbed by the GRA, SWCNT or SWCNT+GRA. Nanomaterials changed the number and behavior of water molecules adjacent to both MnP and its substrates, which was not due to the destruction of H-bond network formed by sensitive regions and water molecules. The present results are useful for understanding the molecular basis of pollutant biodegradation affected by the nanomaterials in the environment, and are also helpful in assessing the risks of these materials to the environment.

Biodegradation of Carbon Nanotubes, Graphene, and Their Derivatives

Carbon nanotubes (CNTs), graphene (GRA), and their derivatives are promising materials for a wide range of applications such as pollutant removal, enzyme immobilization, bioimaging, biosensors, and drug delivery and are rapidly increasing in use and increasingly mass produced. The biodegradation of carbon nanomaterials by microbes and enzymes is now of great importance for both reducing their toxicity to living organisms and removing them from the environment. Here we review recent progress in the biodegradation field from the point of view of the primary microbes and enzymes that can degrade these nanomaterials, along with experimental and molecular simulation methods for the exploration of nanomaterial degradation. Further efforts should primarily aim toward expanding the repertoire of microbes and enzymes and exploring optimal conditions for the degradation of nanomaterials.

Single-walled carbon nanotube release affects the microbial enzyme-catalyzed oxidation processes of organic pollutants and lignin model compounds in nature

The question how microbial enzyme-catalyzed oxidation processes of organic pollutants and lignin model compounds (LMCs) are affected by the release of single-walled carbon nanotube (SWCNT) into the environment remains to be addressed at the molecular level. We have, therefore concentrated the effects of SWCNT on some important properties associated with enzyme activity and function during microbial oxidation of polycyclic aromatic hydrocarbons (benzo(a)pyrene, acenaphthene and anthracene), LMCs (2,6-dimethoxyphenol, guaiacol and veratryl alcohol) and β-hexachlorocyclohexane, including the behaviour of water molecules, hydrogen bonds (HBs) and hydrophobic interactions (HYs) between ligand and the enzyme, and conformational dynamics in N- and C-terminus. Our study revealed that SWCNT significantly affected the behaviour of water molecules within 5 Å of both these substrates and their respective enzymes during oxidation (p < 0.01), by increasing or decreasing the water number near them. SWCNT tended to significantly enhance or reduce the stability of atom pairs that formed the HBs and HYs (p < 0.01). N- and C-terminus conformations underwent transitions between positive and negative states or between positive state or between negative state in all analyzed complexes. Significant conformational transitions were found for all C-terminus, but only for a part of N-terminus after the inclusion of the SWCNT. These results showed that SWCNT release would significantly affect the microbial enzyme-catalyzed processes of organic pollutants and LMCs in nature.