Biodegradation of phenol and its derivatives by engineered bacteria: current knowledge and perspectives

Biodegradation of phenol-contaminated soil and plant growth promotion by Myroides xuanwuensis H13

Physicochemical methods for remediating phenol-contaminated soils are costly and inefficient, making biodegradation an environmentally friendly alternative approach. This study aims to screen for potential phenol-degrading bacteria and to verify the removal capacities of a selected strain in a bioaugmentation experiment at the greenhouse level using Brassica chinensis L. (Chinese cabbage) as the model plant and phenol-contaminated soil. In parallel, pot experiments were conducted using a collaborative approach based on this model system. We found that Myroides xuanwuensis strain H13 showed a high degradation capability, with a 97.67% efficiency in degrading 100 mg/L phenol. Under shaking flask conditions, H13 facilitated the solubilization of tricalcium phosphate and potassium feldspar powder. Pot experiments suggested a phenol removal percentage of 89.22% and enhanced availability of soil phosphorus and potassium for plants with H13 inoculation. In this case, the abundance of soil microbes and the activity of soil enzymes significantly increased as well. Furthermore, both photosynthesis and the antioxidant system in Chinese cabbage were enhanced following H13 inoculation, resulting in its increased yield and quality. Partial least squares path modeling revealed that H13 can primarily affect plant root growth, with a secondary impact on photosynthesis. These findings highlight the potential of biodegradation from phenol-degrading bacteria as a promising strategy for efficient phenol removal from soil while promoting plant growth and health.IMPORTANCEThis study is significant for environmental remediation and agriculture by its exploration of a more environmentally friendly and cost-effective bio-strategy in treating phenol-contaminated soil. These findings have essential implications for environmental remediation efforts and sustainable agriculture. By utilizing the biodegradation capabilities of Myroides xuanwuensis strain H13, it is possible to remove phenol contaminants from the soil efficiently, reducing their negative effects. Furthermore, the enhanced growth and health of the Chinese cabbage plants indicate the potential of this approach to promote sustainable crop production.

Recent advances in clay minerals for groundwater pollution control and remediation

Clay minerals are abundant on Earth and have been crucial to the advancement of human civilization. The ability of clay minerals to absorb chemicals is frequently utilized to remove hazardous compounds from aquatic environments. Moreover, clay-based adsorbent products are both environmentally acceptable and affordable. This study provides an overview of advances in clay minerals in the field of groundwater remediation and related predictions. The existing literature was examined using data and information aggregation approaches. Keyword clustering analysis of the relevant literature revealed that clay minerals are associated with groundwater utilization and soil pollution remediation. Principal component analysis was used to assess the relationships among clay mineral modification methods, pollutant properties, and the Langmuir adsorption capacity (Qmax). The results demonstrated that pollutant properties affect the Qmax of pollutants adsorbed by clay minerals. Systematic cluster analysis was utilized to classify the collected data and investigate the relationships. The pollution adsorption mechanism of the unique structure of clay minerals was investigated based on the characterization results. Modified clay minerals exhibited changes in surface functional groups, internal structure, and pHpzc. This review provides a summary of recent clay-based materials and their applications in groundwater remediation, as well as discussions of their challenges and future prospects.

Comparative Genomic and Transcriptomic Analysis of Phenol Degradation and Tolerance in Acinetobacter lwoffii through Adaptive Evolution

Microorganism-based methods have been widely applied for the treatment of phenol-polluted environments. The previously isolated Acinetobacter lwoffii NL1 strain could completely degrade 0.5 g/L phenol within 12 h, but not higher concentrations of phenol. In this study, we developed an evolutionary strain NL115, through adaptive laboratory evolution, which possessed improved degradation ability and was able to degrade 1.5 g/L phenol within 12 h. Compared with that of the starting strain NL1, the concentration of degradable phenol by the developed strain increased three-fold; its phenol tolerance was also enhanced. Furthermore, comparative genomics showed that sense mutations mainly occurred in genes encoding alkyl hydroperoxide reductase, phenol hydroxylase, 30S ribosomal protein, and mercury resistance operon. Comparative transcriptomics between A. lwoffii NL115 and NL1 revealed the enrichment of direct degradation, stress resistance, and vital activity processes among the metabolic responses of A. lwoffii adapted to phenol stress. Among these, all the upregulated genes (log2fold-change > 5) encoded peroxidases. A phenotypic comparison of A. lwoffii NL1 and NL115 found that the adapted strain NL115 exhibited strengthened antioxidant capacity. Furthermore, the increased enzymatic activities of phenol hydroxylase and alkyl hydroperoxide reductase in A. lwoffii NL115 validated their response to phenol. Overall, this study provides insight into the mechanism of efficient phenol degradation through adaptive microbial evolution and can help to drive improvements in phenol bioremediation.

An Intelligent Synthetic Bacterium for Chronological Toxicant Detection, Biodegradation, and Its Subsequent Suicide

Modules, toolboxes, and synthetic biology systems may be designed to address environmental bioremediation. However, weak and decentralized functional modules require complex control. To address this issue, an integrated system for toxicant detection and biodegradation, and subsequent suicide in chronological order without exogenous inducers is constructed. Salicylic acid, a typical pollutant in industrial wastewater, is selected as an example to demonstrate this design. Biosensors are optimized by regulating the expression of receptors and reporters to get 2-fold sensitivity and 6-fold maximum output. Several stationary phase promoters are compared, and promoter Pfic is chosen to express the degradation enzyme. Two concepts for suicide circuits are developed, with the toxin/antitoxin circuit showing potent lethality. The three modules are coupled in a stepwise manner. Detection and biodegradation, and suicide are sequentially completed with partial attenuation compared to pre-integration, except for biodegradation, being improved by the replacements of ribosome binding site. Finally, a long-term stability test reveals that the engineered strain maintained its function for ten generations. The study provides a novel concept for integrating and controlling functional modules that can accelerate the transition of synthetic biology from conceptual to practical applications.

Metabolic Pathway of Phenol Degradation of a Cold-Adapted Antarctic Bacteria, Arthrobacter sp

Phenol is an important pollutant widely discharged as a component of hydrocarbon fuels, but its degradation in cold regions is challenging due to the harsh environmental conditions. To date, there is little information available concerning the capability for phenol biodegradation by indigenous Antarctic bacteria. In this study, enzyme activities and genes encoding phenol degradative enzymes identified using whole genome sequencing (WGS) were investigated to determine the pathway(s) of phenol degradation of Arthrobacter sp. strains AQ5-05 and AQ5-06, originally isolated from Antarctica. Complete phenol degradative genes involved only in the ortho-cleavage were detected in both strains. This was validated using assays of the enzymes catechol 1,2-dioxygenase and catechol 2,3-dioxygenase, which indicated the activity of only catechol 1,2-dioxygenase in both strains, in agreement with the results from the WGS. Both strains were psychrotolerant with the optimum temperature for phenol degradation, being between 10 and 15 °C. This study suggests the potential use of cold-adapted bacteria in the bioremediation of phenol pollution in cold environments.

Adsorption of hydroquinone and Pb(II) from water by β-cyclodextrin/polyethyleneimine bi-functional polymer

A novel bi-functional β-cyclodextrin polymer (CD@TCT@PEI) was synthesized for the removal of hydroquinone and Pb(II) from wastewater. The structure and adsorption performance of CD@TCT@PEI towards hydroquinone and Pb(II) were studied comprehensively. Both of the adsorption processes fit the pseudo-second-order kinetic model well. The adsorption isotherms of hydroquinone and Pb(II) could be described well by Langmuir isotherm model, and the maximum adsorption capacities of hydroquinone and Pb(II) are 364.86 and 113.52 mg g^-1, respectively. The adsorption of hydroquinone and Pb(II) on CD@TCT@PEI is an exothermic and spontaneous process. The adsorbed CD@TCT@PEI could be regenerated easily, and can still maintain high adsorption performance after 5 cycles. The electrostatic interaction and coordination interaction account for the adsorption of Pb(II), and inclusion of cyclodextrin and hydrogen-bond interaction are responsible for hydroquinone adsorption. This study provides some insights to design an adsorbent that can simultaneously remove heavy metal ions and organic micropollutants from wastewater.

Pseudomonas phenolilytica sp. nov., a novel phenol-degrading bacterium

This study describes a bacterium strain RBPA9 isolated from a municipality waste dumping area capable of degrading phenol, proposed as a novel species of Pseudomonas. Cells are Gram-negative, rod shaped, aerobic and motile. The genome is 3.92 Mb, and the G + C content is 64.64%. The overall genome relatedness indices such as in silico DNA-DNA hybridization (isDDH), average nucleotide identity (ANI), and average amino acid identity (AAI) values were below 70% and 95-96%, respectively. Phylogenetic analysis based on genome-wide core genes and 16S rRNA gene sequences revealed that strain RBPA9 clustered with Pseudomonas stutzeri ATCC 17588 ^T in both the phylogenetic trees. Maximum growth was recorded at 200 mg /L concentration of phenol which was consumed within 24 h. A gene cluster of phenol degradation pathway was detected. The quantitative real-time PCR (RT-PCR) demonstrated the expression of all the genes required in the meta-cleavage pathway of phenol in RBPA9. Our results reveal that strain RBPA9 represents a novel species for which Pseudomonas phenolilytica sp. nov. is proposed. The type strain is RBPA9^T (= TBRC 15231 ^T = NBRC 115284 ^T).

Light-assisted Ullmann coupling of phenols and aryl halides: The synergetic effect between plasmonic copper nanoparticles and carbon nanotubes from various sources

Utilizing light and plastic wastes as resources to turn the wasted phenols and hazardous aryl halides into value added chemicals seems to be an attractive idea for alleviating the energy crisis and environmental problems. In this work, we loaded plasmonic copper nanoparticles (Cu NPs) onto carbon nanotubes (CNTs) from various sources including commercial CNTs and those derived from plastic wastes. Under visible-light irradiation, the catalyst could efficiently convert phenols and aryl halides to diaryl ethers. Similar with commercial CNTs, excellent activity is also achieved when utilizing CNTs derived from different kinds of plastic wastes as support for the system. Further investigation shows that the visible-light irradiation and light-excited plasmonic Cu NPs are necessary to inhibit the phenol degradation on CNTs and in turn promote the cross-coupling of phenol and aryl halides. Compared with metal oxides and other carbon materials, the excellent capability of CNTs to absorb light, to convert light to heat, and to adsorb both two reactants simultaneously are critical to enhance the activity of Cu NPs, achieving the high yield of diaryl ethers. We believe that this study could provide a novel strategy for catalyst design and generate a more economically-sustainable process.

Biodegradation of a Complex Phenolic Industrial Stream by Bacterial Strains Isolated from Industrial Wastewaters

Molecular and metabolomic tools were used to design and understand the biodegradation of phenolic compounds in real industrial streams. Bacterial species were isolated from an industrial wastewater treatment plant of a phenol production factory and identified using molecular techniques. Next, the biodegradation potential of the most promising strains was analyzed in the presence of a phenolic industrial by-product containing phenol, alfa-methylstyrene, acetophenone, 2-cumylphenol, and 4-cumylphenol. A bacterial consortium comprising Pseudomonas and Alcaligenes species was assessed for its ability to degrade phenolic compounds from the phenolic industrial stream (PS). The consortium adapted itself to the increasing levels of phenolic compounds, roughly up to 1750 ppm of PS; thus, becoming resistant to them. In addition, the consortium exhibited the ability to grow in the presence of PS in repeated batch mode processes. Results from untargeted metabolomic analysis of the culture medium in the presence of PS suggested that bacteria transformed the toxic phenolic compounds into less harmful molecules as a survival mechanism. Overall, the study demonstrates the usefulness of massive sequencing and metabolomic tools in constructing bacterial consortia that can efficiently biodegrade complex PS. Furthermore, it improves our understanding of their biodegradation capabilities.

Antioxidative Responses of Duckweed (Lemna minor L.) to Phenol and Rhizosphere-Associated Bacterial Strain Hafnia paralvei C32-106/3

Duckweed (L. minor) is a cosmopolitan aquatic plant of simplified morphology and rapid vegetative reproduction. In this study, an H. paralvei bacterial strain and its influence on the antioxidative response of the duckweeds to phenol, a recalcitrant environmental pollutant, were investigated. Sterile duckweed cultures were inoculated with H. paralvei in vitro and cultivated in the presence or absence of phenol (500 mg L⁻¹), in order to investigate bacterial effects on plant oxidative stress during 5 days. Total soluble proteins, guaiacol peroxidase expression, concentration of hydrogen peroxide and malondialdehyde as well as the total ascorbic acid of the plants were monitored. Moreover, bacterial production of indole-3-acetic acid (IAA) was measured in order to investigate H. paralvei’s influence on plant growth. In general, the addition of phenol elevated all biochemical parameters in L. minor except AsA and total soluble proteins. Phenol as well as bacteria influenced the expression of guaiacol peroxidase. Different isoforms were associated with phenol compared to isoforms expressed in phenol-free medium. Considering that duckweeds showed increased antioxidative parameters in the presence of phenol, it can be assumed that the measured parameters might be involved in the plant’s defense system. H. paralvei is an IAA producer and its presence in the rhizosphere of duckweeds decreased the oxidative stress of the plants, which can be taken as evidence that this bacterial strain acts protectively on the plants during phenol exposure.

Effect of Nickel as Stress Factor on Phenol Biodegradation by Stenotrophomonas maltophilia KB2

This study focuses on the phenol biodegradation kinetics by Stenotrophomonas maltophilia KB2 in a nickel-contaminated medium. Initial tests proved that a nickel concentration of 33.3 mg·L⁻¹ caused a cessation of bacterial growth. The experiments were conducted in a batch bioreactor in several series: without nickel, at constant nickel concentration and at varying metal concentrations (1.67–13.33 g·m⁻³). For a constant Ni²⁺ concentration (1.67 or 3.33 g·m⁻³), a comparable bacterial growth rate was obtained regardless of the initial phenol concentration (50–300 g·m⁻³). The dependence µ = f (S₀) at constant Ni²⁺ concentration was very well described by the Monod equations. The created varying nickel concentrations experimental database was used to estimate the parameters of selected mathematical models, and the analysis included different methods of determining metal inhibition constant K_IM. Each model showed a very good fit with the experimental data (R² values were higher than 0.9). The best agreement (R² = 0.995) was achieved using a modified Andrews equation, which considers the metal influence and substrate inhibition. Therefore, kinetic equation parameters were estimated: µ_max = 1.584 h⁻¹, K_S = 185.367 g·m⁻³, K_IS = 106.137 g·m⁻³, K_IM = 1.249 g·m⁻³ and n = 1.0706.

Analysis of Phenol Biodegradation in Antibiotic and Heavy Metal Resistant Acinetobacter lwoffii NL1

Phenol is a common environmental contaminant. The purpose of this study was to isolate phenol-degrading microorganisms from wastewater in the sections of the Chinese Medicine Manufactory. The phenol-degrading Acinetobacter lwoffii NL1 was identified based on a combination of biochemical characteristics and 16S rRNA genes. To analyze the molecular mechanism, the whole genome of A. lwoffii NL1 was sequenced, yielding 3499 genes on one circular chromosome and three plasmids. Enzyme activity analysis showed that A. lwoffii NL1 degraded phenol via the ortho-cleavage rather than the meta-cleavage pathway. Key genes encoding phenol hydroxylase and catechol 1,2-dioxygenase were located on a megaplasmid (pNL1) and were found to be separated by mobile genetic elements; their function was validated by heterologous expression in Escherichia coli and quantitative real-time PCR. A. lwoffii NL1 could degrade 0.5 g/L phenol within 12 h and tolerate a maximum of 1.1 g/L phenol, and showed resistance against multiple antibiotics and heavy metal ions. Overall, this study shows that A. lwoffii NL1 can be potentially used for efficient phenol degradation in heavy metal wastewater treatment.

Bioremediation of lignin derivatives and phenolics in wastewater with lignin modifying enzymes: Status, opportunities and challenges

Lignin modifying enzymes from fungi and bacteria are potential biocatalysts for sustainable mitigation of different potentially toxic pollutants in wastewater. Notably, the paper and pulp industry generates enormous amounts of wastewater containing high amounts of complex lignin-derived chlorinated phenolics and sulfonated pollutants. The presence of these compounds in wastewater is a critical issue from environmental and toxicological perspectives. Some chloro-phenols are harmful to the environment and human health, as they exert carcinogenic, mutagenic, cytotoxic, and endocrine-disrupting effects. In order to address these most urgent concerns, the use of oxidative lignin modifying enzymes for bioremediation has come into focus. These enzymes catalyze modification of phenolic and non-phenolic lignin-derived substances, and include laccase and a range of peroxidases, specifically lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), and dye-decolorizing peroxidase (DyP). In this review, we explore the key pollutant-generating steps in paper and pulp processing, summarize the most recently reported toxicological effects of industrial lignin-derived phenolic compounds, especially chlorinated phenolic pollutants, and outline bioremediation approaches for pollutant mitigation in wastewater from this industry, emphasizing the oxidative catalytic potential of oxidative lignin modifying enzymes in this regard. We highlight other emerging biotechnical approaches, including phytobioremediation, bioaugmentation, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based technology, protein engineering, and degradation pathways prediction, that are currently gathering momentum for the mitigation of wastewater pollutants. Finally, we address current research needs and options for maximizing sustainable biobased and biocatalytic degradation of toxic industrial wastewater pollutants.

Biodegradation of aromatic pollutants meets synthetic biology

Ubiquitously distributed microorganisms are natural decomposers of environmental pollutants. However, because of continuous generation of novel recalcitrant pollutants due to human activities, it is difficult, if not impossible, for microbes to acquire novel degradation mechanisms through natural evolution. Synthetic biology provides tools to engineer, transform or even re-synthesize an organism purposefully, accelerating transition from unable to able, inefficient to efficient degradation of given pollutants, and therefore, providing new solutions for environmental bioremediation. In this review, we described the pipeline to build chassis cells for the treatment of aromatic pollutants, and presented a proposal to design microbes with emphasis on the strategies applied to modify the target organism at different level. Finally, we discussed challenges and opportunities for future research in this field.

Removal of wastewater phenolic compounds with triethylenetetramine functionalized polystyrene resin

A polyamine functionalized polystyrene resin (PSATA) was prepared via condensation reaction of acetylated polystyrene resin with triethylenetetramine, which, upon NaBH₄ reduction, produced PSATAR. In comparison with the PSATA, the PSATAR with more flexible amine groups shows improved structural properties, and the equilibrium adsorption capacities of phenol, 2-nitrophenol (ONP) and 2,4-dinitrophenol (DNP) in wastewater were up to 1.073, 1.832 and 1.901 mmol/g, respectively. Their adsorption isotherms fit well with the Freundlich model, indicating a multilayer, heterogeneous adsorption nature. Kinetic studies indicated that the adsorption of phenolic compounds conforms to the pseudo-second-order kinetics with the adsorption rate controlled by film diffusion for ONP and DNP, and intra-particle diffusion in the later stage for phenol.

Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology

Continuous contamination of the environment with xenobiotics and related recalcitrant compounds has emerged as a serious pollution threat. Bioremediation is the key to eliminating persistent contaminants from the environment. Traditional bioremediation processes show limitations, therefore it is necessary to discover new bioremediation technologies for better results. In this review we provide an outlook of alternative strategies for bioremediation via synthetic biology, including exploring the prerequisites for analysis of research data for developing synthetic biological models of microbial bioremediation. Moreover, cell coordination in synthetic microbial community, cell signaling, and quorum sensing as engineered for enhanced bioremediation strategies are described, along with promising gene editing tools for obtaining the host with target gene sequences responsible for the degradation of recalcitrant compounds. The synthetic genetic circuit and two-component regulatory system (TCRS)-based microbial biosensors for detection and bioremediation are also briefly explained. These developments are expected to increase the efficiency of bioremediation strategies for best results.

What would a synthetic connectome look like?

A major challenge of contemporary neuroscience is to unravel the structure of the connectome, the ensemble of neural connections that link between different functional units of the brain, and to reveal how this structure relates to brain function. This thriving area of research largely follows the general tradition in biology of reverse-engineering, which consists of first observing and characterizing a biological system or process, and then deconstructing it into its fundamental building blocks in order to infer its modes of operation. However, a complementary form of biology has emerged, synthetic biology, which emphasizes construction-based forward-engineering. The synthetic biology approach comprises the assembly of new biological systems out of elementary biological parts. The rationale is that the act of building a system can be a powerful method for gaining deep understanding of how that system works. As the fields of connectomics and synthetic biology are independently growing, I propose to consider the benefits of combining the two, to create synthetic connectomics, a new form of neuroscience and a new form of synthetic biology. The goal of synthetic connectomics would be to artificially design and construct the connectomes of live behaving organisms. Synthetic connectomics could serve as a unifying platform for unraveling the complexities of brain operation and perhaps also for generating new forms of artificial life, and, in general, could provide a valuable opportunity for empirically exploring theoretical predictions about network function. What would a synthetic connectome look like? What purposes would it serve? How could it be constructed? This review delineates the novel notion of a synthetic connectome and aims to lay out the initial steps towards its implementation, contemplating its impact on science and society.

Construction of an Escherichia coli strain to degrade phenol completely with two modified metabolic modules

Phenol is a common water pollutant because of its broad industrial applications. Biological method is a promising alternative to conventional physical and chemical methods for removing this toxic pollutant from the environment. In this study, two metabolic modules were introduced into Escherichia coli, the widely used host for various genetic manipulations, to elucidate the metabolic capacity of E. coli for phenol degradation. The first module catalysed the conversion of phenol to catechol, whereas the second module cleaved catechol into the three carboxylic acid circulating intermediates by the ortho-cleavage pathway. Phenol was completely degraded and imported into the tricarboxylic acid cycle by the engineered bacteria. Proteomics analysis showed that all genes in the phenol degradation pathway were over-expressed and affected cell division and energy metabolism of the host cells. Phenol in coking wastewater was degraded powerfully by BL-phe/cat. The engineered E. coli can improve the removal rate and shorten the processing time for phenol removal and has considerable potential in the treatment of toxic and harmful pollutants.