Biodegradation of phenol by a halotolerant versatile yeast Candida tropicalis SDP-1 in wastewater and soil under high salinity conditions

Collaboration of bacterial consortia for biodegradation of high concentration phenol and potential application of machine learning

Mixed culture of microorganisms is an effective method to remove high concentration of phenol in wastewater. At present, it is still a challenge for microorganisms to remove high-concentration phenol from wastewater. In this study, a phenol-degrading consortium was isolated, which could rapidly degrade 1800 mg/L phenol within 30 h, and the highest phenol degradation concentration was 2000 mg/L. Further exploration of how microbial consortium cooperates to promote phenol biodegradation was studied: the core bacteria of the microbial consortium was relatively stable during phenol degradation; the bacteria could improve the adaptability to environment and metabolic ability of phenol, by producing more surfactants and betaine, thereby improving the degradation rate. The determination coefficient (R2) in the machine learning model showed that the back propagation artificial neural network (BP-ANN) can predict the biodegradation of phenol under different conditions, saving time and economic costs. This study explains how microbial consortium cooperates to degrade phenol from the aspects of microbial consortium composition and metabolic analysis, which provides a theoretical basis for mixed culture microorganisms to degrade pollutants.

The mechanism of survival and degradation of phenol by Acinetobacter pittii in an extremely acidic environment

The treatment efficiency of acidic phenol-containing wastewater is hindered by the absence of efficient acid-resistant phenol-degrading bacteria, and the acid-resistant mechanism of such bacteria remains poorly studied. In this study, the acid-resistant strain Hly3 was used as a research model to investigate its ability to degrade phenol and its underlying mechanism of acid resistance. Strain Hly3 exhibited robust acid resistance, capable of surviving in extremely acidic environments (pH 3) and degrading 1700 mg L-1 phenol in 72 h. Through the physiological response analysis of strain Hly3 to pH, the results indicated: firstly, the strain could reduce the relative permeability of the cell membrane and increase EPS secretion to prevent H+ from entering the cell (shielding effect); secondly, the strain could accumulate more buffering substances to neutralize the intracellular H+ (neutralization effect); thirdly, the strain could expel H+ from the cell by enhancing H+-ATPase activity (pumping effect); finally, the strain produced more active scavengers to reduce the toxicity of acid stress on cells (antioxidant effect). Subsequently, combining liquid chromatography-mass spectrometry (LC-MS) technology with exogenous addition experiments, it was verified that the acid resistance mechanism of microorganisms is achieved through the activation of acid-resistant response systems by glutamine, thereby enhancing functions such as shielding, neutralization, efflux, and antioxidation. This study elucidated the acid resistance mechanism of Acinetobacter pittii, providing a theoretical basis and guidance for the treatment of acidic phenol-containing wastewater.

Taxonomic identification, phenol biodegradation and soil remediation of the strain Rhodococcus sacchari sp. nov. Z13T

Phenols are highly toxic chemicals that are extensively used in industry and produce large amounts of emissions. Notably, phenols released into the soil are highly persistent, causing long-term harm to human health and the environment. In this study, a gram-positive, aerobic, and rod-shaped bacterial strain, Z13T, with efficient phenol degradation ability, was isolated from the soil of sugarcane fields. Based on the physiological properties and genomic features, strain Z13T is considered as a novel species of the genus Rhodococcus, for which the name Rhodococcus sacchari sp. nov. is proposed. The type strain is Z13T (= CCTCC AB 2022327T = JCM 35797T). This strain can use phenol as its sole carbon source. Z13T was able to completely degrade 1200 mg/L phenol within 20 h; the maximum specific growth rate was μmax = 0.93174 h-1, and the maximum specific degradation rate was qmax = 0.47405 h-1. Based on whole-genome sequencing and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, strain Z13T contains a series of phenol degradation genes, including dmpP, CatA, dmpB, pcaG, and pcaH, and can metabolize aromatic compounds. Moreover, the potential of strain Z13T for soil remediation was investigated by introducing Z13T into simulated phenol-contaminated soil, and the soil microbial diversity was analyzed. The results showed that 100% of the phenol in the soil was removed within 7.5 d. Furthermore, microbial diversity analysis revealed an increase in the relative species richness of Oceanobacillus, Chungangia, and Bacillus.

Competitive mechanism of salt-tolerance/degradation-performance of organic pollutant in bacteria: Na+/H+ antiporters contribute to salt-stress resistance but impact phenol degradation

Phenolic-laden wastewater is typically characterized by its high toxicity and high salinity, imposing serious limits on the application of bioremediation. Although a few halotolerant microorganisms have been reported to degrade phenol, their removal efficiency on high concentrations of phenol remains unsatisfactory. What's more, the deep interaction molecular mechanism of salt-tolerance/phenol-degradation performance has not been clearly revealed. Here, a halotolerant strain Aeribacillus pallidus W-12 employed a meta-pathway to efficiently degrade high concentration of phenol even under high salinity conditions. Investigation of salt-tolerance strategy indicated that four Na+/H+ antiporters, which are widely distributed in bacteria, synergistically endowed the strain with excellent salt adaptability. All these antiporters differentially but positively responded to salinity changes and induction of phenol, forming a synergistic transport effect on salt ions and phenol. In-depth analysis revealed a competitive relationship between salt tolerance and degradation performance, which significantly impaired the degradation efficiency at relatively high salinity. The efficient degradation performance of W-12 under different phenol concentrations and salinity conditions indicated its bioremediation potential for multiple types of phenolic wastewater. Collectively, the competitive mechanism of salt tolerance and degradation performance enlightens a new strategy of introducing or re-constructing Na+/H+ antiporters to further improve bioremediation efficiency of hypersaline organic wastewater.

An effective strategy for biodegradation of high concentration phenol in soil via biochar-immobilized Rhodococcus pyridinivorans B403

High concentration of phenol residues in soil are harmful to human health and ecological safety. However, limited information is available on the in-situ bioremediation of phenol-contaminated soil using biochar as a carrier for bacteria. In this study, bamboo -derived biochar was screened as a carrier to assemble microorganism-immobilized composite with Rhodococcus pyridinivorans B403. Then, SEM used to observe the micromorphology of composite and its bioactivity was detected in solution and soil. Finally, we investigated the effects of free B403 and biochar-immobilized B403 (BCJ) on phenol biodegradation in two types of soils and different initial phenol concentrations. Findings showed that bacterial cells were intensively distributed in/onto the carriers, showing high survival. Immobilisation increased the phenol degradation rate of strain B403 by 1.45 times (37.7 mg/(L·h)). The phenol removed by BCJ in soil was 81% higher than free B403 on the first day. Moreover, the removal of BCJ remained above 51% even at phenol concentration of 1,500 mg/kg, while it was only 15% for free B403. Compared with the other treatment groups, BCJ showed the best phenol removal effect in both tested soils. Our results indicate that the biochar-B403 composite has great potential in the remediation of high phenol-contaminated soil.

Enhanced biodegradation of phenol by microbial collaboration: Resistance, metabolite utilization, and pH stabilization

Mixed culture of microorganisms is an effective method to remove high concentration of phenol from wastewater. Currently, the mechanism of how microorganisms collaborate to enhance the biodegradation of phenol is still a challenge. In this study, the isolated Bacillus subtilis ZWB1 and Bacillus velezensis ZWB2 were co-cultured to enhance phenol biodegradation, and the mechanism of microbial collaboration was further explored. The co-culture of strains could significantly increase the rate (16.7 mg/L·h, 1000 mg/L) and concentration of phenol degradation (1500 mg/L), comparing with mono-culture of ZWB1 (4.2 mg/L·h, 150 mg/L) and ZWB2 (6.9 mg/L·h, 1000 mg/L), among which the highest degraded concentration of phenol for ZWB1 and ZWB2 was 150 and 1000 mg/L. Further, the mechanism of microbial collaboration to enhance phenol biodegradation was raised: the decrease of antioxidant enzymes, and increase of degrading enzymes and surfactants on content after co-culture, assisted the microorganisms in withstanding phenol; Bacillus subtilis ZWB1 used the metabolites of Bacillus velezensis ZWB2 to promote its growth, and further to degrade phenol rapidly; Bacillus subtilis ZWB1 alleviated the damage, which resulted from the pH drop (5.8) of the fermentation broth during phenol degradation that inhibited the growth and degraded ability of Bacillus velezensis ZWB2, making the pH of fermentation broth stable at 7. Metabolic analysis showed that co-culture of strains could produce more alkaline and buffering compounds and pairs, to stabilize pH and reduce the toxicity of acidity on ZWB2, thus increasing the degradation rate. This study explains the mechanism of microbial collaboration on phenol biodegradation from multiple perspectives, especially pH stabilization, which provides a theoretical basis for the degradation of pollutants by co-culture microorganisms.

Elucidated potential of immobilized Janibacter sp. for saline wastewater phenol removal

Phenolic compounds are commonly found in industrial effluents and can be hazardous to organisms even at low concentrations. Over the years, researchers have demonstrated that bioremediation is a cost-effective and environmentally friendly alternative to physicochemical approaches used to remove phenol. The aim of this study was to investigate the removal of phenol from saline wastewaters by a halotolerant strain of the genus Janibacter. For this purpose, bacterial cells were immobilized on different supports, from which mica and zeolite were ultimately chosen due to their higher removal efficiency. The wet weight of immobilized cells per 1 g of mica and zeolite was 0.51 and 0.48 g, respectively. Free cells consumed 100 mg/L of phenol in 88 h, while immobilized cells used it in 40 h. Immobilized cells revealed a higher thermostability and could operate over a wider pH range and salinity. Unlike free cells, immobilized cells could remove 700 mg/L of phenol and could be reused for at least nine cycles. Interestingly the phenol removal efficiency of zeolite-immobilized cells remained unchanged after 4 months of storage at 4 and - 20 °C, which could be of great advantage for industrial applications. Complete destruction of phenol was observed through the meta pathway comprising phenol hydroxylase and catechol 2,3-dioxygenase enzymes. KEY POINTS: • Mica- and zeolite-immobilized cells were able to consume high concentrations of phenol. • Cells immobilized on mica and zeolite had considerable operational and storage stability. • Immobilized cells could be a good candidate for phenol removal in saline environments.

Enhanced exopolysaccharide production of Cordyceps militaris via mycelial cell immobilization on plastic composite support in repeated-batch fermentation

Repeated-batch fermentation with fungal mycelia immobilized in plastic composite support (PCS) eliminates the lag phase during fermentation and improves metabolite productivity. The strategy is implemented herein, and a novel modified PCS is developed to enhance exopolysaccharide (EPS) production from the medicinal fungus Cordyceps militaris. A modified PCS (SYE + PCS) was made by compositing polypropylene (PP) with a nutrient mixture containing soybean hull, peptone, yeast extract, and minerals (SYE+). The use of SYE + PCS has consistent cell productivity throughout the multiple fermentation cycles, which resulted in a more higher cell productivity after second batch compared to unmodified PCS. The cell grown on SYE + PCS also generates a higher yield of EPS (3.36, 6.93, and 5.72 g/L in the first, second, and third fermentation cycles, respectively) up to three-fold higher than the cell immobilized on unmodified PCS. It is also worth noting that the EPS from mycelium grown on SYE + PCS contains up to 2.3-fold higher cordycepin than those on unmodified PCS. The presence of nutrients in SYE + PCS also affects the hydrophobicity and surface roughness of the PC, improving mycelial cell adhesion. This study also provides a preliminary antioxidant activity assessment of EPS from immobilized C. militaris grown with SYE + PCS.

Rapid, stable, and highly-efficient development of salt-tolerant aerobic granular sludge by inoculating magnetite-assisted mycelial pellets

Long cultivation time hinders the industrial applications of aerobic granular sludge (AGS) in treatment of hypersaline wastewater. Mycelial pellets (MPs) have been used to efficiently strengthen the flocculent sludge aggregation and accelerate the formation of AGS. However, the MPs-based AGS was easily crushed or fragmented into several small pieces/granules that brought the uncertainty and extended the transition process to form mature AGS. In this study, magnetite was used to strengthen MPs (halotolerant fungus Cladosporium tenuissimum NCSL-XY8), and co-culture and adsorption type of magnetite-assisted mycelial pellets (CMMPs and AMMPs) were prepared and used for acceleration of salt-tolerant aerobic granular sludge (SAGS) cultivation under 3% salinity conditions. Compared to inoculating MPs, the inoculation of either CMMPs or AMMPs could stably transition to mature SAGS without evident fragmentation, which obviously increased the certainty and stability of SAGS formation. Also, highly-efficient simultaneous nitrogen and carbon removal (∼98% TOC and ∼80% TN removal) could be reached in 8 days. Typically, the granules maintained perfect characteristics (D50 > 1300 μm, D10 > 350 μm, SVI30 < 45 mL/g, and SVI30/SVI5 = 1.0) during the whole cultivation/transition processes (Day 0-55) by using the inoculum of CMMPs. ITS rDNA sequencing revealed the inoculated fungus Cladosporium tenuissimum played key roles in the formation of SAGS. All the phenomena indicated the rapid, stable, and highly-efficient start-up of SAGS could be successfully realized by inoculating CMMPs.

Sustained degradation of phenol under extreme conditions by polyurethane-based Bacillus sp. ZWB3

Phenol is a serious pollutant to the environment, therefore, it is urgent to find a rapid and effective method for its removal. In this study, Bacillus cereus ZWB3 immobilized on a polyurethane (PUF) carrier was studied. The PUF-ZWB3 required only 20 h for the degradation of 1,500 mg L-1 of phenol, shortened by 8 h than the free bacteria. In addition, the PUF-ZWB3 could increase the degradation concentration of phenol from 1,500 to 2,000 mg L-1, and the complete degradation of 2,000 mg L-1 phenol only used 44 h. In addition, the PUF-ZWB3 showed much higher removal of phenol than the free bacteria at different pH values, salt concentrations, and heavy metal ions. Particularly, the PUF-ZWB3 could still completely remove phenol in a strongly alkaline environment, such as pH 10 and 11. In addition, the removal efficiency of phenol by PUF-ZWB3 was still 100% after 10 cycles. This study showed that the PUF immobilization system had great potential in the field of remediation of organic pollution.

Newly isolated halotolerant Aspergillus sp. showed high diesel degradation efficiency under high salinity environment aided with hematite

The contamination of saline soil with hazardous petroleum hydrocarbons is a common problem across coastal areas globally. Bioaugmentation combined with chemical treatment is an emerging remediation technique, but it currently shows low efficiency under high saline environments. In this study, we screened and used a novel halotolerant lipolytic fungal consortium (HLFC) combined with hematite (Fe₂O₃) for the bioremediation of diesel contaminated saline soils. The changes in total petroleum hydrocarbons (TPH) concentrations, enzyme activity, and microbial diversity were compared among different treatments (HLFC, hematite, hematite-HLFC, and control). The results showed that TPH degradation was significantly (P < 0.05) enhanced in hematite-HLFC (47.59-88.01%) and HLFC (24.26-72.04%) amended microcosms across all salinity levels, compared to the treatments of hematite (23.71-66.26%) and control (6.39-55.20%). TPH degradation was positively correlated with lipase and laccase enzyme activities, electrical conductivity, and the water holding capacity of the soil. Analyses of the microbial community structure showed that microbial richness decreased, while evenness increased in HLFC and hematite-HLFC treatments. The relative abundances of Alicyclobacillus, Sediminibacillus, Alcanivorax, Penicillium, Aspergillus, and Candida genera were significantly high in hematite-HLFC and HLFC amended microcosms. Our findings provide a promising new microbial-based technique, which can degrade TPH efficiently in saline soil.

Kinetics investigation of phenolic pollutant degradation via Serratia marcescens ABHI 001 and its application in wastewater treatment

In the present work, kinetic study has been conducted in order to effectively eliminate the p-cresol from wastewater employing isolated bacterial strain Serratia marcescens ABHI001 under batch shake flasks in the concentration varying from 50 to 500 mg/L. Further, effects of various parameters including p-cresol concentration, inoculum dosage, temperature, pH and agitation have been investigated. It was found that 10% v/v inoculum of 24 h age, was effective in degrading p-cresol. Beside this, it was noticed that the concentration of P-cresol above 100 mg/L exhibited an inhibitory effect. The maximum specific growth rate (μmax) was obtained to be 0.360 h-1 for 100 mgL-1 concentration. Further, the experimental results were well fitted with Halden's and Andrew's models and kinetic parameters μmax, KS and Ki in case of Haldane model were calculated to be 0.9697 h-1, 88.07 mgL-1 and 219.9 mgL-1, respectively whereas the corresponding values in case of Andrews's constants were 0.6917 h-1, 62.83 mgL-1 and 307.4 mgL-1, respectively. The yield coefficient for the growth on p-cresol was found to be 0.82.

Rhodococcus: A promising genus of actinomycetes for the bioremediation of organic and inorganic contaminants

Rhodococcus is a genus of actinomycetes that has been explored by the scientific community for different purposes, especially for bioremediation uses. However, the mechanisms governing Rhodococcus-mediated bioremediation processes are far from being fully elucidated. In this sense, this work aimed to compile the recent advances in the use of Rhodococcus for the bioremediation of organic and inorganic contaminants present in different environmental compartments. We reviewed the bioremediation capacity and mechanisms of Rhodococcus spp. in the treatment of polycyclic aromatic hydrocarbons, phenolic substances, emerging contaminants, heavy metals, and dyes given their human health risks and environmental concern. Different bioremediation techniques were discussed, including experimental conditions, treatment efficiencies, mechanisms, and degradation pathways. The use of Rhodococcus strains in the bioremediation of several compounds is a promising approach due to their features, primarily the presence of appropriate enzyme systems, which result in high decontamination efficiencies; but that vary according to experimental conditions. Besides, the genus Rhodococcus contains a small number of opportunistic species and pathogens, representing an advantage from the point of view of safety. Advances in analytical detection techniques and Molecular Biology have been collaborating to improve the understanding of the mechanisms and pathways involved in bioremediation processes. In the context of using Rhodococcus spp. as bioremediation agents, there is a need for more studies that 1) evaluate the role of these actinomycetes on a pilot and field scale; 2) use genetic engineering tools and consortia with other microorganisms to improve the bioremediation efficiency; and 3) isolate new Rhodococcus strains from environments with extreme and/or contaminated conditions aiming to explore their adaptive capabilities for bioremediation purposes.

A study of highly efficient phenol biodegradation by a versatile Bacillus cereus ZWB3 on aerobic condition

As one of the organic pollutants in industrial wastewater, phenol seriously threatens the environment and human health. Among various methods, microbial degradation of phenol possesses the advantages of nontoxicity and no secondary pollution. Therefore, search for microbial resources that can efficiently degrade phenol has become an important issue. In this study, a strain that could efficiently degrade phenol was isolated. The strain was identified as Bacillus cereus based on its morphology, physiological and biochemical features and 16S rRNA sequence analysis. The strain can completely degrade phenol up to 1,500 mg/L within 26 h (57.7 mg·L^-1·h^-1), under the optimum conditions, faster compared with the known degrading bacteria. The strain could efficiently remove phenol at a wide range of temperatures (22-37 °C) and pH (7-9), and Mn²⁺ and Zn²⁺ stress. Interestingly, this strain displayed the potential on microthermal environment, which could degrade 1,200 mg/L phenol within 36 h at 22 °C. Further, the strain had capacity that used a variety of aromatic compounds as the sole carbon source for growth. This study shows a useful biodegradation route on the wastewater treatment under high phenol concentration conditions, providing alternatives for environmental remediation.

Recent developments in the biology and biotechnological applications of halotolerant yeasts

Natural hypersaline environments are inhabited by an abundance of prokaryotic and eukaryotic microorganisms capable of thriving under extreme saline conditions. Yeasts represent a substantial fraction of halotolerant eukaryotic microbiomes and are frequently isolated as food contaminants and from solar salterns. During the last years, a handful of new species has been discovered in moderate saline environments, including estuarine and deep-sea waters. Although Saccharomyces cerevisiae is considered the primary osmoadaptation model system for studies of hyperosmotic stress conditions, our increasing understanding of the physiology and molecular biology of halotolerant yeasts provides new insights into their distinct metabolic traits and provides novel and innovative opportunities for genome mining of biotechnologically relevant genes. Yeast species such as Debaryomyces hansenii, Zygosaccharomyces rouxii, Hortaea werneckii and Wallemia ichthyophaga show unique properties, which make them attractive for biotechnological applications. Select halotolerant yeasts are used in food processing and contribute to aromas and taste, while certain gene clusters are used in second generation biofuel production. Finally, both pharmaceutical and chemical industries benefit from applications of halotolerant yeasts as biocatalysts. This comprehensive review summarizes the most recent findings related to the biology of industrially-important halotolerant yeasts and provides a detailed and up-to-date description of modern halotolerant yeast-based biotechnological applications.

Genomic Analysis and Stability Evaluation of the Phenol-Degrading Bacterium Acinetobacter sp. DW-1 During Water Treatment

Phenol is a toxic organic molecule that is widely detected in the natural environment, even in drinking water sources. Biological methods were considered to be a good tool for phenol removal, especially microbial immobilized technology. However, research on the “seed” bacteria along with microbial community analysis in oligotrophic environment such as drinking water system has not been addressed. In this study, Acinetobacter sp. DW-1 with high phenol degradation ability had been isolated from a drinking water biofilter was used as seeded bacteria to treat phenol micro-polluted drinking water source. Meanwhile, the whole genome of strain DW-1 was sequenced using nanopore technology. The genomic analysis suggests that Acinetobacter sp. DW-1 could utilize phenol via the β-ketoadipate pathway, including the catechol and protocatechuate branches. Subsequently, a bio-enhanced polyhedral hollow polypropylene sphere (BEPHPS) filter was constructed to investigate the stability of the seeded bacteria during the water treatment process. The denatured gradient gel electrophoresis (DGGE) profile and the quantification of phenol hydroxylase gene results indicate that when the BEPHPS filter was operated for 56 days, Acinetobacter sp. was still a persistent and competitive bacterium in the treatment group. In addition, 16S rRNA gene amplicon sequencing results indicate that Acinetobacter sp., as well as Pseudomonas sp., Nitrospira sp., Rubrivivax sp. were the predominant bacteria in the treatment group, which were different from that in the CK group. This study provides a better understanding of the mechanisms of phenol degradation by Acinetobacter sp. DW-1 at the gene level, and provides new insights into the stability of seeded bacteria and its effects on microbial ecology during drinking water treatment.

Alginate modification via click chemistry for biomedical applications

Alginate biopolymers are characterized by favorable properties, of biocompatibility, degradability, and non-toxicity. However, the poor stability properties of alginate have limited its suitability for diverse applications. Recently, click chemistry has generated significant research interest due to its high reaction efficiency, high selectivity for a single product, harmless byproducts, and processing simplicity. Alginate modified using click chemistry enables the production of alginate derivatives with enhanced physical and chemical properties. Herein, we review the employment of click chemistry in the development of alginate-based materials or systems. Various click chemistries were highlighted, including azide and alkyne cycloaddition (e.g. Copper-(I)-catalyzed azide-alkyne cycloaddition (CuAAC), Strain-promoted alkyne-azide cycloaddition (SPAAC)), Diels-Alder reaction (Inverse electron demand Diels-Alder (IEDDA) cycloaddition, Tetrazine-norbornene Diels-Alder reactions), Thiol-ene/yne addition (Free-radical thiol-ene addition click reactions, Thiol-Michael addition click reactions, Thiol-yne addition click reaction), Oxime based click reactions, and other click reactions. Alginate functionalized with click chemistry and its properties were also discussed. The present study shows that click chemistry may be employed in modifying the mechanical strength, biochemical/biological properties of alginate-based materials. Finally, the applications of alginate-based materials in wound dressing, drug delivery, protein delivery, tissue regeneration, and 3D bioprinting were described and the future perspectives of alginates modified with click chemistry, are subsequently presented. This review provides new insights for readers to design structures and expand applications of alginate using click chemistry reactions in a detailed and more rational manner.