Isolation and characterization of tetrahydrofuran-degrading Rhodococcus aetherivorans strain M8

Rapid start-up and excellent performance of anaerobic membrane bioreactor for treating poly (butylene adipate-co-terephthalate) wastewater by using one-step feeding mode

The traditional anaerobic treatment process for highly concentrated, toxic, and acidic poly (butylene adipate-co-terephthalate) (PBAT) wastewater faces challenges. In contrast, the anaerobic membrane bioreactor (AnMBR) offers the advantage of robust performance, but the influence of start-up modes has not been explored. This study investigated the impact of one-step and stepwise startup (gradual dilution of wastewater) strategies in AnMBR treating PBAT wastewater. The results indicated that the one-step startup group achieved COD removal efficiency of 91.2% ± 2.7% and methane conversion rate of 234.7 ± 8.5 mLCH4/gCOD, which were 21.7% and 81.8 mL CH4/gCOD respectively higher than those achieved by the stepwise start-up group. Furthermore, the one-step startup led to the reduction of startup time by 10 days and the decrease in the average membrane fouling cycle by 6.6 days. Compared to the stepwise start-up group, the one-step startup group exhibited a lower abundance of Bacteroidota (11.3%), and a higher abundance of Proteobacteria (27.1%), Chloroflexi (10.5%), and Actinobacteria (11.8%). The one-step startup strategy facilitated the rapid development of a toxicity-tolerant hydrogenotrophic methanogenic pathway. Consequently, the one-step startup method provided a promising approach for the rapid start-up and excellent performance of AnMBR in PBAT wastewater treatment.

A New Discovery on the Potential Stability of Ion-Selective Membranes: The Poison from Tetrahydrofuran

Ion-selective electrodes (ISEs) have widespread use in the fields of clinical and environmental analyses. Tetrahydrofuran (THF) is the most used solvent for the preparation of modern ISEs, equipped with ion-selective membranes (ISMs). Until now, the influence of impurities in THF toward potentiometric instability of ion-selective membrane based ISEs was probably associated with the presence of either residual water or peroxide. To address this issue, most literature recommends redistilling THF prior to use in the preparation of the potentiometric membranes. Current study reveals that the actual THF impurity that is responsible for potential instability in the ISM includes products from the oxidation of THF, which contains the hydroxyl group and possibly carbonyl group with a boiling point of above 200 °C. The density functional theory calculation supported pathway of the chemical reaction of THF oxidation, hence, the chemical structure of the uncertain impurities was predicted. The underlying reason for the deteriorating potential stability of the ISEs is proposed as the significant hydrophilicity of these impurities that affect the partitioning of the ion sensing components in the membrane, thus enhancing the leaching of the membrane components from the membrane phase. This finding explains why redistillation of aged THF is advised.

Efficacy of Continuous Flow Reactors for Biological Treatment of 1,4-Dioxane Contaminated Textile Wastewater Using a Mixed Culture

The goal of this study was to evaluate the biodegradation of 1,4–dioxane using a mixed biological culture grown in textile wastewater sludge with 1,4–dioxane as the sole carbon source. The conditions for the long-term evaluation of 1,4–dioxane degradation were determined and optimized by batch scale analysis. Moreover, Monod’s model was used to determine the biomass decay rate and unknown parameters. The soluble chemical oxygen demand (sCOD) was used to determine the concentration of 1,4–dioxane in the batch test, and gas chromatography/mass spectrometry (GC/MS) was used to measure the concentrations via long-term wastewater analysis. Two types of reactors (continuous stirred reactor (CSTR) and plug flow reactor (PFR)) for the treatment of 1,4–dioxane from textile wastewater were operated for more than 120 days under optimized conditions. These used the mixed microbial culture grown in textile wastewater sludge and 1,4–dioxane as the sole carbon source. The results indicated efficient degradation of 1,4–dioxane by the mixed culture in the presence of a competitive inhibitor, with an increase in degradation time from 13.37 h to 55 h. A specific substrate utilization rate of 0.0096 mg 1,4–dioxane/mg MLVSS/h was observed at a hydraulic retention time of 20 h for 20 days of operation in a biomass concentration of 3000 mg/L produced by the mixed microbial culturing process. In the long-term analysis, effluent concentrations of 3 mg/L and <1 mg/L of 1,4–dioxane were observed for CSTR and PFR, respectively. The higher removal efficacy of PFR was due to the production of more MLVSS at 4000 mg/L compared to the outcome of 3000 mg/L in CSTR in a competitive environment.

A multicomponent THF hydroxylase initiates tetrahydrofuran degradation in Cupriavidus metallidurans ZM02

Tetrahydrofuran (THF) has been recognized as a water contaminant because of its human carcinogenicity, extensive use, and widespread distribution. Previously reported multicomponent monooxygenases (MOs) involved in THF degradation were highly conserved, and all of them were from Gram-positive bacteria. In this study, a novel THF-degrading gene cluster (dmpKLMNOP) encoding THF hydroxylase was identified on the chromosome of a newly isolated Gram-negative THF-degrading bacterium, Cupriavidus metallidurans ZM02, and functionally characterized. Transcriptome sequencing and RT-qPCR demonstrated that the expression of dmpKLMNOP was upregulated during the growth of strain ZM02 on THF or phenol. The deletion of oxygenase alpha or beta subunit or the reductase component disrupted the degradation of THF but did not affect the utilization of its hydroxylated product 2-hydroxytetrahydrofuran. Cupriavidus pinatubonensis JMP134 heterologously expressing dmpKLMNOP from strain ZM02 could grow on THF, indicating that the THF hydroxylase Dmp_ZM02KLMNOP is responsible for the initial degradation of THF. Furthermore, the THF and phenol oxidation activities of crude enzyme extracts were detected, and the highest THF and phenol catalytic activities were 1.38±0.24 μmol min^-1 mg^-1 and 1.77±0.37 μmol min^-1 mg^-1, respectively, with the addition of NADPH and Fe²⁺. The characterization of THF hydroxylase associated with THF degradation enriches our understanding of THF-degrading gene diversity and provides a novel potential enzyme for the bioremediation of THF-containing pollutants. IMPORTANCE Multicomponent MOs catalyzing the initial hydroxylation of THF are vital rate-limiting enzymes in the THF degradation pathway. Previous studies of THF degradation gene clusters have focused on Gram-positive bacteria, and the molecular mechanism of THF degradation in Gram-negative bacteria has rarely been reported. In this study, a novel THF hydroxylase encoded by dmpKLMNOP in strain ZM02 was identified to be involved in both THF and phenol degradation. Our findings provide new insights into the THF-degrading gene cluster and enzymes in Gram-negative bacteria.

Thiamine-Mediated Cooperation Between Auxotrophic Rhodococcus ruber ZM07 and Escherichia coli K12 Drives Efficient Tetrahydrofuran Degradation

Tetrahydrofuran (THF) is a universal solvent widely used in the synthesis of chemicals and pharmaceuticals. As a refractory organic contaminant, it can only be degraded by a small group of microbes. In this study, a thiamine auxotrophic THF-degrading bacterium, Rhodococcus ruber ZM07, was isolated from an enrichment culture H-1. It was cocultured with Escherichia coli K12 (which cannot degrade THF but can produce thiamine) and/or Escherichia coli K12ΔthiE (which can neither degrade THF nor produce thiamine) with or without exogenous thiamine. This study aims to understand the interaction mechanisms between ZM07 and K12. We found that K12 accounted for 30% of the total when cocultured and transferred with ZM07 in thiamine-free systems; in addition, in the three-strain (ZM07, K12, and K12ΔthiE) cocultured system without thiamine, K12ΔthiE disappeared in the 8th transfer, while K12 could still stably exist (the relative abundance remained at approximately 30%). The growth of K12 was significantly inhibited in the thiamine-rich system. Its proportion was almost below 4% after the fourth transfer in both the two-strain (ZM07 and K12) and three-strain (ZM07, K12, and K12ΔthiE) systems; K12ΔthiE’s percentage was higher than K12’s in the three-strain (ZM07, K12, and K12ΔthiE) cocultured system with exogenous thiamine, and both represented only a small proportion (less than 1% by the fourth transfer). The results of the coculture of K12 and K12ΔthiE in thiamine-free medium indicated that intraspecific competition between them may be one of the main reasons for the extinction of K12ΔthiE in the three-strain (ZM07, K12, and K12ΔthiE) system without exogenous thiamine. Furthermore, we found that ZM07 could cooperate with K12 through extracellular metabolites exchanges without physical contact. This study provides novel insight into how microbes cooperate and compete with one another during THF degradation.

Removal of gaseous tetrahydrofuran via a three-phase airlift bioreactor loaded with immobilized cells of GFP-tagged Pseudomonas oleovorans GDT4

Tetrahydrofuran (THF) is a common highly toxic cyclic aliphatic ether that frequently exists in waste gases. Removal of gaseous THF is a serious issue with important environmental ramifications. A novel three-phase airlift bioreactor (TPAB) loaded with immobilized cells was developed for efficient THF removal from gas streams. An effective THF-degrading transformant, Pseudomonas oleovorans GDT4, which contains the pTn-Mod-OTc-gfp plasmid and was tagged with a green fluorescent protein (GFP), was constructed. Continuous treatment of THF-containing waste gases was succeeded by the GFP-labelled cells immobilized with calcium alginate and activated carbon fiber in the TPAB for 60 days with >90% removal efficiency. The number of fluorescent cells in the beads reached 1.7 × 10¹¹ cells·g^-1 of bead on day 10, accounting for 83.3% of the total number of cells. The amount further increased to 3.0 × 10¹¹ cells·g^-1 of bead on day 40. However, it decreased to 2.5 × 10¹¹ cells·g^-1 of bead with a substantial increase in biomass in the liquid because of cell leakage and hydraulic shock. PCR-DGGE revealed that P. oleovorans was the dominant microorganism throughout the entire operation. The maximum elimination capacity was affected by empty bed residence time (EBRT). The capacity was only 25.9 g m^-3·h^-1 at EBRT of 80 s, whereas it reached 37.8 g m^-3·h^-1 at EBRT of 140 s. This work provides an alternative method for full-scale removal of gaseous THF and presents a useful tool for determining the biomass of a specific degrader in immobilized beads.

Biodegradation of Tetrahydrofuran by the Newly Isolated Filamentous Fungus Pseudallescheria boydii ZM01

Tetrahydrofuran (THF) is widely used as a precursor for polymer syntheses and a versatile solvent in industries. THF is an environmental hazard and carcinogenic to humans. In the present study, a new THF-degrading filamentous fungus, Pseudallescheria boydii ZM01, was isolated and characterized. Strain ZM01 can tolerate a maximum THF concentration of 260 mM and can completely degrade 5 mM THF in 48 h, with a maximum THF degradation rate of 133.40 mg THF h⁻¹ g⁻¹ dry weight. Growth inhibition was not observed when the initial THF concentration was below 150 mM, and the maximum THF degradation rate was still maintained at 118.21 mg THF h⁻¹ g⁻¹ dry weight at 50 mM THF, indicating the great potential of this strain to degrade THF at high concentrations. The initial key metabolic intermediate 2-hydroxytetrahydrofuran was detected and identified by gas chromatography (GC) analyses for the first time during the THF degradation process. Analyses of the effects of initial pH, incubation temperature, and heavy metal ions on THF degradation revealed that strain ZM01 can degrade THF under a relatively wide range of conditions and has good degradation ability under low pH and Cu²⁺ stress, suggesting its adaptability and applicability for industrial wastewater treatment.

Isolation and characterization of 2-butoxyethanol degrading bacterial strains

A total of 11 bacterial strains capable of completely degrading 2-butoxyethanol (2-BE) were isolated from forest soil, a biotrickling filter, a bioscrubber, and activated sludge, and identified by 16S rRNA gene sequence analysis. Eight of these strains belong to the genus Pseudomonas; the remaining three strains are Hydrogenophaga pseudoflava BOE3, Gordonia terrae BOE5, and Cupriavidus oxalaticus BOE300. In addition to 2-BE, all isolated strains were able to grow on 2-ethoxyethanol and 2-propoxyethanol, ethanol, n-hexanol, ethyl acetate, 2-butoxyacetic acid (2-BAA), glyoxylic acid, and n-butanol. Apart from the only gram-positive strain isolated, BOE5, none of the strains were able to grow on the nonpolar ethers diethyl ether, di-n-butyl ether, n-butyl vinyl ether, and dibenzyl ether, as well as on 1-butoxy-2-propanol. Strains H. pseudoflava BOE3 and two of the isolated pseudomonads, Pseudomonas putida BOE100 and P. vancouverensis BOE200, were studied in more detail. The maximum growth rates of strains BOE3, BOE100, and BOE200 at 30 °C were 0.204 h-1 at 4 mM, 0.645 h-1 at 5 mM, and 0.395 h-1 at 6 mM 2-BE, respectively. 2-BAA, n-butanol, and butanoic acid were detected as potential metabolites during the degradation of 2-BE. These findings indicate that the degradation of 2-BE by the isolated gram-negative strains proceeds via oxidation to 2-BAA with subsequent cleavage of the ether bond yielding glyoxylate and n-butanol. Since Gordonia terrae BOE5 was the only strain able to degrade nonpolar ethers like diethyl ether, the degradation pathway of 2-BE may be different for this strain.

Draft Genome Sequence of Rhodococcus aetherivorans JCM 14343T, a Bacterium Capable of Degrading Recalcitrant Noncyclic and Cyclic Ethers

Here, we report the draft genome sequence of Rhodococcus aetherivorans JCM 14343^T, which possesses the versatile ability to degrade recalcitrant noncyclic and cyclic ether compounds. The 4.2-Mbp genome of this bacterium contains alkane hydroxylase and propane monooxygenase genes involved in the degradation of noncyclic and cyclic ethers, respectively.

Here, we report the draft genome sequence of Rhodococcus aetherivorans JCM 14343^T, which possesses the versatile ability to degrade recalcitrant noncyclic and cyclic ether compounds. The 4.2-Mbp genome of this bacterium contains alkane hydroxylase and propane monooxygenase genes involved in the degradation of noncyclic and cyclic ethers, respectively.

Metabolite Cross-Feeding between Rhodococcus ruber YYL and Bacillus cereus MLY1 in the Biodegradation of Tetrahydrofuran under pH Stress

Bacterial consortia are among the most basic units in the biodegradation of environmental pollutants. Pollutant-degrading strains frequently encounter different types of environmental stresses and must be able to survive with other bacteria present in the polluted environments. In this study, we proposed a noncontact interaction mode between a tetrahydrofuran (THF)-degrading strain, Rhodococcus ruber YYL, and a non-THF-degrading strain, Bacillus cereus MLY1. The metabolic interaction mechanism between strains YYL and MLY1 was explored through physiological and molecular studies and was further supported by the metabolic response profile of strain YYL, both monocultured and cocultured with strain MLY1 at the optimal pH (pH 8.3) and under pH stress (pH 7.0), through a liquid chromatography-mass spectrometry-based metabolomic analysis. The results suggested that the coculture system resists pH stress in three ways: (i) strain MLY1 utilized acid metabolites and impacted the proportion of glutamine, resulting in an elevated intracellular pH of the system; (ii) strain MLY1 had the ability to degrade intermediates, thus alleviating the product inhibition of strain YYL; and (iii) strain MLY1 produced some essential micronutrients for strain YYL to aid the growth of this strain under pH stress, while strain YYL produced THF degradation intermediates for strain MLY1 as major nutrients. In addition, a metabolite cross-feeding interaction with respect to pollutant biodegradation is discussed.IMPORTANCE Rhodococcus species have been discovered in diverse environmental niches and can degrade numerous recalcitrant toxic pollutants. However, the pollutant degradation efficiency of these strains is severely reduced due to the complexity of environmental conditions and limitations in the growth of the pollutant-degrading microorganism. In our study, Bacillus cereus strain MLY1 exhibited strong stress resistance to adapt to various environments and improved the THF degradation efficiency of Rhodococcus ruber YYL by a metabolic cross-feeding interaction style to relieve the pH stress. These findings suggest that metabolite cross-feeding occurred in a complementary manner, allowing a pollutant-degrading strain to collaborate with a nondegrading strain in the biodegradation of various recalcitrant compounds. The study of metabolic exchanges is crucial to elucidate mechanisms by which degrading and symbiotic bacteria interact to survive environmental stress.

Novel tetrahydrofuran (THF) degradation-associated genes and cooperation patterns of a THF-degrading microbial community as revealed by metagenomic

Our understanding of the tetrahydrofuran (THF) degradation in complex environment is limited. The majority of THF degrading genes reported are group V soluble diiron monooxygenases and share greater than 95% homology with one another. In this study, we used sole-carbon-source incubation combined with high-throughput metagenomic sequencing to investigate this contaminant's degradation in environmental samples. We identified as-yet-uncultivated microbe from the genera Pseudonocardia and fungi Scedosporium sp. (Scedosporium sp. was successfully isolated) as THF degraders as containing THF degradation genes, while microbes from the genera Bordetella, Pandoraea and Rhodanobacter functioned as main cooperators by utilizing acidic intermediates and providing anti-acid mechanisms. Furthermore, a 9387-bp THF degradation cluster designated thmX from the as-yet-uncultivated Pseudonocardia (with 6 main ORFs and with 79-93% amino acid sequence identity with previously reported clusters) was discovered. We also found a THF-degrading related cytochrome P450 monooxygenase from the genus Scedosporium and predicted its cognate reductase for the first time. All the genes and clusters mentioned above were successfully amplified from samples and cloned into the suitable expression vectors. This study will provide novel insights for understanding of THF degradation mechanisms under acid stress conditions and mining new THF degradation genes.

pH Stress-Induced Cooperation between Rhodococcus ruber YYL and Bacillus cereus MLY1 in Biodegradation of Tetrahydrofuran

Microbial consortia consisting of cooperational strains exhibit biodegradation performance superior to that of single microbial strains and improved remediation efficiency by relieving the environmental stress. Tetrahydrofuran (THF), a universal solvent widely used in chemical and pharmaceutical synthesis, significantly affects the environment. As a refractory pollutant, THF can be degraded by some microbial strains under suitable conditions. There are often a variety of stresses, especially pH stress, that inhibit the THF-degradation efficiency of microbial consortia. Therefore, it is necessary to study the molecular mechanisms of microbial cooperational degradation of THF. In this study, under conditions of low pH (initial pH = 7.0) stress, a synergistic promotion of the THF degradation capability of the strain Rhodococcus ruber YYL was found in the presence of a non-THF degrading strain Bacillus cereus MLY1. Metatranscriptome analysis revealed that the low pH stress induced the strain YYL to up-regulate the genes involved in anti-oxidation, mutation, steroid and bile acid metabolism, and translation, while simultaneously down-regulating the genes involved in ATP production. In the co-culture system, strain MLY1 provides fatty acids, ATP, and amino acids for strain YYL in response to low pH stress during THF degradation. In return, YYL shares the metabolic intermediates of THF with MLY1 as carbon sources. This study provides the preliminary mechanism to understand how microbial consortia improve the degradation efficiency of refractory furan pollutants under environmental stress conditions.

1,4-Dioxane degradation potential of members of the genera Pseudonocardia and Rhodococcus

In recent years, several strains capable of degrading 1,4-dioxane have been isolated from the genera Pseudonocardia and Rhodococcus. This study was conducted to evaluate the 1,4-dioxane degradation potential of phylogenetically diverse strains in these genera. The abilities to degrade 1,4-dioxane as a sole carbon and energy source and co-metabolically with tetrahydrofuran (THF) were evaluated for 13 Pseudonocardia and 12 Rhodococcus species. Pseudonocardia dioxanivorans JCM 13855^T, which is a 1,4-dioxane degrading bacterium also known as P. dioxanivorans CB1190, and Rhodococcus aetherivorans JCM 14343^T could degrade 1,4-dioxane as the sole carbon and energy source. In addition to these two strains, ten Pseudonocardia strains could degrade THF, but no Rhodococcus strains could degrade THF. Of the ten Pseudonocardia strains, Pseudonocardia acacia JCM 16707^T and Pseudonocardia asaccharolytica JCM 10410^T degraded 1,4-dioxane co-metabolically with THF. These results indicated that 1,4-dioxane degradation potential, including degradation for growth and by co-metabolism with THF, is possessed by selected strains of Pseudonocardia and Rhodococcus, although THF degradation potential appeared to be widely distributed in Pseudonocardia. Analysis of soluble di-iron monooxygenase (SDIMO) α-subunit genes in THF and/or 1,4-dioxane degrading strains revealed that not only THF and 1,4-dioxane monooxygenases but also propane monooxygenase-like SDIMOs can be involved in 1,4-dioxane degradation.

Dynamic metabolic and transcriptional profiling of Rhodococcus sp. strain YYL during the degradation of tetrahydrofuran

Although tetrahydrofuran-degrading Rhodococcus sp. strain YYL possesses tetrahydrofuran (THF) degradation genes similar to those of other tetrahydrofuran-degrading bacteria, a much higher degradation efficiency has been observed in strain YYL. In this study, nuclear magnetic resonance (NMR)-based metabolomics analyses were performed to explore the metabolic profiling response of strain YYL to exposure to THF. Exposure to THF slightly influenced the metabolome of strain YYL when yeast extract was present in the medium. The metabolic profile of strain YYL over time was also investigated using THF as the sole carbon source to identify the metabolites associated with high-efficiency THF degradation. Lactate, alanine, glutarate, glutamate, glutamine, succinate, lysine, trehalose, trimethylamine-N-oxide (TMAO), NAD(+), and CTP were significantly altered over time in strain YYL grown in 20 mM THF. Real-time quantitative PCR (RT-qPCR) revealed changes in the transcriptional expression levels of 15 genes involved in THF degradation, suggesting that strain YYL could accumulate several disturbances in osmoregulation (trehalose, glutamate, glutamine, etc.), with reduced glycolysis levels, an accelerated tricarboxylic acid cycle, and enhanced protein synthesis. The findings obtained through (1)H NMR metabolomics analyses and the transcriptional expression of the corresponding genes are complementary for exploring the dynamic metabolic profile in organisms.

Successful bioaugmentation of an activated sludge reactor with Rhodococcus sp. YYL for efficient tetrahydrofuran degradation

The exchange of tetrahydrofuran (THF)-containing wastewater should significantly affect the performance of an activated sludge system. In this study, the feasibility of using THF-degrading Rhodococcus sp. strain YYL to bioaugment an activated sludge system treating THF wastewater was explored. As indicated by a DGGE analysis, strain YYL alone could not dominate the system, with the concentration of mixed liquor suspended solids (MLSS) decreasing to nearly half of the initial concentration after 45 d, and the microbial diversity was found to be significantly reduced. However, after the reactor was augmented with the mixed culture of strain YYL and two bacilli initially coexisting in the enriched isolation source, strain YYL quickly became dominant in the system and was incorporated into the activated sludge. The concentration of MLSS increased from 2.1g/L to 7.3g/L in 20 d, and the efficiency of THF removal from the system was remarkably improved. After the successful bioaugmentation, more than 95% of THF was completely removed from the wastewater when 20mM THF was continuously loaded into the system. In conclusion, our research first demonstrates that bioaugmentation of activated sludge system for THF degradation is feasible but that successful bioaugmentation should utilize a THF-degrading mixed culture as the inoculum, in which the two bacilli might help strain YYL colonize in activated sludge by co-aggregation.