Glyoxylate metabolism is a key feature of the metabolic degradation of 1,4-dioxane by Pseudonocardia dioxanivorans strain CB1190

Delignified porous wood as biofilm support for 1,4-dioxane-degrading bacterial consortium

Delignified porous wood samples were used as carriers for biofilm formation of a bacterial consortium with the ability to degrade 1,4-dioxane (DX). The delignification treatment of the natural wood resulted in higher porosity, formation of macropores, increase in surface roughness and hydrophilicity of the treated wood pieces. These superior properties of two types of treated carriers (respectively, A and B) compared to the untreated wood resulted in 2.19 ± 0.52- and 2.66 ± 0.23-fold higher growth of biofilm. Moreover, analysis of the fatty acid profiles indicated an increase in proportion of the saturated fatty acids during the biofilm formation, characterising an enhancement in rigidity and hydrophobicity of the biofilms. DX initial concentration of 100 mg/L was completely degraded (detection limit 0.01 mg/L) in 24 and 32 h using the treated A and B woods, while only 25.84 ± 5.95% was removed after 32 h using the untreated wood. However, fitting the DX biodegradation data to the Monod model showed a lower maximum specific growth rate for biofilm (0.0276 ± 0.0018 1/h) versus planktonic (0.0382 ± 0.0024 1/h), because of gradual accumulation of inactive cells in the biofilm. Findings of this study can contribute to the knowledge of biofilm formation regarding the physical/chemical properties of biofilm carriers and be helpful to the ongoing research on bioremediation of DX.

Isolation and characterization of pure cultures for metabolizing 1,4-dioxane in oligotrophic environments

1,4-Dioxane concentration in most contaminated water is much less than 1 mg/L, which cannot sustain the growth of most reported 1,4-dioxane-metabolizing pure cultures. These pure cultures were isolated following enrichment of mixed cultures at high concentrations (20 to 1,000 mg/L). This study is based on a different strategy: 1,4-dioxane-metabolizing mixed cultures were enriched by periodically spiking 1,4-dioxane at low concentrations (≤1 mg/L). Five 1,4-dioxane-metabolizing pure strains LCD6B, LCD6D, WC10G, WCD6H, and WD4H were isolated and characterized. The partial 16S rRNA gene sequencing showed that the five bacterial strains were related to Dokdonella sp. (98.3%), Acinetobacter sp. (99.0%), Afipia sp. (99.2%), Nitrobacter sp. (97.9%), and Pseudonocardia sp. (99.4%), respectively. Nitrobacter sp. WCD6H is the first reported 1,4-dioxane-metabolizing bacterium in the genus of Nitrobacter. The net specific growth rates of these five cultures are consistently higher than those reported in the literature at 1,4-dioxane concentrations <0.5 mg/L. Compared to the literature, our newly discovered strains have lower half-maximum-rate concentrations (1.8 to 8.2 mg-dioxane/L), lower maximum specific 1,4-dioxane utilization rates (0.24 to 0.47 mg-dioxane/(mg-protein ⋅ d)), higher biomass yields (0.29 to 0.38 mg-protein/mg-dioxane), and lower decay coefficients (0.01 to 0.02 d-1). These are characteristics of microorganisms living in oligotrophic environments.

A novel pbd gene cluster responsible for pyrrole and pyridine ring cleavage in Rhodococcus ruber A5

Pyridine and pyrrole, which are regarded as recalcitrant chemicals, are released into the environment as a result of industrial manufacturing processes, posing serious hazards to both the environment and human health. However, the pyrrole degradation mechanism and the pyridine-degrading gene in Rhodococcus are unknown. Herein, a highly efficient pyridine and pyrrole degradation strain Rhodococcus ruber A5 was isolated. Strain A5 completely degraded 1000 mg/L pyridine in a mineral salt medium within 24 h. The pyridine degradation of strain A5 was optimized using the BoxBehnken design. The optimum degradation conditions were found to be pH 7.15, temperature 28.06 ℃, and inoculation amount 1290.94 mg/L. The pbd gene clusters involved in pyridine degradation were discovered via proteomic analysis. The initial ring cleavage of pyridine and pyrrole in strain A5 was carried out by the two-component flavin-dependent monooxygenase PbdA/PbdE. The degradation pathways of pyridine and pyrrole were proposed by the identification of metabolites and comparisons of homologous genes. Additionally, homologous pbd gene clusters were found to exist in different bacterial genomes. Our study revealed the ring cleavage mechanisms of pyrrole and pyridine, and strain A5 was identified as a promising resource for pyridine bioremediation.

Biodegradation of 1,4-dioxane in a continuous-flow bioelectrochemical reactor by biofilm of Pseudonocardia dioxanivorans CB1190 and microbial community on conductive carriers

Bioelectrochemical degradation is an environmentally friendly, cost-effective and controllable way of providing electron acceptor to the microorganisms. A two-chamber continuous-flow bioelectrochemical reactor (BER) was developed in this study. The objective was to investigate the potential for enhancing the bioelectrochemical degradation of 1,4-dioxane (DX) by Pseudonocardia dioxanivorans CB1190 (CB1190) and microbial community biofilm on conductive and non-conductive carriers in low potentials (1.0-1.2 V) and currents (<2 mA). In the case of CB1190, biodegradation experiments at 1.0 V did not result in any observable change in DX removal efficiency (32.63 ± 2.48%) compared to the 0.0 V (31.69 ± 2.33%). However, the removal efficiency was much higher at 1.2 V (59.08 ± 0.86%). The higher removal at 1.2 V was attributed to an increase in dissolved oxygen (DO) concentration from 3.77 ± 0.33 mg/L at 0.0 V to 5.40 ± 0.11 mg/L at 1.2 V, which resulted from water electrolysis. In the case of microbial community, on the other hand, DX removal efficiency increased at 1.0 V (30.98 ± 1.10%) compared to 0.0 V (23.40 ± 1.02%) that can be attributed to a simultaneous increase in microbial activity from 2389 ± 118.5 ngATP/mgVSS at 0.0 V to 2942 ± 109 ngATP/mgVSS at 1.0 V. Analysis of the changes in microbial composition indicated enrichment of Alistipes and Lutispora at 1.0 V due to the ability of these genera to directly transfer electrons with conductive surface. On the other hand, no change was observed in the microbial community in the case of non-conductive carriers. Results of this study showed that electro-assisted biodegradation of DX at low potentials is possible through two different mechanisms (oxygen production and direct electron transfer with electrode) which makes this technique flexible and cost-effective. The novelty of this work lies in exploring the use of electrical assistance to enhance the biodegradation of DX in the presence of CB1190 and the microbial community. This study more specifically investigated lower potential than required water electrolysis potential, allowing microorganisms to be stimulated through mechanisms unrelated to oxygen generation.

Efficient biodegradation of 1,4-dioxane commingled with additional organic compound: Role of interspecies interactions within consortia

Microbial consortia-mediated biodegradation of 1,4-dioxane (1,4-D), an emerging water contaminant, is always a superior choice over axenic cultures. Thus, better understanding of the functions of coexisting microbes and their interspecies interactions within the consortia is crucial for predicting biodegradation efficiency and designing efficient 1,4-D-degrading microbial consortia. This study evaluated how microbial community compositions and interspecies interactions govern the microbial consortia-mediated 1,4-D biodegradation by investigating the biodegradability and microbial community dynamics of both enriched (N112) and synthetic (SCDs and SCDNs) microbial consortia in the absence or presence of additional organic compound (AOC). In the absence of AOC, N112 exhibited 100% 1,4-D biodegradation efficiency at a rate of 12.5 mg/L/d, whereas the co-occurrence of AOC resulted in substrate-dependent biodegradation inhibition and thereby reduced the biodegradation efficiency and activity (2.0-10.0 mg/L/d). The coexistence and negative influence of certain low-abundant non-degraders on both 1,4-D-degraders and key non-degraders in N112 was identified as the prime cause behind such biodegradation inhibition. Comparing with N112, SCDN-1 composed of 1,4-D-degraders and key non-degraders significantly improved the 1,4-D biodegradation efficiency in the presence of AOC, confirming the absence of negative influence of low-abundant non-degraders and cooperative interactions between 1,4-D-degraders and key non-degraders in SCDN-1. On the contrary, both two-species and three-species SCDs comprised of only 1,4-D-degraders resulted in lower 1,4-D biodegradation efficiency as compared to SCDN-1 under all treatment conditions, while max. 91% 1,4-D biodegradation occurred by SCDs in the absence of AOC. These results were attributed to the negative interaction among 1,4-D-degraders and the absence of complementary roles of key non-degraders in SCDs. The findings improve our understanding of how interspecies interactions can regulate the intrinsic abilities and functions of coexisting microbes during biodegradation in complex environments and provide valuable guidelines for designing highly efficient and robust microbial consortia for practical bioremediation of 1,4-D like emerging organic contaminants.

Remedial strategies for abating 1,4-dioxane pollution-special emphasis on diverse biotechnological interventions

1,4-dioxane is a heterocyclic ether used as a polar industrial solvent and are released as waste discharges. 1,4-dioxane deteriorates health and quality, thereby attracts concern by the environment technologists. The need of attaining sustainable development goals have resulted in search of an eco-friendly and technically viable treatment strategy. This extensive review is aimed to emphasis on the (a) characteristics of 1,4-dioxane and their occurrence in the environment as well as their toxicity, (b) remedial strategies, such as physico-chemical treatment and advanced oxidation techniques. Special reference to bioremediation that involves diverse microbial strains and their mechanism are highlighted in this review. The role of macronutrients, stimulants and other abiotic cofactors in the biodegradation of 1,4-dioxane is discussed lucidly. We have critically discussed the inducible enzymes, enzyme-based remediation, distinct instrumental method of analyses to know the fate of intermediates produced from 1,4-dioxane biotransformation. This comprehensive survey also tries to put forth the different toxicity assessment tools used in evaluating the extent of detoxification of 1,4-dioxane achieved through biotransforming mechanism. Conclusively, the challenges, opportunities, techno-economic feasibility and future prospects of implementing 1,4-dioxane through biotechnological interventions are also discussed.

Network and meta-omics reveal the cooperation patterns and mechanisms in an efficient 1,4-dioxane-degrading microbial consortium

1,4-Dioxane is an emerging wastewater contaminant with probable human carcinogenicity. Our current understanding of microbial interactions during 1,4-dioxane biodegradation process in mixed cultures is limited. Here, we applied metagenomic, metatranscriptomic and co-occurrence network analyses to unraveling the microbial cooperation between degrader and non-degraders in an efficient 1,4-dioxane-degrading microbial consortium CH1. A 1,4-dioxane-degrading bacterium, Ancylobacter polymorphus ZM13, was isolated from CH1 and had a potential of being one of the important degraders due to its high relative abundance, highly expressed monooxygenase genes tmoABCDEF and high betweenness centrality of networks. The strain ZM13 cooperated obviously with 6 bacterial genera in the network, among which Xanthobacter and Mesorhizobium could be involved in the intermediates metabolism with responsible genes encoding alcohol dehydrogenase (adh), aldehyde dehydrogenase (aldh), glycolate oxidase (glcDEF), glyoxylate carboligase (gcl), malate synthase (glcB) and 2-isopropylmalate synthase (leuA) differentially high-expressed. Also, 1,4-dioxane facilitated the shift of biodiversity and function of CH1, and those cooperators cooperated with ZM13 in the way of providing amino acids or fatty acids, as well as relieving environmental stresses to promote biodegradation. These results provide new insights into our understandings of the microbial interactions during 1,4-dioxane degradation, and have important implications for predicting microbial cooperation and constructing efficient and stable synthetic 1,4-dioxane-degrading consortia for practical remediation.

Response surface algorithm for improved biotransformation of 1,4-dioxane using Staphylococcus capitis strain AG

The present investigation reports the biotransformation of an endrocrine disrupting agent; 1,4-dioxane through bacterial metabolism. Initially, potential bacterial isolates capable of surviving with minimum 1,4-dioxane were screened from industrial wastewater. Thereafter, screening was done to isolate a bacteria which can biotransform higher concentration (1000 mg/L) of 1,4-dioxane. Morphological and biochemical features were examined prior establishing their phylogenetic relationships and the bacterium was identified as Staphylococcus capitis strain AG. Biotransformation experiments were tailored using response surface tool and predictions were made to elucidate the opimal conditions. Critical factors influencing bio-transformation efficiency such as tetrahydrofuran, availability of 1,4-dioxane and inoculum size were varied at three different levels as per the central composite design for ameliorating 1,4-dioxane removal. Functional attenuation of 1,4-dioxane by S. capitis strain AG were understood using spectroscopic techniques were significant changes in the peak positions and chemical shifts were visualized. Mass spectral profile revealed that 1.5 (% v/v) S. capitis strain AG could completely (∼99%) remove 1000 mg/L 1,4-dioxane, when incubated with 2 μg/L tetrahydrofuran for 96 h. The toxicity of 1,4-dioxane and biotransformed products by S. capitis strain AG were tested on Artemia salina. The results of toxicity tests revealed that the metabolic products were less toxic as they exerted minimal mortality rate after 48 h exposure. Thus, this research would be the first to report the response prediction and precise tailoring of 1,4-dioxane biotransformation using S. captis strain AG.

Environmental Potential for Microbial 1,4-Dioxane Degradation Is Sparse despite Mobile Elements Playing a Role in Trait Distribution

1,4-Dioxane (dioxane) is an emerging contaminant of concern for which bioremediation is seen as a promising solution. To date, eight distinct gene families have been implicated in dioxane degradation, though only dioxane monooxygenase (DXMO) from Pseudonocardia dioxanivorans is routinely used as a biomarker in environmental surveys. In order to assess the functional and taxonomic diversity of bacteria capable of dioxane degradation, we collated existing, poorly-organized information on known biodegraders to create a curated suite of biomarkers with confidence levels for assessing 1,4-dioxane degradation potential. The characterized enzyme systems for dioxane degradation are frequently found on mobile elements, and we identified that many of the curated biomarkers are associated with other hallmarks of genomic rearrangements, indicating lateral gene transfer plays a role in dissemination of this trait. This is contrasted by the extremely limited phylogenetic distribution of known dioxane degraders, where all representatives belong to four classes within three bacterial phyla. Based on the curated set of expanded biomarkers, a search of more than 11,000 publicly available metagenomes identified a sparse and taxonomically limited distribution of potential dioxane degradation proteins. Our work provides an important and necessary structure to the current knowledge base for dioxane degradation and clarifies the potential for natural attenuation of dioxane across different environments. It further highlights a disconnect between the apparent mobility of these gene families and their limited distributions, indicating dioxane degradation may be difficult to integrate into a microorganism's metabolism. IMPORTANCE New regulatory limits for 1,4-dioxane in groundwater have been proposed or adopted in many countries, including the United States and Canada, generating a direct need for remediation options as well as better tools for assessing the fate of dioxane in an environment. A comprehensive suite of biomarkers associated with dioxane degradation was identified and then leveraged to examine the global potential for dioxane degradation in natural and engineered environments. We identified consistent differences in the dioxane-degrading gene families associated with terrestrial, aquatic, and wetland environments, indicating reliance on a single biomarker for assessing natural attenuation of dioxane is likely to miss key players. Most environments do not currently host the capacity for dioxane degradation-the sparse distribution of dioxane degradation potential highlights the need for bioaugmentation approaches over biostimulation of naturally occurring microbial communities.

Enabling Efficient Genetic Manipulations in a Rare Actinomycete Pseudonocardia alni Shahu

Pseudonocardia species are emerging as important microorganisms of global concern with unique and increasingly significant ecological roles and represent a prominent source of bioactive natural products, but genetic engineering of these organisms for biotechnological applications is greatly hindered due to the limitation of efficient genetic manipulation tools. In this regard, we report here the establishment of an efficient genetic manipulation system for a newly isolated strain, Pseudonocardia alni Shahu, based on plasmid conjugal transfer from Escherichia coli to Pseudonocardia. Conjugants were yielded upon determining the optimal ratio between the donor and recipient cells, and designed genome modifications were efficiently accomplished, including exogenous gene integration based on an integrative plasmid and chromosomal stretch removal by homologous recombination using a suicidal non-replicating vector. Collectively, this work has made the P. alni Shahu accessible for genetic engineering, and provided an important reference for developing genetic manipulation methods in other rare actinomycetes.

Evaluation of natural attenuation of 1,4-dioxane in groundwater using a 14C assay

Monitored Natural Attenuation (MNA) is a preferred remedy for sites contaminated with 1,4-dioxane due to its low cost and limited environmental impacts compared to active remediation. Having a robust estimate of the rate at which biodegradation occurs is an essential component of assessing MNA. In this study, an assay was developed using ¹⁴C-labeled 1,4-dioxane to measure rate constants for biodegradation based on accumulation of ¹⁴C products. Purification of the ¹⁴C-1,4-dioxane stock solution lowered the level of ¹⁴C impurities to below 1% of the total ¹⁴C activity. This enabled determination of rate constants in groundwater as low as 0.0021 yr^-1, equating to a half-life greater than 300 years. Of the 54 groundwater samples collected from 10 sites in the US, statistically significant rate constants were determined with the ¹⁴C assay for 24. The median rate constant was 0.0138 yr^-1 (half-life = 50 yr); the maximum rate constant was 0.367 yr^-1 (half-life = 1.9 yr). The results confirmed that biodegradation of 1,4-dioxane is occurring at 9 of the 10 sites sampled, albeit with considerable variability in the level of activity. The specificity of the assay was confirmed using acetylene and the absence of oxygen to inhibit monooxygenases.

Identification of the phylotypes involved in cis-dichloroethene and 1,4-dioxane biodegradation in soil microcosms

Co-contamination with chlorinated compounds and 1,4-dioxane has been reported at many sites. Recently, there has been an increased interest in bioremediation because of the potential to degrade multiple contaminants concurrently. Towards improving bioremediation efficacy, the current study examined laboratory microcosms (inoculated separately with two soils) to determine the phylotypes and functional genes associated with the biodegradation of two common co-contaminants (cis-dichloroethene [cDCE] and 1,4-dioxane). The impact of amending microcosms with lactate on cDCE and 1,4-dioxane biodegradation was also investigated. The presence of either lactate or cDCE did not impact 1,4-dioxane biodegradation one of the two soils. Lactate appeared to improve the initiation of the biological removal of cDCE in microcosms inoculated with either soil. Stable isotope probing (SIP) was then used to determine which phylotypes were actively involved in carbon uptake from cDCE and 1,4-dioxane in both soil communities. The most enriched phylotypes for ¹³C assimilation from 1,4-dioxane included Rhodopseudomonas and Rhodanobacter. Propane monooxygenase was predicted (by PICRUSt2) to be dominant in the 1,4-dioxane amended microbial communities and propane monooxygenase gene abundance values correlated with other enriched (but less abundant) phylotypes for ¹³C-1,4-dioxane assimilation. The dominant enriched phylotypes for ¹³C assimilation from cDCE included Bacteriovorax, Pseudomonas and Sphingomonas. In the cDCE amended soil microcosms, PICRUSt2 predicted the presence of DNA encoding glutathione S-transferase (a known cDCE upregulated enzyme). Overall, the work demonstrated concurrent removal of cDCE and 1,4-dioxane by indigenous soil microbial communities and the enhancement of cDCE removal by lactate. The data generated on the phylotypes responsible for carbon uptake (as determined by SIP) could be incorporated into diagnostic molecular methods for site characterization. The results suggest concurrent biodegradation of cDCE and 1,4-dioxane should be considered for chlorinated solvent site remediation.

Adaption and Degradation Strategies of Methylotrophic 1,4-Dioxane Degrading Strain Xanthobacter sp. YN2 Revealed by Transcriptome-Scale Analysis

Biodegradation of 1,4-dioxane (dioxane) contamination has gained much attention for decades. In our previous work, we isolated a highly efficient dioxane degrader, Xanthobacter sp. YN2, but the underlying mechanisms of its extraordinary degradation performance remained unresolved. In this study, we performed a comparative transcriptome analysis of YN2 grown on dioxane and citrate to elucidate its genetic degradation mechanism and investigated the transcriptomes of different dioxane degradation stages (T0, T24, T48). We also analyzed the transcriptional response of YN2 over time during which the carbon source switched from citrate to dioxane. The results indicate that strain YN2 was a methylotroph, which provides YN2 a major advantage as a pollutant degrader. A large number of genes involved in dioxane metabolism were constitutively expressed prior to dioxane exposure. Multiple genes related to the catabolism of each intermediate were upregulated by treatment in response to dioxane. Glyoxylate metabolism was essential during dioxane degradation by YN2, and the key intermediate glyoxylate was metabolized through three routes: glyoxylate carboligase pathway, malate synthase pathway, and anaplerotic ethylmalonyl-CoA pathway. Genes related to quorum sensing and transporters were significantly upregulated during the early stages of degradation (T0, T24) prior to dioxane depletion, while the expression of genes encoding two-component systems was significantly increased at late degradation stages (T48) when total organic carbon in the culture was exhausted. This study is the first to report the participation of genes encoding glyoxalase, as well as methylotrophic genes xoxF and mox, in dioxane metabolism. The present study reveals multiple genetic and transcriptional strategies used by YN2 to rapidly increase biomass during growth on dioxane, achieve high degradation efficiency and tolerance, and adapt to dioxane exposure quickly, which provides useful information regarding the molecular basis for efficient dioxane biodegradation.

In-Depth Computational Analysis of Natural and Artificial Carbon Fixation Pathways

In the recent years, engineering new-to-nature CO2- and C1-fixing metabolic pathways made a leap forward. New, artificial pathways promise higher yields and activity than natural ones like the Calvin-Benson-Bassham (CBB) cycle. The question remains how to best predict their in vivo performance and what actually makes one pathway "better" than another. In this context, we explore aerobic carbon fixation pathways by a computational approach and compare them based on their specific activity and yield on methanol, formate, and CO2/H2 considering the kinetics and thermodynamics of the reactions. Besides pathways found in nature or implemented in the laboratory, this included two completely new cycles with favorable features: the reductive citramalyl-CoA cycle and the 2-hydroxyglutarate-reverse tricarboxylic acid cycle. A comprehensive kinetic data set was collected for all enzymes of all pathways, and missing kinetic data were sampled with the Parameter Balancing algorithm. Kinetic and thermodynamic data were fed to the Enzyme Cost Minimization algorithm to check for respective inconsistencies and calculate pathway-specific activities. The specific activities of the reductive glycine pathway, the CETCH cycle, and the new reductive citramalyl-CoA cycle were predicted to match the best natural cycles with superior product-substrate yield. However, the CBB cycle performed better in terms of activity compared to the alternative pathways than previously thought. We make an argument that stoichiometric yield is likely not the most important design criterion of the CBB cycle. Still, alternative carbon fixation pathways were paretooptimal for specific activity and product-substrate yield in simulations with C1 substrates and CO2/H2 and therefore hold great potential for future applications in Industrial Biotechnology and Synthetic Biology.

Treatment of 1,4-dioxane-containing water using carriers immobilized with indigenous microorganisms in landfill leachate treatment sludge: A laboratory-scale reactor study

1,4-Dioxane (DX) is a contaminant of emerging concern in aquatic environments, and is frequently found in landfill leachate. As a biological method applicable to landfill leachate treatment facilities, the feasibility of DX treatment using carriers immobilized with microorganisms indigenous to landfill leachate treatment sludge was explored through laboratory-scale reactor experiments by introducing carriers prepared via microorganism immobilization in the aeration tank of a leachate treatment facility. Three different carrier materials were used to immobilize microorganisms, and a model DX-containing water (10 mg/L) was treated under continuous feeding. Biological DX removal to < 0.5 mg/L was achieved using all carrier types, thereby adhering to the effluent standard for landfill leachate in Japan, which confirms the usefulness of the proposed method. However, weaker aeration and enhanced DX loading drastically impaired the DX removal performance depending on the carrier materials. This suggests the importance of carrier selection and control of the operational variables to ensure stable and effective DX removal. Microbial community analyses revealed that Pseudonocardia with thm genes may largely contribute to the initial oxidation of DX, irrespective of the carrier type, suggesting the importance of this population for the continuous treatment of low DX concentrations with mixed microbial consortia.

Bio-conversion of CO2 into biofuels and other value-added chemicals via metabolic engineering

Carbon dioxide (CO₂) occurs naturally in the atmosphere as a trace gas, which is produced naturally as well as by anthropogenic activities. CO₂ is a readily available source of carbon that in principle can be used as a raw material for the synthesis of valuable products. The autotrophic organisms are naturally equipped to convert CO₂ into biomass by obtaining energy from sunlight or inorganic electron donors. This autotrophic CO₂ fixation has been exploited in biotechnology, and microbial cell factories have been metabolically engineered to convert CO₂ into biofuels and other value-added bio-based chemicals. A variety of metabolic engineering efforts for CO₂ fixation ranging from basic copy, paste, and fine-tuning approaches to engineering and testing of novel synthetic CO₂ fixing pathways have been demonstrated. In this paper, we review the current advances and innovations in metabolic engineering for bio-conversion of CO₂ into bio biofuels and other value-added bio-based chemicals.

Identification of novel 1,4-dioxane degraders and related genes from activated sludge by taxonomic and functional gene sequence analysis

This study used integrated omics technologies to investigate the potential novel pathways and enzymes for 1,4-dioxane degradation by a consortium enriched from activated sludge of a domestic wastewater treatment plant. An unclassified genus belonging to Xanthobacteraceae increased significantly after magnetic nanoparticle-mediated isolation for 1,4-dioxane degraders. Species with relatively higher abundance (> 0.3%) were identified to present high metabolic activities in the biodegradation process through shotgun sequencing. The functional gene investigations revealed that Xanthobacter sp. 91, Xanthobacter sp. 126, and a Rhizobiales strain carried novel 1,4-dioxane-hydroxylating monooxygenase genes. Xanthobacter sp. 126 contained the genes coding for glycolate oxidase, which was the main enzyme responsible for utilization of 1,4-dioxane intermediates through the TCA cycle, and further proven by the specific glycolate oxidase inhibitor, α-hydroxy-2-pyridinemethanesulfonic acid. An expanded and detailed degradation pathway of 1,4-dioxane was proposed on the basis of the three major intermediates (2-hydroxy-1,4-dioxane, ethylene glycol, and oxalic acid) confirmed by metabolomics. These findings of microbial community and function as well as the novel pathway will be valuable in predicting natural attenuation or reconstruction of a bacterial consortium for enhanced remediation of 1,4-dioxane-contaminated sites as well as wastewater treatment.

Isolation and Characterization of Novel Bacteria Capable of Degrading 1,4-Dioxane in the Presence of Diverse Co-Occurring Compounds

Biodegradation is found to be a promising, cost-effective and eco-friendly option for the treatment of industrial wastewater contaminated by 1,4-dioxane (1,4-D), a highly stable synthetic chemical and probable human carcinogen. This study aimed to isolate, identify, and characterize metabolic 1,4-D-degrading bacteria from a stable 1,4-D-degrading microbial consortium. Three bacterial strains (designated as strains TS28, TS32, and TS43) capable of degrading 1,4-D as a sole carbon and energy source were isolated and identified as Gram-positive Pseudonocardia sp. (TS28) and Gram-negative Dokdonella sp. (TS32) and Afipia sp. (TS43). This study, for the first time, confirmed that the genus Dokdonella is involved in the biodegradation of 1,4-D. The results reveal that all of the isolated strains possess inducible 1,4-D-degrading enzymes and also confirm the presence of a gene encoding tetrahydrofuran/dioxane monooxygenase (thmA/dxmA) belonging to group 5 soluble di-iron monooxygenases (SDIMOs) in both genomic and plasmid DNA of each of the strains, which is possibly responsible for the initial oxidation of 1,4-D. Moreover, the isolated strains showed a broad substrate range and are capable of degrading 1,4-D in the presence of additional substrates, including easy-to-degrade compounds, 1,4-D biodegradation intermediates, structural analogs, and co-contaminants of 1,4-D. This indicates the potential of the isolated strains, especially strain TS32, in removing 1,4-D from contaminated industrial wastewater containing additional organic load. Additionally, the results will help to improve our understanding of how multiple 1,4-D-degraders stably co-exist and interact in the consortium, relying on a single carbon source (1,4-D) in order to develop an efficient biological 1,4-D treatment system.

Degradation of 1,4-Dioxane by Xanthobacter sp. YN2

1,4-Dioxane is a highly toxic and carcinogenic pollutant found worldwide in groundwater and soil environments. Several microorganisms have been isolated by their ability to grow on 1,4-dioxane; however, low 1,4-dioxane tolerance and slow degradation kinetics remain obstacles for their use in 1,4-dioxane bioremediation. We report here the isolation and characterization of a new strain, Xanthobacter sp. YN2, capable of highly efficient 1,4-dioxane degradation. High degradation efficiency and high tolerance to 1,4-dioxane make this new strain an ideal candidate for the biodegradation of 1,4-dioxane in various treatment facilities. The maximum degradation rate of 1,4-dioxane was found to be 1.10 mg-1,4-dioxane/h mg-protein. Furthermore, Xanthobacter sp. YN2 was shown to grow in the presence of higher than 3000 mg/L 1,4-dioxane with little to no degradation inhibition. In addition, Xanthobacter sp. YN2 could grow on and degrade 1,4-dioxane at pH ranges 5 to 8 and temperatures between 20 and 40 °C. Xanthobacter sp. YN2 was also found to be able to grow on a variety of other substrates including several analogs of 1,4-dioxane. Genome sequence analyses revealed the presence of two soluble di-iron monooxygenase (SDIMO) gene clusters, and regulation studies determined that all of the genes in these two clusters were upregulated in the presence of 1,4-dioxane. This study provides insights into the bacterial stress response and the highly efficient biodegradation of 1,4-dioxane as well as the identification of a novel Group-2 SDIMO.

Impact of Zero-Valent Iron on Freshwater Bacterioplankton Metabolism as Predicted from 16S rRNA Gene Sequence Libraries

The application of zero-valent iron particles (ZVI) for the treatment of heavily polluted environment and its biological effects have been studied for at least two decades. Still, information on the impact on bacterial metabolic pathways is lacking. This study describes the effect of microscale and nanoscale ZVI (mZVI and nZVI) on the abundance of different metabolic pathways in freshwater bacterial communities. The metabolic pathways were inferred from metabolism modelling based on 16S rRNA gene sequence data using paprica pipeline. The nZVI changed the abundance of numerous metabolic pathways compared to a less influencing mZVI. We identified the 50 most affected pathways, where 31 were related to degradation, 17 to biosynthesis, and 2 to detoxification. The linkage between pathways was two times higher in nZVI samples compared to mZVI, and was specifically higher considering the arsenate detoxification II pathway. Limnohabitans and Roseiflexus were linked to the same pathways in both nZVI and mZVI. The prediction of metabolic pathways increases our knowledge of the impacts of nZVI and mZVI on freshwater bacterioplankton.

Substrate Diversity of L-Threonic Acid Dehydrogenase Homologs

Despite physiological importance of aldonic sugar acids for living organisms, little is known about metabolic pathways of these compounds. Here, we investigated the functional diversity of homologs of L-threonic acid dehydrogenase (ThrDH; UniProt ID: Q0KBC7), an enzyme composed of two NAD-binding domains (PF14833 and PF03446). Ten ThrDH homologs with different genomic context were studied; seven new enzymatic activities were identified, such as (R)-pantoate dehydrogenase, L-altronic acid dehydrogenase, 6-deoxy-L-talonate dehydrogenase, L-idonic acid dehydrogenase, D-xylonic acid dehydrogenase, D-gluconic acid dehydrogenase, and 2-hydroxy-3-oxopantoate reductase activities. Two associated metabolic pathways were identified: L-idonic acid dehydrogenase was found to be involved in the degradation of L-idonic acid through oxidation/decarboxylation in Agrobacterium radiobacter K84, while 2-hydroxy-3-oxopantoate reductase was found to participate in D-glucarate catabolism through dehydration/cleavage in Ralstonia metallidurans CH34.

Greenhouse gases emissions from duckweed pond system treating polyester resin wastewater containing 1,4-dioxane and heavy metals

Phytoremediation of polyester resin wastewater containing 1,4-dioxane and heavy metals using Lemna gibba (L.gibba) was enhanced by incorporation of perforated polyethylene carrier materials (PCM) onto the duckweed pond (DWP) system. The DWP module was operated at a hydraulic retention times (HRTs) of 2, 4 and 6 days and as well as 1,4-dioxane loading rate of 16, 25 and 48 g/m³.d. The maximum removal efficiency of 54 ± 2.5% was achieved for 1,4-dioxane at an HRT of 6 days and loading rate of 16 g1,4-dioxane/m³.d. Similarly, the DWP system provided removal efficiencies of 28.3 ± 2.1, 93.2 ± 7.6, 95.7 ± 8.9 and 93.6 ± 4.9% for Cd²⁺, Cu²⁺, Zn²⁺ and Ni²⁺ at influent concentration of 0.037 ± 0.01, 1.2 ± 0.9, 27.2 ± 4.7 and 4.6 ± 1.2 mg/L respectively. The structural analysis by Fourier-transform infrared spectroscopy (FTIR) clearly displayed a reduction of 1,4- dioxane in the treated effluent. A strong peak was detected for L. gibba plants at frequency of 3417.71 cm^-1 due to N-H stretching, which confirm the proposed mechanism of partially conversion of 1,4-dioxane into amino acids. Glycine, serine, aspartic, threonine and alanine content were increased in L. gibba by values of 35 ± 2.2, 40 ± 3.2, 48 ± 3.7, 31 ± 2.8, and 56 ± 4.1%, respectively. The contribution of DWP unit as a greenhouse gases (GHG) emissions were relatively low (1.65 gCO₂/Kg BOD_removed.d., and 18.3 gCO₂/Kg _biomass.d) due to photosynthesis process, low excess sludge production and consumption of CO₂ for nitrification process (1.4 gCO₂/kgN _removed.d). Based on these results, it is recommended to apply such a technology for treatment of polyester resin wastewater containing 1,4-dioxane and heavy metals at a HRT not exceeding 6 days.

Bioaugmenting the poplar rhizosphere to enhance treatment of 1,4-dioxane

1,4-Dioxane is a highly mobile and persistent groundwater pollutant that often forms large dilute plumes. Because of this, utilizing aggressive pump-and-treat and ex-situ technologies such as advanced oxidation can be prohibitively expensive. In this study, we bioaugmented the poplar rhizosphere with dioxane-degrading bacteria Mycobacterium dioxanotrophicus PH-06 or Pseudonocardia dioxanivorans CB1190 to enhance treatment of 1,4-dioxane in bench-scale experiments. All treatments tested removed 10 mg/L dioxane to near health advisory levels (<4 μg/L). However, PH-06-bioaugmented poplar significantly outperformed all other treatments, reaching <4 μg/L in only 13 days. Growth curve experiments confirmed that PH-06 could not utilize root extract as an auxiliary carbon source for growth. Despite this limitation, our findings suggest that PH-06 is a strong bioaugmentation candidate to enhance the treatment of dioxane by phytoremediation. In addition, we confirmed that CB1190 could utilize both 1,4-dioxane and root extract as substrates. Finally, we demonstrated the large-scale production of these two strains for use in the field. Overall, this study shows that combining phytoremediation and bioaugmentation is an attractive strategy to treat dioxane-contaminated groundwater to low risk-based concentrations (~1 μg/L).

Enhanced long-term attenuation of 1,4-dioxane in bioaugmented flow-through aquifer columns

Long term natural attenuation of 1,4-dioxane (dioxane) and its enhanced biodegradation after bioaugmentation with Pseudonocardia dioxanivorans CB1190 were assessed using flow-through aquifer columns. Natural attenuation of dioxane was not observed even after 2 years of acclimation. However, dioxane removal was observed in the bioaugmented columns (34% when the influent was 200 µg/L and 92% for 5 mg/L). The thmA gene that encodes the tetrahydrofuran monooxygenase that initiates dioxane degradation by CB1190 was only detected at the inoculation port and persisted for months after inoculation, implying the resiliency of bioaugmentation and its potential to offer long-term enhanced biodegradation capabilities. However, due to extensive clumping and limited mobility of CB1190, the augmented catabolic potential may be restricted to the immediate vicinity of the inoculation port. Accordingly, bioaugmentation with CB1190 seems more appropriate for the establishment of biobarriers. Bioaugmentation efficiency was associated with the availability of oxygen. Aeration of the column influent to increase dissolved oxygen significantly improved dioxane removal (p < 0.05), suggesting that (for sites with oxygen-limiting conditions) bioaugmentation can benefit from engineered approaches for delivering additional oxygen.

Investigating promising substrates for promoting 1,4-dioxane biodegradation: effects of ethane and tetrahydrofuran on microbial consortia

Cometabolic biodegradation of 1,4-dioxane (dioxane) in the presence of primary substrates is a promising strategy for treating dioxane at environmentally relevant concentrations. Seven aqueous amendments (i.e., tetrahydrofuran (THF), butanone, acetone, 1-butanol, 2-butanol, phenol and acetate) and five gaseous amendments (i.e., C₁-C₄ alkanes and ethylene) were evaluated as the primary substrates for dioxane degradation by mixed microbial consortia. The aqueous amendments were tested in microcosm bottles and the gaseous amendments were tested in a continuous-flow membrane biofilm reactor with hollow fibers pressurized by the gaseous amendments. Ethane was found to be the most effective gaseous substrate and THF was the only aqueous substrate that promoted dioxane degradation. A diverse microbial community consisting of several putative dioxane degraders-Mycobacterium, Flavobacterium and Bradyrhizobiaceae-were enriched in the presence of ethane. This is the first study showing that ethane was the most effective substrate among the short-chain alkanes and it promoted dioxane degradation by enriching dioxane-degraders that did not harbor the well-known dioxane/tetrahydrofuran monooxygenase.

Enrichment and Analysis of Stable 1,4-dioxane-Degrading Microbial Consortia Consisting of Novel Dioxane-Degraders

Biodegradation of 1,4-dioxane, a water contaminant of emerging concern, has drawn substantial attention over the last two decades. A number of dioxane-degraders have been identified, though many of them are unable to metabolically utilize 1,4-dioxane. Moreover, it is considered more preferable to use microbial consortia rather than the pure strains, especially in conventional bioreactors for industrial wastewater treatment. In the present study, a stable 1,4-dioxane-degrading microbial consortium was enriched, namely 112, from industrial wastewater by nitrate mineral salt medium (NMSM). The consortium 112 is capable of utilizing 1,4-dioxane as a sole carbon and energy source, and can completely degrade 1,4-dioxane up to 100 mg/L. From the consortium 112, two 1,4-dioxane-degrading bacterial strains were isolated and identified, in which the Variovorax sp. TS13 was found to be a novel 1,4-dioxane-degrader that can utilize 100 mg/L of 1,4-dioxane. The efficacy of the consortium 112 was increased significantly when we cultured the consortium with mineral salt medium (MSM). The new consortium, N112, could utilize 1,4-dioxane at a rate of 1.67 mg/L·h. The results of the ribosomal RNA intergenic spacer analysis (RISA) depicted that changes in the microbial community structure of consortium 112 was the reason behind the improved degradation efficiency of consortium N112, which was exhibited as a stable and effective microbial consortium with a high potential for bioremediation of the dioxane-impacted sites and contaminated industrial wastewater.

1,4-Dioxane as an emerging water contaminant: State of the science and evaluation of research needs

1,4-Dioxane has historically been used to stabilize chlorinated solvents and more recently has been found as a contaminant of numerous consumer and food products. Once discharged into the environment, its physical and chemical characteristics facilitate migration in groundwater, resulting in widespread contamination of drinking water supplies. Over one-fifth of U.S. public drinking water supplies contain detectable levels of 1,4-dioxane. Remediation efforts using common adsorption and membrane filtration techniques have been ineffective, highlighting the need for alternative removal approaches. While the data evaluating human exposure and health effects are limited, animal studies have shown chronic exposure to cause carcinogenic responses in the liver across multiple species and routes of exposure. Based on this experimental evidence, the U.S. Environmental Protection Agency has listed 1,4-dioxane as a high priority chemical and classified it as a probable human carcinogen. Despite these health concerns, there are no federal or state maximum contaminant levels for 1,4-dioxane. Effective public health policy for this emerging contaminant requires additional information about human health effects, chemical interactions, environmental fate, analytical detection, and treatment technologies. This review highlights the current state of knowledge, key uncertainties, and data needs for future research on 1,4-dioxane.

Alternative fate of glyoxylate during acetate and hexadecane metabolism in Acinetobacter oleivorans DR1

The glyoxylate shunt (GS), involving isocitrate lyase (encoded by aceA) and malate synthase G (encoded by glcB), is known to play important roles under several conditions including oxidative stress, antibiotic defense, or certain carbon source metabolism (acetate and fatty acids). Comparative growth analyses of wild type (WT), aceA, and glcB null-strains revealed that aceA, but not glcB, is essential for cells to grow on either acetate (1%) or hexadecane (1%) in Acinetobacter oleivorans DR1. Interestingly. the aceA knockout strain was able to grow slower in 0.1% acetate than the parent strain. Northern Blot analysis showed that the expression of aceA was dependent on the concentration of acetate or H₂O₂, while glcB was constitutively expressed. Up-regulation of stress response-related genes and down-regulation of main carbon metabolism-participating genes in a ΔaceA mutant, compared to that in the parent strain, suggested that an ΔaceA mutant is susceptible to acetate toxicity, but grows slowly in 0.1% acetate. However, a ΔglcB mutant showed no growth defect in acetate or hexadecane and no susceptibility to H₂O₂, suggesting the presence of an alternative pathway to eliminate glyoxylate toxicity. A lactate dehydrogenase (LDH, encoded by a ldh) could possibly mediate the conversion from glyoxylate to oxalate based on our RNA-seq profiles. Oxalate production during hexadecane degradation and impaired growth of a ΔldhΔglcB double mutant in both acetate and hexadecane-supplemented media suggested that LDH is a potential detoxifying enzyme for glyoxylate. Our constructed LDH-overexpressing Escherichia coli strain also showed an important role of LDH under lactate, acetate, and glyoxylate metabolisms. The LDH-overexpressing E. coli strain, but not wild type strain, produced oxalate under glyoxylate condition. In conclusion, the GS is a main player, but alternative glyoxylate pathways exist during acetate and hexadecane metabolism in A. oleivorans DR1.

Simulation of in situ biodegradation of 1,4-dioxane under metabolic and cometabolic conditions

Bioaugmentation is an option for aerobic remediation of groundwater contaminated with 1,4-dioxane. One approach uses microbes that cometabolize 1,4-dioxane following growth on a primary substrate (e.g., propane), whereas another uses microbes (e.g., Pseudonocardia dioxivorans CB1190) capable of using 1,4-dioxane as a sole substrate. The relative merits of these approaches are difficult to distinguish based on field data alone, and theoretical analyses of these processes have yet to be published. The objective of this study was to compare these remediation options using a transport model that incorporates advection, dispersion and biodegradation reactions described by multi-substrate Monod kinetics and co-inhibition effects. The transport model was coupled to an approximate steady-state air sparging simulation used to estimate gas (propane and oxygen) distribution at the field scale. The model was calibrated with field data for 1,4-dioxane and propane concentrations from a previously reported pilot study. The two remediation approaches were evaluated under different conditions that vary the initial concentration of 1,4-dioxane and the loading rates of oxygen, propane, and biomass. The metrics used to evaluate the remediation success were the time to reach an average 1,4-dioxane concentration of 1 μg L^-1 and the percent of 1,4-dioxane biodegraded after 10 years of simulation. Results indicate that the initial concentration of 1,4-dioxane strongly influences which remediation approach is more effective. When initial concentrations were <10 mg L^-1, propane-driven cometabolism led to faster remediation; whereas metabolic biodegradation was faster when initial concentrations were 10 mg L^-1 or higher. Below 0.25 mg L^-1, the viability of metabolic biodegradation improved, although cometabolism by propanotrophs still required less time to reach 1 μg L^-1. Biomass injection rates had a strong effect on the rate of metabolism but not cometabolism because continuous input of primary substrate supported growth of propanotrophs. The performance of both cultures was negatively affected by a decrease in oxygen injection rate. The endogenous decay coefficient and the dispersion rate for biomass had a significant impact on cometabolic and metabolic biodegradation of 1,4-dioxane. The maximum specific rate for cometabolism of 1,4-dioxane, the dispersion rate for 1,4-dioxane, and effective porosity also had significant effects on the time to achieve remediation with propanotrophs.

Microbial Community Analysis Provides Insights into the Effects of Tetrahydrofuran on 1,4-Dioxane Biodegradation

Tetrahydrofuran (THF) is known to induce the biodegradation of 1,4-dioxane (dioxane), an emerging contaminant, but the mechanisms by which THF affects dioxane biodegradation in microbial communities are not well understood. To fill this knowledge gap, changes in the microbial community structure in microcosm experiments with synthetic medium and landfill leachate were examined over time using 16S rRNA gene amplicon sequencing and functional gene quantitative PCR assays. The overarching hypothesis being tested was that THF promoted dioxane biodegradation by increasing the abundance of dioxane-degrading bacteria in the consortium. The data revealed that in experiments with synthetic medium, the addition of THF significantly increased the abundance of Pseudonocardia, a genus with several representatives that can grow on both dioxane and THF, and of Rhodococ cus ruber, a species that can use THF as the primary growth substrate while cometabolizing dioxane. However, in similar experiments with landfill leachate, only R. ruber was significantly enriched. When the THF concentration was higher than the dioxane concentration, THF competitively inhibited dioxane degradation since dioxane degradation was negligible, while the dioxane-degrading bacteria and the corresponding THF/dioxane monooxygenase gene copies increased by a few orders of magnitude.IMPORTANCE Widespread in groundwater and carcinogenic to humans, 1,4-dioxane (dioxane) is attracting significant attention in recent years. Advanced oxidation processes can effectively remove dioxane but require high energy consumption and operation costs. Biological removal of dioxane is of particular interest due to the ability of some bacteria to mineralize dioxane at a low energy cost. Although dioxane is generally considered recalcitrant to biodegradation, more than 20 types of bacteria can degrade dioxane as the sole electron donor substrate or the secondary electron donor substrate. In the latter case, tetrahydrofuran (THF) is commonly studied as the primary electron donor substrate. Previous work has shown that THF promotes dioxane degradation at a low THF concentration but inhibits dioxane degradation at a high THF concentration. Our work expanded on the previous work by mechanically examining the effects of THF on dioxane degradation in a microbial community context.

Microbial Genes for a Circular and Sustainable Bio-PET Economy

Plastics have become an important environmental concern due to their durability and resistance to degradation. Out of all plastic materials, polyesters such as polyethylene terephthalate (PET) are amenable to biological degradation due to the action of microbial polyester hydrolases. The hydrolysis products obtained from PET can thereby be used for the synthesis of novel PET as well as become a potential carbon source for microorganisms. In addition, microorganisms and biomass can be used for the synthesis of the constituent monomers of PET from renewable sources. The combination of both biodegradation and biosynthesis would enable a completely circular bio-PET economy beyond the conventional recycling processes. Circular strategies like this could contribute to significantly decreasing the environmental impact of our dependence on this polymer. Here we review the efforts made towards turning PET into a viable feedstock for microbial transformations. We highlight current bottlenecks in degradation of the polymer and metabolism of the monomers, and we showcase fully biological or semisynthetic processes leading to the synthesis of PET from sustainable substrates.

Abiotic and bioaugmented granular activated carbon for the treatment of 1,4-dioxane-contaminated water

1,4-Dioxane is a probable human carcinogen and an emerging contaminant that has been detected in surface water and groundwater resources. Many conventional water treatment technologies are not effective for the removal of 1,4-dioxane due to its high water solubility and chemical stability. Biological degradation is a potentially low-cost, energy-efficient approach to treat 1,4-dioxane-contaminated waters. Two bacterial strains, Pseudonocardia dioxanivorans CB1190 (CB1190) and Mycobacterium austroafricanum JOB5 (JOB5), have been previously demonstrated to break down 1,4-dioxane through metabolic and co-metabolic pathways, respectively. However, both CB1190 and JOB5 have been primarily studied in laboratory planktonic cultures, while most environmental microbes grow in biofilms on surfaces. Another treatment technology, adsorption, has not historically been considered an effective means of removing 1,4-dioxane due to the contaminant's low K_oc and K_ow values. We report that the granular activated carbon (GAC), Norit 1240, is an adsorbent with high affinity for 1,4-dioxane as well as physical dimensions conducive to attached bacterial growth. In abiotic batch reactor studies, 1,4-dioxane adsorption was reversible to a large extent. By bioaugmenting GAC with 1,4-dioxane-degrading microbes, the adsorption reversibility was minimized while achieving greater 1,4-dioxane removal when compared with abiotic GAC (95-98% reduction of initial 1,4-dioxane as compared to an 85-89% reduction of initial 1,4-dioxane, respectively). Bacterial attachment and viability was visualized using fluorescence microscopy and confirmed by amplification of taxonomic genes by quantitative polymerase chain reaction (qPCR) and an ATP assay. Filtered samples of industrial wastewater and contaminated groundwater were also tested in the bioaugmented GAC reactors. Both CB1190 and JOB5 demonstrated 1,4-dioxane removal greater than that of the abiotic adsorbent controls. This study suggests that bioaugmented adsorbents could be an effective technology for 1,4-dioxane removal from contaminated water resources.

Identification of active and taxonomically diverse 1,4-dioxane degraders in a full-scale activated sludge system by high-sensitivity stable isotope probing

1,4-Dioxane is one of the most common and persistent artificial pollutants in petrochemical industrial wastewaters and chlorinated solvent groundwater plumes. Despite its possible biological treatment in natural environments, the identity and dynamics of the microorganisms involved are largely unknown. Here, we identified active and diverse 1,4-dioxane-degrading microorganisms from activated sludge by high-sensitivity stable isotope probing of rRNA. By rigorously analyzing 16S rRNA molecules in RNA density fractions of ¹³C-labeled and unlabeled 1,4-dioxane treatments, we discovered 10 significantly ¹³C-incorporating microbial species from the complex microbial community. 16S rRNA expression assays revealed that 9 of the 10 species, including the well-known degrader Pseudonocardia dioxanivorans, an ammonia-oxidizing bacterium and phylogenetically novel bacteria, increased their metabolic activities shortly after exposure to 1,4-dioxane. Moreover, high-resolution monitoring showed that, during a single year of operation of the full-scale activated sludge system, the nine identified species exhibited yearly averaged relative abundances of 0.001–1.523%, and yet showed different responses to changes in the 1,4-dioxane removal efficiency. Hence, the co-existence and individually distinct dynamics of various 1,4-dioxane-degrading microorganisms, including hitherto unidentified species, played pivotal roles in the maintenance of the biological system removing the recalcitrant pollutant.

1,4-Dioxane degradation characteristics of Rhodococcus aetherivorans JCM 14343

Rhodococcus aetherivorans JCM 14343 can degrade 1,4-dioxane as a sole carbon and energy source. This study aimed to characterize this 1,4-dioxane degradation ability further, and assess the potential use of the strain for 1,4-dioxane removal in industrial wastewater. Strain JCM 14343 was able to degrade 1,4-dioxane inducibly, and its 1,4-dioxane degradation was also induced by tetrahydrofuran and 1,4-butanediol. The demonstration that 1,4-butanediol not only induced but also enhanced 1,4-dioxane degradation was a novel finding of this study. Although strain JCM 14343 appeared not to be an effective 1,4-dioxane degrader considering the maximum specific 1,4-dioxane degradation rate (0.0073 mg-dioxane/mg-protein/h), half saturation concentration (59.2 mg/L), and cell yield (0.031 mg-protein/mg-1,4-dioxane), the strain could degrade over 1100 mg/L of 1,4-dioxane and maintain its degradation activity at a wide range of temperature (5-40 °C) and pH (4-9) conditions. This suggests the usefulness of strain JCM 14343 in 1,4-dioxane treatment under acidic and cold conditions. In addition, 1,4-dioxane degradation experiments in the presence of ethylene glycol (EG) or other cyclic ethers revealed that 1,4-dioxane degradation by strain JCM 14343 was inhibited in the presence of other cyclic ethers, but not by EG, suggesting certain applicability of strain JCM 14343 for industrial wastewater treatment.

Associating potential 1,4-dioxane biodegradation activity with groundwater geochemical parameters at four different contaminated sites

1,4-Dioxane (dioxane) is a groundwater contaminant of emerging concern for which bioremediation may become a practical remediation strategy. Therefore, it is important to advance our heuristic understanding of geochemical parameters that are most influential on the potential success of intrinsic bioremediation of dioxane-impacted sites. Here, Pearson's and Spearman's correlation and linear regression analyses were conducted to discern associations between 1,4-dioxane biodegradation activity measured in aerobic microcosms and groundwater geochemical parameters at four different contaminated sites. Dissolved oxygen, which is known to limit dioxane biodegradation, was excluded as a limiting factor in this analysis. Biodegradation activity was positively associated with dioxane concentrations (p < 0.01; R < 0.70) as well as the number of catabolic thmA gene copies (p < 0.01; R = 0.80) encoding dioxane monooxygenase. Thus, whereas environmental factors such as pH, temperature, and nutrients may influence dioxane biodegradation, these parameters did not exert as strong of an influence on potential biodegradation activity as the in situ concentration of substrate dioxane at the time of sampling. This analysis infers that aerobic sites with higher dioxane concentrations are more likely to select and sustain a thriving population of dioxane degraders, while sites with relatively low dioxane concentrations would be more difficult to attenuate naturally and may require alternative remediation strategies.

Characterization of newly isolated Pseudonocardia sp. N23 with high 1,4-dioxane-degrading ability

This study was conducted to elucidate the 1,4-dioxane degradation characteristics of a newly isolated 1,4-dioxane-degrading bacterial strain and evaluate the applicability of the strain to biological 1,4-dioxane removal from wastewater. A bacterial strain (designated strain N23) capable of degrading 1,4-dioxane as the sole carbon and energy source was isolated from an enrichment culture prepared from 1,4-dioxane-contaminated groundwater. Strain N23 was phylogenetically identified as belonging to the genus Pseudonocardia, based on 16S rRNA gene sequencing. 1,4-Dioxane degradation experiments revealed that strain N23 is capable of constitutive 1,4-dioxane degradation. Further, this strain exhibited the highest specific 1,4-dioxane degradation rate of 0.230 mg-1,4-dioxane (mg-protein)^-1 h^-1 among 1,4-dioxane-degrading bacteria with constitutively expressed degrading enzymes reported to date. In addition, strain N23 was shown to degrade up to 1100 mg L^-1 of 1,4-dioxane without significant inhibition, and to maintain a high level of 1,4-dioxane degradation activity under a wide pH (pH 3.8-8.2) and temperature (20-35 °C) range. In particular, the specific 1,4-dioxane degradation rate, even at pH 3.8, was 83% of the highest rate at pH 7.0. In addition, strain N23 was capable of utilizing ethylene glycol and diethylene glycol, which are both considered to be present in 1,4-dioxane-containing industrial wastewater, as the sole carbon source. The present results indicate that strain N23 exhibits the potential for 1,4-dioxane removal from industrial wastewater.

Mechanism of 1,4-dioxane microbial degradation revealed by 16S rRNA and metatranscriptomic analyses

1,4-Dioxane (dioxane), a probable human carcinogen, often exists in industrial wastewater and domestic sewage. In this study, we applied 16S rRNA and metatranscriptomic methods to analyze the dioxane biodegradation mechanism by activated sludge. Tetrahydrofuran (THF) was added as an essential co-metabolite to promote the degradation of dioxane. We found the dioxane removal ratio increased with increasing THF concentrations. When the THF concentration increased from 60.0 to 200.0 mg/L, the dioxane degradation rate was stable. Three additions of ∼60.0 mg/L THF resulted in better dioxane degradation than one addition of 200 mg/L THF. Ammonia-oxidizing and denitrifying bacteria with methane monooxygenases (MOs) and ammonia MOs played the most important roles during the degradation of dioxane. Kyoto Encyclopedia of Genes and Genomes metabolic pathway and functional genes analyses showed that the activated sludge system was complex and stable when dioxane was added. In future studies, primers should be designed to identify specific bacteria and functional MO genes, which would help reveal the function of various bacteria and their MOs during dioxane degradation.

Synergistic Treatment of Mixed 1,4-Dioxane and Chlorinated Solvent Contaminations by Coupling Electrochemical Oxidation with Aerobic Biodegradation

Biodegradation of the persistent groundwater contaminant 1,4-dioxane is often hindered by the absence of dissolved oxygen and the co-occurrence of inhibiting chlorinated solvents. Using flow-through electrolytic reactors equipped with Ti/IrO₂-Ta₂O₅ mesh electrodes, we show that combining electrochemical oxidation with aerobic biodegradation produces an overadditive treatment effect for degrading 1,4-dioxane. In reactors bioaugmented by Pseudonocardia dioxanivorans CB1190 with 3.0 V applied, 1,4-dioxane was oxidized 2.5 times faster than in bioaugmented control reactors without an applied potential, and 12 times faster than by abiotic electrolysis only. Quantitative polymerase chain reaction analyses of CB1190 abundance, oxidation-reduction potential, and dissolved oxygen measurements indicated that microbial growth was promoted by anodic oxygen-generating reactions. At a higher potential of 8.0 V, however, the cell abundance near the anode was diminished, likely due to unfavorable pH and/or redox conditions. When coupled to electrolysis, biodegradation of 1,4-dioxane was sustained even in the presence of the common co-contaminant trichloroethene in the influent. Our findings demonstrate that combining electrolytic treatment with aerobic biodegradation may be a promising synergistic approach for the treatment of mixed contaminants.

Draft Genome Sequence of Pseudonocardia sp. Strain N23, a 1,4-Dioxane-Degrading Bacterium

Pseudonocardia sp. strain N23 is a 1,4-dioxane-degrading bacterium that is capable of utilizing 1,4-dioxane as the sole carbon and energy source. Here, we report the draft genome sequence of strain N23, with a size of 6.5 Mbp, to identify the genes associated with 1,4-dioxane degradation.

1,4-Dioxane-degrading consortia can be enriched from uncontaminated soils: prevalence of Mycobacterium and soluble di-iron monooxygenase genes

Two bacterial consortia were enriched from uncontaminated soil by virtue of their ability to grow on 1,4‐dioxane (dioxane) as a sole carbon and energy source. Their specific dioxane degradation rates at 30°C, pH = 7 (i.e. 5.7 to 7.1 g‐dioxane per g‐protein per day) were comparable to those of two dioxane‐metabolizing archetypes: Pseudonocardia dioxanivoransCB1190 and Mycobacterium dioxanotrophicusPH‐06. Based on 16S rRNA sequencing, Mycobacterium was the dominant genus. Acetylene inhibition tests suggest that dioxane degradation was mediated by monooxygenases. However, qPCR analyses targeting the tetrahydrofuran/dioxane monooxygenase gene (thmA/dxmA) (which is, to date, the only sequenced dioxane monooxygenase gene) were negative, indicating that other (as yet unknown) catabolic gene(s) were responsible. DNA sequence analyses also showed threefold to sevenfold enrichment of group 5 and group 6 soluble di‐iron monooxygenase (SDIMO) genes relative to the original soil samples. Whereas biodegradation of trace levels of dioxane is a common challenge at contaminated sites, both consortia degraded dioxane at low initial concentrations (300 μg l⁻¹) below detectable levels (5 μg l⁻¹) in bioaugmented microcosms prepared with impacted groundwater. Overall, this work shows that dioxane‐degrading bacteria (and the associated natural attenuation potential) exist even in some uncontaminated soils, and may be enriched to broaden bioaugmentation options for sites experiencing insufficient dioxane catabolic capacity.

Whole-Genome Sequence of the 1,4-Dioxane-Degrading Bacterium Mycobacterium dioxanotrophicus PH-06

We report here the complete genome sequence of Mycobacterium dioxanotrophicus PH-06, which is capable of using 1,4-dioxane as a sole source of carbon and energy. The reported sequence will enable the elucidation of this novel metabolic pathway and the development of molecular biomarkers to assess bioremediation potential at contaminated sites.

Hindrance of 1,4-dioxane biodegradation in microcosms biostimulated with inducing or non-inducing auxiliary substrates

A microcosm study was conducted to assess two biostimulation strategies (relative to natural attenuation) to bioremediate 1,4-dioxane contamination at a site in west Texas. Dioxane concentrations were relatively low (<300 μg/L), which represents a potential challenge to sustain and induce specific degraders. Thus, biostimulation was attempted with an auxiliary substrate known to induce dioxane-degrading monooxygenases (i.e., tetrahydrohyran [THF]) or with a non-inducing growth substrate (1-butanol [1-BuOH]). Amendment of 1-BuOH (100 mg/L) to microcosms that were not oxygen-limited temporarily enhanced dioxane biodegradation by the indigenous microorganisms. However, this stimulatory effect was not sustained by repeated amendments, which might be attributed to i) the inability of 1-BuOH to induce dioxane-degrading enzymes, ii) curing of catabolic plasmids, iii) metabolic flux dilution and catabolite repression, and iv) increased competition by commensal bacteria that do not degrade dioxane. Experiments with the archetype dioxane degrader Pseudonocardia dioxanivorans CB1190 repeatedly amended with 1-BuOH (500 mg/L added weekly for 4 weeks) corroborated the partial curing of catabolic plasmids (9.5 ± 7.4% was the plasmid retention ratio) and proliferation of derivative segregants that lost their ability to degrade dioxane. Addition of THF (300 μg/L) also had limited benefit due to competitive inhibition; significant dioxane degradation occurred only when the THF concentration decreased below approximately 160 μg/L. Overall, these results illustrate the importance of considering the possibility of unintentional hindrance of catabolism associated with the addition of auxiliary carbon sources to bioremediate aquifers impacted with trace concentrations of dioxane.

Identification and characterization of 1,4-dioxane-degrading microbe separated from surface seawater by the seawater-charcoal perfusion apparatus

To determine the concentration of soluble 1,4-dioxane during biodegradation, a new method using of high-performance liquid chromatography equipped with a hydrophilic interaction chromatography column was developed. The developed method enabled easy and rapid determination of 1,4-dioxane, even in saline medium. Microbes capable of degrading 1,4-dioxane were selected from the seawater samples by the seawater-charcoal perfusion apparatus. Among 32 candidate 1,4-dioxane degraders,, strain RM-31 exhibited the strongest 1,4-dioxane degradation ability. 16S rDNA sequencing and the similarity analysis of strain RM-31 suggested that this organism was most closely related to Pseudonocardia carboxydivorans. This species is similar to Pseudonocardia dioxanivorans, which has previously been reported as a 1,4-dioxane degrader. Strain RM-31 could degrade 300 mg/L within 2 days. As culture incubation times increasing, the residual 1,4-dioxane concentration was decreasing and the total protein contents extracted from growth cells were increasing. The optimum initial pH of the broth medium and incubation temperature for 1,4-dioxane degradation were pH 6-8 and 25 °C. The biodegradation rate of 1,4-dioxane by strain RM-31 at 25 °C in broth medium with 3 % NaCl was almost 20 % faster than that without NaCl. It was probably a first bacteria from the seawater that can exert a strong degrading ability.

Role of Glyoxylate Shunt in Oxidative Stress Response

The glyoxylate shunt (GS) is a two-step metabolic pathway (isocitrate lyase, aceA; and malate synthase, glcB) that serves as an alternative to the tricarboxylic acid cycle. The GS bypasses the carbon dioxide-producing steps of the tricarboxylic acid cycle and is essential for acetate and fatty acid metabolism in bacteria. GS can be up-regulated under conditions of oxidative stress, antibiotic stress, and host infection, which implies that it plays important but poorly explored roles in stress defense and pathogenesis. In many bacterial species, including Pseudomonas aeruginosa, aceA and glcB are not in an operon, unlike in Escherichia coli In P. aeruginosa, we explored relationships between GS genes and growth, transcription profiles, and biofilm formation. Contrary to our expectations, deletion of aceA in P. aeruginosa improved cell growth under conditions of oxidative and antibiotic stress. Transcriptome data suggested that aceA mutants underwent a metabolic shift toward aerobic denitrification; this was supported by additional evidence, including up-regulation of denitrification-related genes, decreased oxygen consumption without lowering ATP yield, increased production of denitrification intermediates (NO and N2O), and increased cyanide resistance. The aceA mutants also produced a thicker exopolysaccharide layer; that is, a phenotype consistent with aerobic denitrification. A bioinformatic survey across known bacterial genomes showed that only microorganisms capable of aerobic metabolism possess the glyoxylate shunt. This trend is consistent with the hypothesis that the GS plays a previously unrecognized role in allowing bacteria to tolerate oxidative stress.

Pilot test of biological removal of 1,4-dioxane from a chemical factory wastewater by gel carrier entrapping Afipia sp. strain D1

A pilot-scale (120 L) bioreactor system using a gel carrier-entrapped pure bacterial strain, Afipia sp. strain D1, capable of degrading 1,4-dioxane as a sole carbon and energy source was constructed and applied to treat real industrial wastewater containing 1,4-dioxane from a chemical factory. Although the wastewater not only contained high concentrations of 1,4-dioxane but also considerable amounts of other organic compounds (73 mg-TOCL(-1) on average), the bioreactor could efficiently remove 1,4-dioxane without significant inhibitory effects. The reactor startup could be completed within approximately 1 month by increasing the 1,4-dioxane loading rate (0.09-0.47 kg-dioxanem(-3)d(-1)) in a stepwise manner. Effective 1,4-dioxane removal was stably maintained for 3 months with an influent 1,4-dioxane of 570-730 mg L(-1), giving an average effluent concentration and removal rate of 3.4 mg L(-1) and 0.46 kg-dioxanem(-3)d(-1), respectively. A 1,4-dioxane loading fluctuation between 0.14 and 0.72 kg-dioxanem(-3)d(-1) did not significantly affect its removal, and more than 99% removal efficiency was constantly maintained. The Monod model could well describe the relationship between the effluent 1,4-dioxane concentration and 1,4-dioxane removal rates of the bioreactors, showing that the half-saturation constant (Ks) was 28 mg L(-1).