Biodegradation Of Contaminants Research Articles

Semi-rational design of nitroarene dioxygenase for catalytic ability toward 2,4-dichloronitrobenzene.

Rieske non-heme dioxygenase family enzymes play an important role in the aerobic biodegradation of nitroaromatic pollutants, but no active dioxygenases are available in nature for initial reactions in the degradation of many refractory pollutants like 2,4-dichloronitrobenzene (24DCNB). Here, we report the engineering of hotspots in 2,3-dichloronitrobenzene dioxygenase from Diaphorobacter sp. strain JS3051, achieved through molecular dynamic simulation analysis and site-directed mutagenesis, with the aim of enhancing its catalytic activity toward 24DCNB. The computationally predicted activity scores were largely consistent with the detected activities in wet experiments. Among them, the two most beneficial mutations (E204M and M248I) were obtained, and the combined mutant reached up to a 62-fold increase in activity toward 24DCNB, generating a single product, 3,5-dichlorocatechol, which is a naturally occurring compound. In silico analysis confirmed that residue 204 affected the substrate preference for meta-substituted nitroarenes, while residue 248 may influence substrate preference by interaction with residue 295. Overall, this study provides a framework for manipulating nitroarene dioxygenases using computational methods to address various nitroarene contamination problems.IMPORTANCEAs a result of human activities, various nitroaromatic pollutants continue to enter the biosphere with poor degradability, and dioxygenation is an important kickoff step to remove toxic nitro-groups and convert them into degradable products. The biodegradation of many nitroarenes has been reported over the decades; however, many others still lack corresponding enzymes to initiate their degradation. Although rieske non-heme dioxygenase family enzymes play extraordinarily important roles in the aerobic biodegradation of various nitroaromatic pollutants, prediction of their substrate specificity is difficult. This work greatly improved the catalytic activity of dioxygenase against 2,4-dichloronitrobenzene by computer-aided semi-rational design, paving a new way for the evolution strategy of nitroarene dioxygenase. This study highlights the potential for using enzyme structure-function information with computational pre-screening methods to rapidly tailor the catalytic functions of enzymes toward poorly biodegradable contaminants.

Unravelling the role of the group 6 soluble di-iron monooxygenase (SDIMO) SmoABCD in alkane metabolism and chlorinated alkane degradation.

Soluble di-iron monooxygenases (SDIMOs) are multi-component enzymes catalysing the oxidation of various substrates. These enzymes are characterized by high sequence and functional diversity that is still not well understood despite their key role in biotechnological processes including contaminant biodegradation. In this study, we analysed a mutant of Rhodoccocus aetherivorans BCP1 (BCP1-2.10) characterized by a transposon insertion in the gene smoA encoding the alpha subunit of the plasmid-located SDIMO SmoABCD. The mutant BCP1-2.10 showed a reduced capacity to grow on propane, lost the ability to grow on butane, pentane and n-hexane and was heavily impaired in the capacity to degrade chloroform and trichloroethane. The expression of the additional SDIMO prmABCD in BCP1-2.10 probably allowed the mutant to partially grow on propane and to degrade it, to some extent, together with the other short-chain n-alkanes. The complementation of the mutant, conducted by introducing smoABCD in the genome as a single copy under a constitutive promoter or within a plasmid under a thiostreptone-inducible promoter, allowed the recovery of the alkanotrophic phenotype as well as the capacity to degrade chlorinated n-alkanes. The heterologous expression of smoABCD allowed a non-alkanotrophic Rhodococcus strain to grow on pentane and n-hexane when the gene cluster was introduced together with the downstream genes encoding alcohol and aldehyde dehydrogenases and a GroEL chaperon. BCP1 smoA gene was shown to belong to the group 6 SDIMOs, which is a rare group of monooxygenases mostly present in Mycobacterium genus and in a few Rhodococcus strains. SmoABCD originally evolved in Mycobacterium and was then acquired by Rhodococcus through horizontal gene transfer events. This work extends the knowledge of the biotechnologically relevant SDIMOs by providing functional and evolutionary insights into a group 6 SDIMO in Rhodococcus and demonstrating its key role in the metabolism of short-chain alkanes and degradation of chlorinated n-alkanes.

Enhancing in situ biodegradation in groundwater using pump and treat remediation: a proof of concept and modelling analysis of controlling variables.

A remediation approach which uses pump and treatment (PAT) to enhance the biodegradation of organic contaminants by increasing dispersive mixing between plumes and groundwater was evaluated for a phenol-contaminated aquifer, using a reactive transport model which simulates kinetic reactions between an electron donor (ED) in the plume and electron acceptor (EA) in the groundwater. The influence of system design and operation was examined in six modelling scenarios. Injection or extraction of groundwater increases biodegradation above no action and the location, pumping rate, and distance between well(s) are important variables which influence biodegradation. An increase in pumping rate, distance of the wells from the plume centreline, and changing the flow direction increase dispersive mixing between the plume and groundwater. This increases plume spreading and the plume fringe interface, providing a greater flux of dissolved EAs for biodegradation. In general, injection of groundwater containing natural EAs enhances biodegradation more than extraction. The enhancement of biodegradation is sensitive to the relative fluxes of ED and EA, as controlled by the arrangement of the wells. In the best performing scenario, biodegradation was enhanced by 128%, compared with no action.

Electrode potential regulates extracellular polymer secretion enhanced tetracycline removal

Bacteria colonized on solid electrode developing electroactive biofilm (EAB) has been shown to promote the contaminants biodegradation. Regulating electrode potential can improve the stability of extracellular electron transfer (EET), but how the electrode potential regulating the extracellular polymer secretion and the tetracycline (TC) removal has not been fully studied. Here, EAB cultured at 0 V was used to study the degradation mechanism of TC at different electrode potentials. Results showed that −0.1 V was the optimized electrode potential for TC biodegradation compared with 0.1 V, 0 V and −0.3 V, which was 28 % higher than that without electric field. Stimulation of electric field can retain proper extracellular polymer (EPS) to relieve the poison of TC, while excessive extracellular polysaccharide (PS) at 0 V have hindered the contact between microorganisms and TC, thus limited electron transfer and reduced the TC biodegradation efficiency. Excessively negative potential (−0.3 V) will restrict the electron transfer which was not conducive to the biodegradation of organic pollutants. Microbial community analysis revealed that TC addition have refreshed the EAB structure, Dokdonella and Norank_f_Rikenellaceae replaced Geobacter as the dominant species in EAB to promote TC biodegradation. The variation of metabolic pathway was suggested that the up-regulation of pyruvate metabolism and ubiquinone synthesis at −0.1 V have promoted the TC removal. This study has provided theoretical support for the electrode potential regulating the extracellular polymer secretion and promoting the pollution bioremediation.

Natural attenuation of dissolved petroleum fuel constituents in a fractured Chalk aquifer: contaminant mass balance with probabilistic analysis

A plume-scale mass balance is developed to assess the natural attenuation (NA) of dissolved organic contaminants in fractured, dual-porosity aquifers. This methodology can be used to evaluate contaminant distribution within the aquifer, plume source term, contaminant biodegradation and plume status. The approach is illustrated for a site on the UK Upper Chalk aquifer impacted by petroleum fuel containing methyl tert -butyl ether (MTBE) and tert -amyl methyl ether (TAME). Variability in site investigation data and uncertainty in the mass balance were assessed using probabilistic analysis. The analysis shows that benzene, toluene, m/p-xylene and o-xylene (BTEX) compounds are biodegraded primarily by denitrification and sulfate reduction in the aquifer, with an equivalent plume-scale first-order biodegradation rate of 0.49 a −1 . Other biodegradation processes are less important. Sorption contributes to hydrocarbon attenuation in the aquifer but is less important for MTBE and TAME. Uncertainty in the plume source term and site hydrogeological parameters had the greatest effect on the mass balance. The probabilistic analysis enabled the most likely long-term composition of the plume source term to be deduced and provided a site-specific estimate of contaminant mass flux for the prediction of plume development. The mass balance methodology provides a novel approach to improve NA assessments for petroleum hydrocarbons and other organic contaminants in these aquifer settings. Supplementary material: Plume organic chemistry, aquifer hydraulic conductivity and probability distribution functions used for mass balance inputs are available at https://doi.org/10.6084/m9.figshare.c.7016429 Thematic collection: This article is part of the Monitoring the aquifers collection available at: https://www.lyellcollection.org/topic/collections/monitoring-the-aquifers

Depth-dependent variations of physicochemical properties of sedimentary dissolved organic matter and the influence on the elimination of typical pharmaceuticals

Sedimentary dissolved organic matter (DOM) could exert a significant influence on the transformation of trace organic contaminants. However, the variations of sedimentary DOM properties with depth and their impact on trace organic contaminants biodegradation remain unclear. In this study, the qualitative changes in DOM properties with depth were assessed using spectral techniques. Specifically, within the sediment range of 0–30 cm, humic acid and fulvic acid fractions exhibited higher degrees of humification and aromatization at 10–20 cm, while hydrophilic fractions showed higher degrees of humification and aromatization at 20–30 cm. Furthermore, electrochemical methods were employed to quantitatively assess the electron transfer capacity of sedimentary DOM at different depths, which displayed consistent variation trend with humification and aromatization degree. The high degree of humification and aromatization, along with strong electron-accepting capability of DOM, significantly enhanced the biodegradation rates of tetracycline and ritonavir. To gain deeper insights into the influence of molecular composition of DOM on its properties, two-dimensional gas chromatography-quadrupole mass spectrometry analysis revealed that quinones and phenolic hydroxyl compounds govern the redox reactivity of DOM. Simulated experiment of DOM-mediated biodegradation of typical pharmaceuticals confirmed the role of quinones and phenolic hydroxyl groups in the redox reactivity of DOM.

Robust calculus for biotransformation in wastewater generalised across thousands of chemicals and conditions

Environmental context Decades of research tried to understand the inherent complexity of biodegradation of contaminants. We describe calculus of biodegradation driven by bioavailability, redox, geometry and acclimation (adaptation) of microbiota. We tested predictions for thousands of contaminants across wastewater treatment plants, explaining up to 70% of the variance in observations. This competes with more intensive methods, and enables more efficient monitoring, experimentation and data interpretation. Rationale Release of harmful contaminants of emerging concern (CECs) in the environment prompts possible adverse toxicological effects. Increasing population, water use and process wastewater generation require more efficient removal of contaminants that allows for effluent discharge within environmental regulatory limits. Wastewater treatment plants (WWTPs) can remove hazardous contaminants, limiting unwanted release. Fine-tuning WWTP settings to fit the location, time, season, wastewater type, etc. may enhance removals to reduce CEC concentrations and toxic pressures. Methodology For this purpose, we need robust tools to calculate removal efficiencies. We studied influences of operational settings and CEC properties on their removal in WWTPs. For this purpose, we parameterised thermochemical properties of CECs: for their (1) speciation and acidification, (2) (re/im)mobilisation due to (de)sorption into solid/water, (3) redox-mediated biotransformation and (4) acclimation of biomass so to utilise metabolic pathways for biotransformation. By combining these parameters, we developed an energy-based framework for calculating biotransformation rates. Results We evaluated our calculus using removal efficiency (%) data for 373 measurements of 60 CECs in 14 different Dutch WWTPs and an additional 667 CECs in 49 WWTPs across the world. Our prediction precision, R2 ≈ 0.65 (P < 10−5), captures influences of wastewater characteristics (multiple measurements for each WWTP). It is higher than R2-values of modelling approaches currently available. Our model explains CEC removal with appreciative certainty. We identified outliers during evaluation. These outliers were attributed mostly to back-transformation and uncertainty in long-term background concentrations of contaminants, causing consequent acclimation of microbial consortia. Discussion Biodegradability and CEC-degrading biomass can be estimated from concentration and environmental residence time. Our framework and underlying parametrisations have a mechanistic basis, utilising simple WWTP operational information (CEC concentration, temperature, suspended solids concentration, oxygen demand, etc.). Thereby, our work has wide potential for implementation. Our approach can supplement current fate assessment for CECs for improved environmental risk assessments. We conclude by discussing the potential for removal enhancement.

Influence of a biodegradable contaminant on the mechanical recycling of a low‐density polyethylene sample

AbstractMechanical recycling of oil‐derived polymers is certainly our best option to reduce pollution, save raw materials, and protect ourselves and the environment from the adverse effects of waste disposal. However, the presence of contaminants, including other types of plastics, that are mixed in during the recycling collection process or during the mechanical waste sorting stage could adversely affect the quality of the recycled product, leading to the recycling of a poor‐quality secondary material. In this work, the influence of a biodegradable contaminant on the mechanical recycling of a low‐density polyethylene (LDPE) sample was investigated by rheological (shear and non‐isothermal elongation) and mechanical analyses. The results showed that 2% of the contaminant is able to influence the rheological, shear, and isothermal elongation properties of recycled LDPE, while the results of the mechanical tests showed that after one extrusion cycle, the main tensile properties were not significantly affected by the presence of the contaminant, but after only two cycles of extrusions, some significant reduction in the final properties began to appear. In short, the presence of 2% of a biodegradable co‐polyester in a LDPE matrix gives rise to a more pronounced decay of the rheological and mechanical properties, but, after two extrusion steps, both rheological and mechanical properties seem still useful for the production of film.Highlights To what extent the contaminant affects the quality and usability of the recycled LDPE; The effects of contamination on the LDPE sample during the recycling process; Reduction in properties, compromising product quality; Compromised product quality after only two additional processing steps; Important implications for the recycling industry.

Acetylenotrophic and Diazotrophic Bradyrhizobium sp. Strain I71 from Trichloroethylene-Contaminated Soils

Acetylene (C2H2) is a trace constituent of Earth’s modern atmosphere and is used by acetylenotrophic microorganisms as their sole carbon and energy source (Akob et al. 2018) Acetylenotrophs hydrate acetylene through a reaction catalyzed by acetylene hydratase, which is a heterogeneous class of enzymes. As of 2018, there were 15 known strains of acetylenotrophs including aerobic species affiliated with the Actinobacteria, and Firmicutes and anaerobic species affiliated with the Desulfobacterota. However, we hypothesized that there was an unknown diversity of acetylenotrophs in nature. We recently expanded the known distribution of acetylenotrophs via the isolation of the aerobic acetylenotroph, Bradyrhizobium sp. strain I71, from trichloroethylene (TCE)-contaminated soils (Akob et al. 2022). Strain I71 is a member of the class Alphaproteobacteria, and this is the first observation of an aerobic acetylenotroph in the Proteobacteria phylum. The isolate grows via heterotrophic and acetylenotrophic metabolism, and is diazotrophic, capable of nitrogen fixation. Acetylenotrophy and nitrogen fixation are the only two enzymatic reactions known to transform acetylene, and this is only the second isolate known to carry out both reactions (Akob et al. 2017, Baesman et al. 2019). Members of Bradyrhizobium are well studied for their abilities to improve plant health and increase crop yields by providing bioavailable nitrogen. The unique capability of Bradyrhizobium sp. strain I71 to utilize acetylene may increase the genus’ economic impact beyond agriculture as acetylenotrophy is closely linked to bioremediation of chlorinated contaminants (Mao et al. 2017, Gushgari-Doyle et al. 2021). Based on genome, cultivation, and protein prediction analysis, the ability to consume acetylene is likely not widespread within the genus Bradyrhizobium. These findings suggest that the suite of phenotypic capabilities of strain I71 may be unique and make it a good candidate for further study in several research avenues such as contaminant biodegradation and nutrient cycling.

Composting post-anaerobic digestion for emerging contaminant biodegradation: Impacts of operating conditions.

Sustainable manure management technologies are needed, and combining anaerobic digestion (AD) for energy generation and aerobic composting (AC) to stabilize digestate and remove emerging contaminants (ECs), including veterinary pharmaceuticals and steroid hormones, is promising. This study identified post-AD, AC operating conditions that maximized degradation of study ECs, expected to be present in cattle manure digested using treated municipal wastewater as the water source. Study ECs included sulfamethoxazole (SMX), chlortetracycline (CTC), oxytetracycline (OTC), estrone (E1), and naproxen (NPX). Composting conditions were simulated in bench-scale reactors, with microorganisms from digestate produced in an AD system (25L scale), by varying temperatures, pH, and carbon source compositions (representing food waste/manure co-digestion with different residence times). Results indicate maximum SMX biodegradation occurred at 35°C, pH 7, and with high levels of easily degradable carbon (≥99%, 99%, and 98%), and maximum E1 biodegradation occurred at 35°C, and with low levels of easily degradable carbon (≥97% and 99%). Abiotic degradation was responsible for the nearly complete removal of tetracyclines under all conditions and for partial degradation of NPX (between 20% and 48%). Microorganisms originating from the AD system putatively capable of SMX and E1 biodegradation, or of contributing to biodegradation during the AC phase, were identified, including phylotypes previously shown to biodegrade SMX (Brevundimonas and Alcaligenes).

Advancing biodegradation of petroleum contaminants by indigenous microbial consortia through assembly strategy innovations

Our demand for petroleum has challenged Earth's ecosystems, causing extensive water and soil pollution. Petroleum contamination treatment technology has relied on a range of biochemical processes to treat hydrocarbon-contaminated wastes, of which microbial degradation is one of the most economical and ecological. Engineered microbialconsortia can solve complex and difficult-to-degrade contaminants. However, the functional stability of consortia is challenged during long-term co-cultivation. Here, we introduced a novel strategy to design a stable consortium for degrading hydrocarbon pollutants, developed from ecological coexistence theory and trait-based method. Specifically, the degradation rate of the consortium constructed using the five strains was 31.54% higher than that of a single strain in a 6% (m/v) petroleum concentration after 16 days of co-culture. Besides, molecular characterization of the composition and transformation of petroleum-based substances further reveals the functional stability of consortium and the degradation mechanism and pattern of hydrocarbons by the consortium. Two independent soil experiments showed that the treatment of oil-contaminated soil by consortia from the indigenous microbiota maximizes the removal of hydrocarbon contaminants. Collectively, this strategy is generally applicable, facilitates the design of engineered microbial consortia, and provides a foundation for solving environmental pollution.

BIOSURFACTANTS: POSSIBLE ROLES IN ENVIRONMENTAL MANAGEMENT -A REVIEW

Recent years have seen a rise in interest in biosurfactants, which are surface-active compounds produced by microorganisms that affect surfaces, particularly the surface tension of liquid-vapor interfaces. Due to their ability to emulsify and solubilize hydrophobic compounds as result of their amphipathic nature, biosurfactants are useful in degradation of hydrocarbon and are therefore applicable in oil spill management. Because they are biodegradable, have low toxicity, work well at high or low pH levels, and are more environmentally friendly than their chemical equivalents, biosurfactants have merits over their chemical counterparts. Biosurfactants are adaptable materials with a wide range of uses in the biodegradation and bioremediation of environmental contaminants. In addition, they have uses in pharmaceutical, food, and other industries. The continuous interest in biosurfactants results from these benefits and their vast variety of applications. Hydrophobic pollutants such as hydrocarbons and their derivatives are the major environmental issues due to their poor degradation but the use of biosurfactants can enhance their microbial degradation. When microorganisms try to use substrates like hydrocarbon as a source of carbon, they produce a variety of compounds called biosurfactants that help the diffusion into the cell. This review discusses the roles of these microbial products as veritable tools in environmental management with particular emphasis on the roles of biosurfactants in the sanitation of petroleum pollution and bioremediation of soils contaminated by pesticides.

Nitrification-denitrification co-metabolism in an algal-bacterial aggregates system for simultaneous pyridine and nitrogen removal

Photosynthetic oxygenation in algal-bacterial symbiotic (ABS) system was mainly concerned to enhance contaminant biodegradation by developing an aerobic environment, while the role of nitrification-denitrification involved is often neglected. In this study, an algal-bacterial aggregates (ABA) system was developed with algae and activated sludge (PBR-1) to achieve simultaneous pyridine and nitrogen removal. In PBR-1, as high as 150 mg·L−1 pyridine could be completely removed at hydraulic residence time of 48 h. Besides, total nitrogen (TN) removal efficiency could be maintained above 80%. Nitrification-denitrification was verified as the crucial process for nitrogen removal, accounting for 79.3% of TN removal at 180 μmol·m−2·s−1. Moreover, simultaneous pyridine and nitrogen removal was enhanced through nitrification-denitrification co-metabolism in the ABA system. Integrated bioprocesses in PBR-1 including photosynthesis, pyridine biodegradation, carbon and nitrogen assimilation, and nitrification-denitrification, were revealed at metabolic and transcriptional levels. Fluorescence in situ hybridization analysis indicated that algae and aerobic species were located in the surface layer, while denitrifiers were situated in the inner layer. Microelectrode analysis confirmed the microenvironment of ABA with dissolved oxygen and pH gradients, which was beneficial for simultaneous pyridine and nitrogen removal. Mechanism of nitrification-denitrification involved in pyridine and nitrogen removal was finally elucidated under the scale of ABA.

Biodegradation of soil agrochemical contamination mitigates the direct horizontal transfer risk of antibiotic resistance genes to crops

Microorganisms can drive a substrate-specific biodegradation process to mitigate soil contamination resulting from extensive agrochemical usage. However, microorganisms with high metabolic efficiency are capable of adapting to the co-occurrence of non-substrate contaminants in the soil (particularly antibiotics). Therefore, the utilization of active microorganisms for biodegradation raises concerns regarding the potential risk of antibiotic resistance development. Here, the horizontal transfer risk of antibiotic-resistance genes (ARGs) in the soil-plant biota was assessed during biodegradation by the newly isolated Proteus terrae ZQ02 (which shortened the half-life of fungicide chlorothalonil from 9.24 d to 2.35 d when exposed to tetracycline). Based on metagenomic analyses, the distribution of ARGs and mobile genetic elements (MGEs) was profiled. The ARGs shared with ∼118 core genes and mostly accumulated in the rhizosphere and maize roots. After ZQ02 was inoculated, the core genes of ARGs reduced significantly in roots. In addition, the Pseudomonas and Proteus genera were identified as the dominant microbial hosts of ARGs and MGEs after ZQ02 adoption. The richness of major ARG hosts increased in soil but barely changed in the roots, which contributed to the mitigation of hosts-mediated ARGs transfer from soil to maize. Finally, the risk of ARGs has been assessed. Compared with the regular planting system, the number of risky ARGs declined from 220 (occupied 4.77 % of the total ARGs) to 143 (occupied 2.67 %) after biodegradation. Among these, 23 out of 25 high-risk genes were aggregated in the soil whereas only 2 genes were identified in roots, which further verified the low antibiotic resistance risk for crop after biodegradation. In a nutshell, this work highlights the critical advantage of ZQ02-based biodegradation that alleviating the ARGs transfer risks from soil to crop, which offers deeper insights into the versatility and feasibility of bioremediation techniques in sustainable agriculture.

The microbial oxidation of pharmaceuticals in an anaerobic aqueous environment: Effect of dissolved organic matter fractions from different sources

Previous studies have demonstrated the importance of dissolved organic matter (DOM) on the biodegradation of trace organic contaminants occurred in the hyporheic zone. However, the role of diverse DOM fractions with distinct physicochemical properties on the biodegradation of pharmaceuticals under reducing conditions is scarcely known. To address this knowledge gap, DOMs derived from road-deposited sediment, soil, and active sludge (namely allochthonous DOM) and algae (namely autochthonous DOM) were collected and isolated into different fractions. Thereafter, the effect of DOM fractions on the anaerobic microbial oxidation of two typical pharmaceuticals, i.e., ritonavir (RTV) and tetracycline (TC) was explored by using simulated anaerobic microcosms. Mechanistic insights into how DOM fractions from different sources influence pharmaceutical biodegradation processes were provided by optical and electrochemical analyses. Results showed that humic acid and fulvic acid fractions from allochthonous DOM could enhance the biodegradation of TC (12.2 % per mgC/L) and RTV (14.5 % per mgC/L), while no significant impact was observed for that of hydrophilic fractions. However, autochthonous DOM promoted the biodegradation of TC (4.17 % per mgC/L) and inhibited that of RTV. Mechanistic analysis showed that the higher of humification and aromatization level of DOM components, the stronger their promotive effect on the biodegradation of TC and RTV. Further, the promotive mechanism could be attributed to the response of quinone moieties in DOM as extracellular electron acceptors that yields more energy to support microbial metabolism. These results provide a more comprehensive understanding of diverse DOM fractions mediating microbial anaerobic oxidation of trace organic pollutants, and extend our insights into contamination control and remediation technologies.

Cold adapted Pseudomonas: ecology to biotechnology.

The cold adapted microorganisms, psychrophiles/psychrotolerants, go through several modifications at cellular and biochemical levels to alleviate the influence of low temperature stress conditions. The low temperature environments depend on these cold adapted microorganisms for various ecological processes. The ability of the microorganisms to function in cold environments depends on the strategies directly associated with cell metabolism, physicochemical constrains, and stress factors. Pseudomonas is one among such group of microorganisms which is predominant in cold environments with a wide range of ecological and biotechnological applications. Bioformulations of Pseudomonas spp., possessing plant growth promotion and biocontrol abilities for application under low temperature environments, are well documented. Further, recent advances in high throughput sequencing provide essential information regarding the prevalence of Pseudomonas in rhizospheres and their role in plant health. Cold adapted species of Pseudomonas are also getting recognition for their potential in biodegradation and bioremediation of environmental contaminants. Production of enzymes and bioactive compounds (primarily as an adaptation mechanism) gives way to their applications in various industries. Exopolysaccharides and various biotechnologically important enzymes, produced by cold adapted species of Pseudomonas, are making their way in food, textiles, and pharmaceuticals. The present review, therefore, aims to summarize the functional versatility of Pseudomonas with particular reference to its peculiarities along with the ecological and biotechnological applications.

Characterization of Hsp17, a Novel Small Heat Shock Protein, in Sphingomonas melonis TY under Heat Stress.

Bacteria are constantly exposed to a variety of environmental stresses. Temperature is considered one of the most important environmental factors affecting microbial growth and survival. As ubiquitous environmental microorganisms, Sphingomonas species play essential roles in the biodegradation of organic contaminants, plant protection, and environmental remediation. Understanding the mechanism by which they respond to heat shock will help further improve cell resistance by applying synthetic biological strategies. Here, we assessed the transcriptomic and proteomic responses of Sphingomonas melonis TY to heat shock and found that stressful conditions caused significant changes in functional genes related to protein synthesis at the transcriptional level. The most notable changes observed were increases in the transcription (1,857-fold) and protein expression (11-fold) of Hsp17, which belongs to the small heat shock protein family, and the function of Hsp17 in heat stress was further investigated in this study. We found that the deletion of hsp17 reduced the capacity of the cells to tolerate high temperatures, whereas the overexpression of hsp17 significantly enhanced the ability of the cells to withstand high temperatures. Moreover, the heterologous expression of hsp17 in Escherichia coli DH5α conferred to the bacterium the ability to resist heat stress. Interestingly, its cells were elongated and formed connected cells following the increase in temperature, while hsp17 overexpression restored their normal morphology under high temperature. In general, these results indicate that the novel small heat shock protein Hsp17 greatly contributes to maintaining cell viability and morphology under stress conditions. IMPORTANCE Temperature is generally considered the most important factor affecting metabolic functions and the survival of microbes. As molecular chaperones, small heat shock proteins can prevent damaged protein aggregation during abiotic stress, especially heat stress. Sphingomonas species are widely distributed in nature, and they can frequently be found in various extreme environments. However, the role of small heat shock proteins in Sphingomonas under high-temperature stress has not been elucidated. This study greatly enhances our understanding of a novel identified protein, Hsp17, in S. melonis TY in terms of its ability to resist heat stress and maintain cell morphology under high temperature, leading to a broader understanding of how microbes adapt to environmental extremes. Furthermore, our study will provide potential heat resistance elements for further enhancing cellular resistance as well as the synthetic biological applications of Sphingomonas.

Enhanced biodegradation of crude oil contamination by indigenous bacterial consortium under real conditions

This study was performed to evaluate the efficiency of using locally isolated bacteria to degrade crude oil in sea water-based medium. The bacteria were isolated from water samples taken from different sea environments (Mediterranean, Aegean, Marmara, and Black Sea). The experiments for crude oil degradation were carried out in small volume (100 mL sea water medium in 250 mL shaking flasks) or large volume (14 L sea water-based medium in a plastic container). Furthermore, the media were not sterilized and remained open to the environment (non-sterile conditions). On the other hand, the media were shaken at a low speed of 50 rpm to mimic sea conditions. Of twelve bacterial isolates, four isolates (PB1, PB4, PB6, and PB7) having higher oil degradation potential were selected. According to 16S rRNA analysis, the isolates PB4 and PB6 were identified as, respectively, Rhodococcus qingshengii and Alcanivorax venustensis, and the other two isolates (PB1 and PB7) as Pseudomonas sabulinigri. When the usability of four isolates alone or as a co-culture for crude oil degradation was tested, co-cultures were found to cause more crude oil degradation than individual bacterial cultures. Among the co-cultures, the maximum degradation of crude oil was achieved with the association of PB6 + PB4. During the experiments, carbon sources and minerals were not supplemented to the sea water medium, and even the supplementation of only nitrogen source (especially ammonium sulphate) was determined to significantly enhance the crude oil degradation potential of the bacterial consortium (PB6 + PB4). Spectrophotometric analyses (OD225) demonstrated that crude oil degradation continued up to 12th day in small volume but 16th day in large volume. GC-MS analyses revealed that co-culture of PB6 and PB4 degraded 100% of C9–C12 and C16–C29 hydrocarbons and 85% of C13–C15 hydrocarbons.

Improved degradation of petroleum contaminants in hydraulic fracturing flowback and produced water using laccase immobilized on functionalized biochar

Large quantities of hydraulic fracturing flowback and produced water (HF-FPW) represent an important environmental issue owing to their inclusion of toxic petroleum contaminants. Enzymatic degradation is a promising approach for treating these pollutants. However, the low stability and poor reusability of free enzymes greatly inhibit their applications. This study investigated the effect of biochar-immobilized laccases on the biodegradation of petroleum contaminants in HF-FPW. Acid functionalization of corn straw biochar increased its surface area and pore volume, allowing it to adsorb additional laccase on the surface. Biochar-immobilized laccase exhibited a high tolerance to a low pH and high temperatures and retained >81.0% of its relative activity at 4 °C for 20 d. In addition, the immobilized laccase displayed reusability after six reaction cycles, retaining 40.9% of its activity. Supplementation with immobilized laccase substantially improved microbial growth and fluorescein diacetate hydrolase activity in HF-FPW, which were up to 25.5 times and 4.9 times higher than those of the free laccase treatment, respectively. The immobilized laccase also elevated the transcription levels of degradation genes such as rub and xylE, and greatly enhanced the biodegradation of n-alkanes (reduction from 112.4 mg/L to 41.9 mg/L) and polycyclic aromatic hydrocarbons (reduction from 2606.2μg/L to 1526.6μg/L). Full-length 16S rRNA gene sequencing revealed that Pseudomonas stutzeri, Pseudomonas balearica, and Stenotrophomonas maltophilia dominated the microbial community and were potential functional populations. This study represents the first attempt of utilizing biochar-immobilized laccase to treat HF-FPW and has important implications for efforts to develop strategies for HF-FPW remediation.

Reviewing the Bioremediation of Contaminants in Groundwater: Investigations over 40 Years Provide Insights into What's Achievable.

Biodegradation and biotransformation of contaminants in groundwater commonly occurs naturally. However, natural biodegradation rates can be slow leading to elongated contaminant plumes and prolonged risks that demand greater remedial intervention. Enhancement of the biodegradation of contaminants in groundwater can be induced by the addition of amendments to change the geochemical conditions to those that are more favorable for indigenous or added biota. Enhancing biodegradation requires collocation of the contaminant of concern with the 'right' microbial communities under the 'right' geochemical conditions, so that the microbiota thrive and bio-transform, degrade or lock up the contaminant of interest. This is most easily achievable at laboratory or bench scale where mixing is easily performed, and mass transfer limitations are minimized. However, inducing such changes at field scale in aquifers is non-trivial - amendments do not easily mix into groundwater because it is a laminar (non-turbulent) and low-energy flow environment. Bioaugmentation of cultured or genetically modified organisms have also been considered to add to groundwater to enhance contaminant degradation rates. Here we provide an overview of research studies over approximately 40 years that highlight the progression of understanding from natural biodegradation of plumes in groundwater to active bioremediation efforts that have been variably successful at field scale. Investigated contaminants providing insights include petroleum hydrocarbons, chlorinated and brominated hydrocarbons, ammonium, metals, munition compounds, atrazine and per- and polyfluorinated alkyl substances. The redox and electron acceptor/donor conditions that are inducive to biodegradation for a range of contaminants are highlighted. Biodegradation is challenged by the availability of electron donors/acceptors in the core of plumes and on plume fringes. Cases for bioaugmentation are identified. A long history of investigations provides examples of the importance of amendment delivery mechanisms, scale-up from laboratory to field, and field-scale demonstration of the effectiveness of groundwater bioremediation technologies. Advantages and disadvantages of remedial approaches are tabulated. The value and contributions of integrative modelling advances are identified. The literature review and example cases provide a deep understanding of what scale of bioremediation might be achievable for groundwater plumes. Limitations to bioremediation strategies outlined here will help direct future efforts. Addressing the sources of groundwater plumes as well as bioremediation of the plume itself will achieve more effective outcomes. Twelve 'lessons learnt' are synthesized from the review.