Engineering non-conservative substrate recognition sites of extradiol dioxygenase: Computation guided design to diversify and accelerate degradation of aromatic compounds.

Extradiol dioxygenases (EDOs) catalyzing meta-cleavage of catecholic compounds promise an effective way to detoxify aromatic pollutants. This work reported a novel scenario to engineer our recently identified Type I EDO from Tcu3516 for a broader substrate scope and enhanced activity, which was based on 2,3-dihydroxybiphenyl (2,3-DHB)-liganded molecular docking of Tcu3516 and multiple sequence alignment with other 22 Type I EDOs. 11 non-conservative residues of Tcu3516 within 6 Å distance to the 2,3-DHB ligand center were selected as potential hotspots and subjected to semi-rational design using 6 catecholic analogues as substrates; the mutants V186L and V212N returned with progressive evolution in substrate scope and catalytic activity. Both mutants were combined with D285A for construction of double mutants and final triple mutant V186L/V212N/D285A. Except for 2,3-DHB (the mutant V186L/D285A gave the best catalytic performance), the triple mutant prevailed all other 5 catecholic compounds for their degradation; affording the catalytic efficiency kcat/Km value increase by 10-30 folds, protein Tm (structural rigidity) increase by 15 °C and the half-life time enhancement by 10 times compared to the wild type Tcu3516. The molecular dynamic simulation suggested that a stabler core and a more flexible entrance are likely accounting for enhanced catalytic activity and stability of enzymes.

A novel circular approach to analyze the challenges associated with micro-nano plastics and their sustainable remediation techniques.

The mismanagement of consumer-discarded plastic waste (CDPW) has raised global environmental concerns about climate change. The COVID-19 outbreak has generated ∼1.6 million tons of plastic waste per day in the form of personal protective equipment (masks, gloves, face shields, and sanitizer bottles). These plastic wastes are either combustible or openly dumped in aquatic and terrestrial environments. Open dumping upsurges emerging contaminants like micro-nano plastics (MNPs) that directly enter the ecosystem and cause severe impacts on flora and fauna. Therefore, it has become an utmost priority to determine sustainable technologies that can degrade or treat MNPs from the environment. The present review assesses the sources and impacts of MNPs, various challenges, and issues associated with their remediation techniques. Accordingly, a novel sustainable circular model is recommended to increase the degradation efficiency of MNPs using biochemical and biological methods. It is also concluded that the proposed model does not only overcome environmental issues but also provides a sustainable secondary resource to meet the sustainable development goals (SDGs).

Bioremediation of lead-contaminated soil by inorganic phosphate-solubilizing bacteria immobilized on biochar.

In this study, a bio-composite (IBWS700) was prepared using inorganic phosphate-solubilizing bacteria (iPSB), which were immobilized on biochar produced from wheat straw (WS700). Further, the bio-remediation effects of the composite for lead (Pb) in soil were also investigated. The presence of different Pb species, physicochemical properties, enzyme activities, and immobilization mechanisms of Pb in soil were also evaluated. Compared to free iPSB and biochar, IBWS700 significantly decreased the lead bio-availability whereas increased the residual fraction, also affected available phosphorus (AP), cation exchange capacity (CEC), organic matter (OM) and activity of urease, alkaline phosphatase, sucrase and catalase. Interestingly, the changes in the enzyme activity, AP and OM performed twice increases with increasing Pb concentration, which was rarely reported. The reason might be attributed to the reconstruction of bacteria communities with high Pb load. Further, the immobilization mechanisms mainly included bio-adsorption and bio-precipitation. SEM revealed that the surface of IBWS700 covered with a large number of heterogeneous colonization of iPSB and white stack after Pb2+ adsorption. FTIR spectra showed that O-H, C-O-P, CO, and C =C could play important roles in bio-adsorption. Moreover, XRD analysis indicated that bio-precipitates were mainly Pb5(PO4)3Cl. In general, the use of IBWS700 could effectively immobilize Pb2+ and improve soil quality.

Environmental pollution, toxicity profile, and physico-chemical and biotechnological approaches for treatment of textile wastewater.

Textile industries discharges a huge quantity of unused synthetic dyes in wastewater leading to increased environmental pollution and pose a great risk to human health. Thus, a significant improvement in effluent quality is required before it is discharged into the environment. Although, several physicochemical methods have been practiced for the efficient color and dyes removal from textile effluents, these approaches have some drawbacks of greater use of expensive chemicals, low sensitivity, formation of excess sludge which also have secondary disposal problem. Thus, there is still a need for energy efficient, affordable, effective, and environmentally friendly treatment technologies. Bioremediation has been considered as a promising an upcoming active field of research for the treatment of unwanted color and target compounds from the contaminated environment. In order to efficient treatment of textile effluent, the main objective of the present study was to isolate and characterize the indigenous microbial isolates from textile industry effluents and sludge samples and investigate their dye removal and decolorization ability along with the influence of various process parameters on effluents decolorization that draining into the open environment.

Comparative assessment of chromate bioremediation potential of Pantoea conspicua and Aspergillus niger.

The recent work aims at the use of Pantoea conspicua (MT5) and Aspergillus niger (CRS3) to assess their bioremediation potential and growth restoration of Helianthus annuus L. under chromate (Cr+6) stress. The growth of the P. conspicua and A. niger was tested in Cr+6 supplemented media. The strains can withstand up to 1200 and 900 ppm respectively in the media and effectively bio-transform it to nontoxic form. Supplemented metal's levels significantly decreased the growth attribute of H. annuus (p< 0.05). On the other hand, P. conspicua and A. niger rescued the host plant by establishing higher colonization frequency with the host roots. Moreover, MT5 bio-transformed the toxic Cr+6 to non-toxic Cr+3 form in the rhizosphere. It also enhanced the host plant growth by producing phytohormones and ceasing Cr uptake and accumulation. Contrarily, CRS3 tends to accumulate and bio-transform metal in their hyphae. Nonetheless, both of the microbes tend to modulate phytohormones production and strengthening antioxidant system of the host. Improvement in the antioxidant system enabled the host plant to produce higher phenolics and flavonoids, and lower peroxidase. The associated plant species also exhibited higher ROS scavenging and lower ROS accumulation. Besides, the strains were able to produce higher amounts of phytohormones, including IAA, GA, and SA. Such activities rendered them as excellent phytostimulants, that can be used as biofertilizers in chromium polluted soils.

Comparative growth analysis of okra (Abelmoschus esculentus) in the presence of PGPR and press mud in chromium contaminated soil.

Chromium is a toxic heavy metal. Plants, animals and human metabolic processes are disturbed due to higher levels of chromium. PGPR are involved in seed germination, growth improvement, metabolic process and in most of the physiological processes of plants. Press mud in soil provides substrate to the microbes. PGPR can convert the more toxic form of Cr (VI) into less toxic form Cr (III). This study was conducted to find out the reduction potential of pre-isolated rhizobacteria and their role in strengthening of plant growth and physiological attributes. Soil collected from the research area was spiked with 20 mg kg-1 of Cr (VI) by using potassium dichromate (K2Cr2O7) salt before sowing. Results revealed that Cr (VI) significantly suppressed the shoot length, root length and photosynthetic rate of okra up to 19, 37 and 31%, respectively. However, inoculation decreases the uptake of Cr (VI) in root and shoot up to 37 and 31% and by press mud 33 and 20%, respectively. Combined application of inoculation and press mud significantly recovered the negative impact of chromium and plant growth was almost at par compared with contaminated treatment without inoculation.

Effect of lignin and plant growth-promoting bacteria (Staphylococcus pasteuri) on microbe-plant Co-remediation: A PAHs-DDTs Co-contaminated agricultural greenhouse study.

Due to the ecological toxicity and environmental residues, how to remove the persistent organic pollutants (POPs), especially of polycyclic-aromatic-hydrocarbons (PAHs) and dichloro-diphenyl-trichloroethanes (DDTs), from agricultural soil has captured the attention of scholars for a long time. To develop an effective and low-cost in situ co-remediation technique, five independent but complementary treatments were used on an over-standard PAHs-DDTs co-contaminated soil in an agricultural greenhouse. Experimental results identified that the combination of microbe (Bacillus methylotrophicus) - plant (Brassica rapa) could remove rhamnolipid activated PAHs and DDTs effectively after enhanced by Staphylococcus pasteuri. Also, the Benzoapyrene and total DDTs residue in Brassica rapa was up to the standard of National (China) food safety. The lignin enhanced the removal of high-rings PAHs and p-p' DDE but reduced soil microbial biomass carbon and soil enzymes activity (polyphenol oxidase, invertase and acid phosphatase). Pearson correlation analysis showed that polyphenol oxidase activity was significantly related to the PAHs/DDTs dissipation rate. Our research suggested a new amendment that could remediate PAHs/DDTs co-contaminated agricultural soil without interrupting crop production, and the polyphenol oxidase activity should be considered as a micro-ecological indicator in this process.

[Interactions among soil biota and their applications in synergistic bioremediation of heavy-metal contaminated soils].

Soil is the material basis for human survival. However, in China, soils are wildly polluted by heavy metals, which poses serious health risks to humans. Bioremediation of heavy-metal contaminated soil is widely considered as a sustainable remediation strategy, but low remediation efficiency is still a scientific bottleneck of bioremediation. There are abundant microorganisms, plants and animals living in soils. Among these soil biota, there are complex interactions to form an intricate food web through material circulation and energy transfer. These interactions among soil biota affect the transportation and transformation of pollutants in soil, and consequently influence the bioremediation efficiency. The synergistic remediation by soil biota combines the advantages of diferent organisms to enhance the efficiency of bioremediation. In this paper, the interactions among soil biota and their influence on heavy-metal transportation and transformation, as well as bioremediation efficiency are reviewed. We also propose perspectives for future researches, including targeted regulating the structure of soil food web, improving the bioremediation efficiency of heavy-metal contaminated soil, and building a synergistic remediation technology with multi-organisms based on food web.

Biofunctionalized nanomaterials for in situ clean-up of hydrocarbon contamination: A quantum jump in global bioremediation research.

Interfacing organic or inorganic nanoparticles with biological entities or molecules or systems with the aim of developing functionalized nano-scale materials or composites for remediation of persistent organic hydrocarbon pollutants (such as monocyclic and polycyclic aromatic hydrocarbons, MAH/PAH) has generated great interest and continues to grow almost unabated. However, the usefulness and potency of these materials or conjugates hinges over several key barriers, including structural assembly with fine-tuned control over nanoparticle/biomolecule ratio, spatial orientation and activity of biomolecules, the nano/bio-interface strategy and hierarchical architecture, water-dispersibility and long term colloidal stability in environmental media, and non-specific toxicity. The present review thus critically analyses, discusses and interprets recently reported attempts and approaches to functionalize nanoparticles with biomolecules. Since there is no comprehensive and critical reviews on the applications of nanotechnology in bioremediation of MAHs/PAHs, this overview essentially captures the current global scenario and vision on the use and future prospects of biofunctionalized nanomaterials with respect to their strategic interactions involved at the nano/bio-interface essential to understand and decipher the structural and functional relationships and their impact on persistent hydrocarbon remediation.

Biotechnological potential and applications of microbial consortia.

Recent advances in microbial consortia present a valuable approach for expanding the scope of metabolic engineering. Systems biology enable thorough understanding of diverse physiological processes of cells and their interactions, which in turn offers insights into the optimal design of synthetic microbial consortia. Yet, the study of synthetic microbial consortia is still in early infancy, facing many unknowns and challenges in intercellular communication and construction of stable and controllable microbial consortia systems. In this review, we comprehensively discussed the recent application of defined microbial consortia in the fields of human health monitoring and medicine exploitation, valuable compounds synthesis, consolidated bioprocessing of lignocellulosic materials and environmental bioremediation. Moreover, the outstanding challenges and future directions to advance the development of high-efficient, stable and controllable synthetic microbial consortia were highlighted.

Pollution, Toxicity and Carcinogenicity of Organic Dyes and their Catalytic Bio-Remediation.

Water pollution due to waste effluents of the textile industry is seriously causing various health problems in humans. Water pollution with pathogenic bacteria, especially Escherichia coli (E. coli) and other microbes is due to the mixing of fecal material with drinking water, industrial and domestic sewage, pasture and agricultural runoff. Among the chemical pollutants, organic dyes due to toxic nature, are one of the major contaminants of industrial wastewater. Adequate sanitation services and drinking quality water would eliminate 200 million cases of diarrhea, which results in 2.1 million less deaths caused by diarrheal disease due to E. coli each year. Nanotechnology is an excellent platform as compared to conventional treatment methods of water treatment and remediation from microorganisms and organic dyes. In the current study, toxicity and carcinogenicity of the organic dyes have been studied as well as the remediation/inactivation of dyes and microorganism has been discussed. Remediation by biological, physical and chemical methods has been reviewed critically. A physical process like adsorption is cost-effective, but can't degrade dyes. Biological methods were considered to be ecofriendly and cost-effective. Microbiological degradation of dyes is cost-effective, eco-friendly and alternative to the chemical reduction. Besides, certain enzymes especially horseradish peroxidase are used as versatile catalysts in a number of industrial processes. Moreover, this document has been prepared by gathering recent research works related to the dyes and microbial pollution elimination from water sources by using heterogeneous photocatalysts, metal nanoparticles catalysts, metal oxides and enzymes.

A biorefinery for valorization of industrial waste-water and flue gas by microalgae for waste mitigation, carbon-dioxide sequestration and algal biomass production.

Massive industrialization all over the globe is the main cause for the generation of huge quantity of wastes such as flue gas and wastewaters. Mindless release of these hazardous wastes into the environment is threatening the health and survival of the mankind. Judicious use of these wastes for microalgal biomass cultivation is recognized as a plausible approach for the creation of a renewable and sustainable process chain for biofuel production. This study was designed to cultivate microalgae utilizing the organic and inorganic nutrients from the industrial wastewater (IWW) and coal-fired flue gas (FG) for simultaneous waste bio-remediation and biomass production for biorefinery application in closed photobioreactors. The two microalgae, Chlorella sp. and Chlorococcum sp. were cultivated in industrial wastewater where varying concentrations of coal-fired FG from 1 to 10% CO2, volume/volume percent (v/v) was supplied to stimulate the mixotrophic growth. Performance of the two microalgae was evaluated in terms of nutrient removal (ammonium, nitrate, phosphate and COD), CO2 fixation, total lipid and carbohydrate content obtained in the integrated mode of process development. The IWW with flue gas (5% CO2 (v/v)) resulted in maximum growth and CO2 fixation. The highest biomass growth (1.52 g L-1) and CO2 fixation (187.65 mg L-1 d-1) of Chlorella sp. with nutrient removal of >70% was observed by 5th day of batch cultivation. Nearly 90% removal of nitrogen resulted in nutrient limitation condition that steered the accumulation of lipid (17-34%) and carbohydrate (21.5-23.1%) in Chlorella and Chlorococcum sp. An overall 1.7 fold improvement in biomass was observed in this process integration compared with control culture. The present study presents a green process for waste remediation, CO2 fixation and production of biomass rich in lipid & carbohydrate content for the development of a green microalgal biorefinery.

Biotechnological potential of Chlorella sp. and Scenedesmus sp. microalgae to endure high CO2 and methane concentrations from biogas.

Biogas, a gaseous effluent from the anaerobic digestion of organic waste, is considered an important source of energy, since it has a composition mainly of methane (CH4; 55-75%) and CO2 (20-60%). Today, CO2 from biogas is an excellent carbon source to induce high microalgal biomass production; however, each microalga strain can have different optimal CO2 concentrations for maximizing their bio-refinery capacity as well as different ability to endure stressful conditions of industrial effluents. This study assessed the bio-refinery capacity of Chlorella sp. and Scenedesmus sp., native of Lago de Chapala, Mexico, from biogas, as well as the effect of high CO2 and methane concentrations on the physiological performance to grow, capture CO2 and biochemical composition of both microalgae cultured under different biogas compositions. The results show that both microalgae have the biotechnological potential to endure biogas compositions of 25% CO2-75% CH4. Under this condition, the biomass production attained by Chlorella sp. and Scenedesmus sp. was 1.77 ± 0.32 and 2.25 ± 0.20 g L-1, respectively, with a biochemical composition mainly of carbohydrates and proteins. Overall, this study demonstrates that both microalgae have the ability to endure the stressful biogas composition without affecting their physiological capacity to capture CO2 and biosynthesize high-value metabolites. Moreover, it is worth highlighting the importance of screening wild-type microalgae from local ecosystems to determine their physiological capacity for each biotechnological application.

Biodegradation of dibenzothiophene by efficient Pseudomonas sp. LKY-5 with the production of a biosurfactant.

A potent bacterial strain capable of degrading dibenzothiophene (DBT) was isolated and evaluated for its characteristics. The strain, designated as LKY-5, is rod-shaped, gram-negative, and occurs mainly in clusters. It was identified as belonging to the Pseudomonas genus based on the 16S rDNA sequence and phylogenic analysis. Determination of its DBT depletion efficiency by gas chromatography revealed that the isolate was able to completely degrade up to 100 mg L-1 DBT within 144 h. The pH values, DBT concentrations, and biomasses in the medium varied significantly in the initial 24 h. A biosurfactant produced by LKY-5 was extracted and identified as a di-rhamnolipid with the formula Rha-Rha-C8-C8:1 by HPLC-ESI-MS/MS. There were 26 metabolites in the DBT degradation process. Pseudomonas sp. LKY-5 exhibited unusually high DBT degradation efficiency via multiple metabolic pathways. Compared with the reported 4S and Kodama pathways, two more expanded metabolic pathways for the degradation of DBT are proposed. The polycyclic aromatic sulfur heterocycles (PASHs) in diesel, such as C1-DBT, C2-DBT, C3-DBT, 4,6-DMDBT, and 2,4,6-TMDBT, can also be degraded with 28.2-42.3% efficiency. The results showed that LKY-5 is an excellent bacterial candidate for the bioremediation of PASH-contaminated sites and sediments.

Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14.

Ensifer (Sinorhizobium) sp. M14 is an efficient arsenic-oxidizing bacterium (AOB) that displays high resistance to numerous metals and various stressors. Here, we report the draft genome sequence and genome-guided characterization of Ensifer sp. M14, and we describe a pilot-scale installation applying the M14 strain for remediation of arsenic-contaminated waters. The M14 genome contains 6874 protein coding sequences, including hundreds not found in related strains. Nearly all unique genes that are associated with metal resistance and arsenic oxidation are localized within the pSinA and pSinB megaplasmids. Comparative genomics revealed that multiple copies of high-affinity phosphate transport systems are common in AOBs, possibly as an As-resistance mechanism. Genome and antibiotic sensitivity analyses further suggested that the use of Ensifer sp. M14 in biotechnology does not pose serious biosafety risks. Therefore, a novel two-stage installation for remediation of arsenic-contaminated waters was developed. It consists of a microbiological module, where M14 oxidizes As(III) to As(V) ion, followed by an adsorption module for As(V) removal using granulated bog iron ores. During a 40-day pilot-scale test in an abandoned gold mine in Zloty Stok (Poland), water leaving the microbiological module generally contained trace amounts of As(III), and dramatic decreases in total arsenic concentrations were observed after passage through the adsorption module. These results demonstrate the usefulness of Ensifer sp. M14 in arsenic removal performed in environmental settings.

Genome of Serratia nematodiphila MB307 offers unique insights into its diverse traits.

A pigment-producing species of Serratia was isolated from the rhizosphere of a heavy metal resistant Cannabis sativa plant growing in effluent-affected soil of Hattar Industrial Estate, Haripur, Pakistan. Here, we report the genome sequence of this bacterium, which has been identified as Serratia nematodiphila on the basis of whole genome comparison using the OrthoANI classification scheme. The bacterium exhibited diverse traits, including plant growth promotion, antimicrobial, bioremediation, and pollutant tolerance capabilities including metal tolerance, azo dye degradation, ibuprofen degradation, etc. Plant growth-promoting exoenzyme production as well as phosphate solubilisation properties were observed. Genes for phosphate solubilisation, siderophore production, and chitin destruction were identified in addition to other industrially important enzymes like nitrilase and lipase. Secondary metabolite producing apparatus for high value chemicals in the whole genome was also analysed. The number of antibiotic resistance genes was then profiled in silico, through a match with Antibiotic Resistant Gene and CAR database. This is the first report of a S. nematodiphila genome from a polluted environment. This could significantly contribute to the understanding of pollution tolerance, antibiotic resistance, association with nematodes, production of bio-pesticide, and their role in plant growth promotion.

Long-term sustainability of microbial-induced CaCO3 precipitation in aqueous media.

Microbially induced CaCO3 precipitation (MICP) via urea hydrolysis is an emerging technique for soil amelioration, building materials rehabilitation and pollutants sequestration amongst other various environmental applications. The successful application of MICP requires the sustainability of the precipitated CaCO3; to which the fate of ammonia, the main by-product of ureolysis, is potentially significante. Ammonia volatilization and biological ammonia oxidation both induce a pH decrease, which, in turn, might cause CaCO3 dissolution. To examine the potential effect of accumulated ammonia on precipitated CaCO3, we conducted a long-term MICP batch experiment, using environmental enrichment cultures of ureolytic bacteria. Here we show that CaCO3 precipitation was completed within 15-27 days, along with a rise in ammonium concentration. Following completion of ureolysis and precipitation, ammonium concentrations decreased, leading to a pH decrease. About 30 days after precipitation was completed, as much as 30% CaCO3 dissolution, was observed. A two-step model, describing urea hydrolysis followed by the removal of ammonia from the precipitation solution, predicted CaCO3 dissolution due to ammonia volatilization. We suggest that ureolytic MICP might result in ammonia volatilization, leading to significant CaCO3 dissolution. These results provide basic insights into the sustainability of ureolytic MICP and should further encourage removal of the accumulated ammonia from the treated site.

Assessment of the immune-modulatory and antimicrobial effects of dietary chitosan on Nile tilapia (Oreochrmis niloticus) with special emphasis to its bio-remediating impacts.

Fish, pathogen and environment are three counterparts who are sharing the same circle of life. To keep fish up to their optimal health, environment should be competently improved and pathogen count/virulence should be seized. Using of bioactive immunostimulants to achieve these objectives is the hypothesis under assessment. Thus, the present study was performed to evaluate the use of shrimp shells derived chitosan as an immunostimulant as well as preventive regime against Aeromonas hydrophila infection of Nile tilapia and to assess its antibacterial/aquatic bio-remediating effects. Results achieved by feeding 1% chitosan as preventive/therapeutic regimes have revealed a remarkably enhanced several innate immunological parameters (e.g., Phagocytic activity/index, NBT, Lysozyme activity and ACH50), increased resistance against A. hydrophila and strikingly improved water quality compared to the 0.5 and 2% chitosan containing diets. Conclusively, experimental results suggest the commercial usage of chitosan as an efficient immunostimulant and bio-remediating agent in aquaculture.

Chronic effects of temperature and nitrate pollution on Daphnia magna: Is this cladoceran suitable for widespread use as a tertiary treatment?

Effluent clarification and disinfection are major challenges in wastewater management. The cladoceran Daphnia magna has been proposed as a cost-effective and ecosystem-friendly option to clarify and disinfect secondary effluents, but its efficacy has not been fully tested under different sewage conditions. The present study explores the effects of temperature and nitrate on the efficacy of D. magna as a tertiary treatment at two different scales (individual assays and microcosms). Individual assays were employed to determine direct effects of temperature and/or nitrate on D. magna cultured in a suspension of organic matter. Using microcosms under the same environmental conditions, we explored the clearing efficacy of D. magna interacting with a natural microbial community. Individual assays revealed that D. magna mortality increased by 17% at 26 °C, 21% at >250 mg NO3(-)/l and by 60% at 26 °C and at >250 mg NO3(-)/l, and individuals displayed reduced body size, filtering rates and fecundity when compared to those at 21 °C and <40 mg NO3(-)/l. Improved performance under these conditions was also mirrored in the microcosms, with a higher density of D. magna (>100 ind/l) at 21 °C and <40 mg NO3(-)/l compared to the number (0-21 ind/l) at 26 °C and/or >250 mg NO3(-)/l. In the microcosms at 21 °C and <40 mg NO3(-)/l, turbidity and the density of bacteria, protists and micro-metazoa decreased in relation to those at 26 °C and/or >250 mg NO3(-)/l. Each treatment developed a unique and characteristic microbial assemblage, and D. magna was identified as the major driver of the community structure of protists and micro-metazoa. This enabled us to determine taxa vulnerability to D. magna grazing, and to re-define their tolerance thresholds for nitrate. In conclusion, this study increases our knowledge of how microbes respond to temperature and nitrate pollution, and highlights that D. magna efficacy as a tertiary treatment can be seriously compromised by variable environmental conditions.