Genetically engineered microorganisms for environmental remediation

Rafeeq, Hamza; Afsheen, Nadia; Rafique, Sadia; Arshad, Arooj; Intsar, Maham; Rehman, Asim Ur; Bilal, Muhammad; Iqbal, Hafiz M.N.

doi:10.1016/j.chemosphere.2022.136751

Cited by 67 publications

(20 citation statements)

References 142 publications

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“…As stated above, efflux pumps are transport proteins involved in the extrusion of hazardous substrates from within the cells into the external environment, and they are linked to bioremediation mechanisms (Sharma et al, 2023). In addition, permease proteins are essential membrane transport mechanisms that allow the introduction of stronger proteins into the bacterial cell through genetic engineering to enhance bioremediation traits (Rafeeq et al 2023). Interestingly, Cho et al (2019) drafted the whole genome of an Arthrobacter oryzae strain from a site not affected by anthropogenic activities and reported that the genome contains many heavy metal resistant genes, so bioremediation may be a central genome-enabled trait of this genera.…”

Section: Resultsmentioning

confidence: 99%

Metagenome Assembled Genomes (MAG) Facilitate a Better Understanding of Microbially-mediated Heavy Metal Resistance in Soils from a Former Nuclear Materials Production Facility

Kommu,

Stothard,

Chukwujindu

et al. 2023

Preprint

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Shotgun metagenomes is a repository of all the genes present in an environmental sample. With recent advancements in bioinformatic techniques, it is now possible to in-silico retrieve sequences that belong to specific taxa, followed by assembly and annotation and the obtained sequences are called as metagenome-assembled genome (MAG), which facilitates better understanding of metabolic and other traits without having to culture the microorganism. We applied the MAG technique using the nf-core/mag pipeline on shotgun metagenome sequences obtained from a soil ecosystem that has long-term co-contamination with radionuclides (mainly uranium), heavy metals (mercury, nickel etc.) and organic compounds. Annotation of MAGs was performed using SPAdes and MEGAHIT and genomes were binned and taxonomically classified using the GTDBTk and CAT toolkits within nf-core/mag. Additional annotations were done using Prokka and Prodigal and the dRep program was used to choose specific MAGs for further analysis. Initial analysis resulted in a total of 254 MAGs which met the high-quality standard with the completeness > 95% and contamination < 5%, accounting for 26.67% of all the MAGs (Fig SI-1). After bin refinement and de-replication, 27 MAGs (18 from Winter season and 9 from Summer season) were reconstructed. These 27 MAGs span across 6 bacterial phyla and the most predominant ones were Proteobacteria, Bacteroidetes, and Cyanobacteria regardless of the season. Overall, the Arthrobacter MAG was found to be one that was robust for further analysis. Over 1749 genes putatively involved in crucial metabolism of elements viz. nitrogen, phosphorous, sulfur and 598 genes encoding enzymes for metals resistance from cadmium, zinc, chromium, arsenic and copper. In summary, this project enhances our understanding of genes conferring resistance to heavy metals in uranium contaminated soils.

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Section: Resultsmentioning

confidence: 99%

Metagenome Assembled Genomes (MAG) Facilitate a Better Understanding of Microbially-mediated Heavy Metal Resistance in Soils from a Former Nuclear Materials Production Facility

Kommu,

Stothard,

Chukwujindu

et al. 2023

Preprint

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“…Given the widespread CO 2 supersaturation, local physical aeration in river channels can degas a mass of CO 2 and CH 4 (Chiu et al., 2021), which would increase the CO 2 emissions from restored rivers. Meanwhile, previous studies suggested that many engineered microorganism inputs during nutrient removal could strongly alter the microbial flora structure and carbon metabolism in urban rivers, resulting more CO 2 and CH 4 production in the water column (Rafeeq et al., 2023; Sharma et al., 2023). Accordingly, our results provide only holistic insights into watershed restoration controls on CO 2 emissions in heavily polluted rivers, and more research on the regulation effect of ecological restoration on riverine carbon emission is needed from several different perspectives.…”

Section: Discussionmentioning

confidence: 99%

Ecological Restoration Effectively Mitigated pCO₂ and CO₂ Evasions From Severely Polluted Urban Rivers

Wang,

Liu

et al. 2023

JGR Biogeosciences

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Urban rivers are significant hotspots of CO2 emissions into the atmosphere, playing important roles in global carbon emission inventories. However, little is known about the effect of ecological restoration on CO2 dynamics in severely polluted urban rivers, and this strongly hindering our understanding of the positive effects of human activities on CO2 emissions in urbanized aquatic ecosystems. We measured CO2 partial pressure (pCO2) and fluxes in nine severely polluted urban rivers with varying degrees of ecological restoration, and assessed the relationships with water physicochemical parameters, pollution levels and basin environmental investment. Our results indicate that urban rivers with high pollution loadings were indeed hotspots of CO2 evasion. However, fully restored rivers had generally lower pCO2 and CO2 emissions than partially restored rivers and were observably lower than unrestored rivers, suggesting that watershed eco‐restoration could effectively reduce CO2 evasion. In particular, environmental investment per unit basin area had a significant negative correlation with CO2 evasion and could explain 51%–85% and 51% of total variability in pCO2 and CO2 fluxes among nine urban rivers respectively, emphasizing the potential benefits of carbon emission regulation resulting from positive environmental management. Nutrient removal and sewage interception during watershed eco‐restoration were key processes reducing pCO2 and CO2 fluxes in polluted urban rivers. pH alteration kept close correlations with pCO2 and acted as a sensitive regulator of CO2 evasion in the nine rivers. We highlight the importance of considering the coupling effects of pollution and restoration on the spatiotemporal variability of CO2 evasion and the uncertainty of related monitoring methods in urban watersheds.

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“…Improved bioremediation results can be achieved by a number of different methods, the choice of which is based on the level of pollution present in the immediate area. Bioremediation can be applied in-situ or ex-situ , whereas the in-situ bioremediation methods are more cost-effective and cause less pollution to be released into the environment ( Rafeeq et al, 2023 ). Bioremediation using bacteria, fungi, yeasts, and algae is being studied.…”

Section: Recent Strategies For Pollutants Remediationmentioning

confidence: 99%

“…Genetically modified microorganisms will have altered cells with efficient adsorption capacity and specificity for target metals ( Wu et al, 2021 ; Rafeeq et al, 2023 ). The use of microbial fuel cells (MFC) and biofilm-based treatment can also be applied.…”

Section: Introductionmentioning

confidence: 99%

Microbial biosorbent for remediation of dyes and heavy metals pollution: A green strategy for sustainable environment

Tripathi

Singh

et al. 2023

Front. Microbiol.

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Toxic wastes like heavy metals and dyes are released into the environment as a direct result of industrialization and technological progress. The biosorption of contaminants utilizes a variety of biomaterials. Biosorbents can adsorb toxic pollutants on their surface through various mechanisms like complexation, precipitation, etc. The quantity of sorption sites that are accessible on the surface of the biosorbent affects its effectiveness. Biosorption’s low cost, high efficiency, lack of nutrient requirements, and ability to regenerate the biosorbent are its main advantages over other treatment methods. Optimization of environmental conditions like temperature, pH, nutrient availability, and other factors is a prerequisite to achieving optimal biosorbent performance. Recent strategies include nanomaterials, genetic engineering, and biofilm-based remediation for various types of pollutants. The removal of hazardous dyes and heavy metals from wastewater using biosorbents is a strategy that is both efficient and sustainable. This review provides a perspective on the existing literature and brings it up-to-date by including the latest research and findings in the field.

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Genetically engineered microorganisms for environmental remediation

Cited by 67 publications

References 142 publications

Metagenome Assembled Genomes (MAG) Facilitate a Better Understanding of Microbially-mediated Heavy Metal Resistance in Soils from a Former Nuclear Materials Production Facility

Metagenome Assembled Genomes (MAG) Facilitate a Better Understanding of Microbially-mediated Heavy Metal Resistance in Soils from a Former Nuclear Materials Production Facility

Ecological Restoration Effectively Mitigated pCO₂ and CO₂ Evasions From Severely Polluted Urban Rivers

Microbial biosorbent for remediation of dyes and heavy metals pollution: A green strategy for sustainable environment

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Genetically engineered microorganisms for environmental remediation

Cited by 67 publications

References 142 publications

Metagenome Assembled Genomes (MAG) Facilitate a Better Understanding of Microbially-mediated Heavy Metal Resistance in Soils from a Former Nuclear Materials Production Facility

Metagenome Assembled Genomes (MAG) Facilitate a Better Understanding of Microbially-mediated Heavy Metal Resistance in Soils from a Former Nuclear Materials Production Facility

Ecological Restoration Effectively Mitigated pCO2 and CO2 Evasions From Severely Polluted Urban Rivers

Microbial biosorbent for remediation of dyes and heavy metals pollution: A green strategy for sustainable environment

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Ecological Restoration Effectively Mitigated pCO₂ and CO₂ Evasions From Severely Polluted Urban Rivers