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Journal articles on the topic 'Metabolism; Bioremediation'

Author: Grafiati
Published: 4 June 2021
Last updated: 15 February 2022

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1

Mao, Xin Yu, Xiao Hou Shao, Jiang Qiang Mao, Chao Yin, Long Wang, Hao Bo Sun, Zhong Lin Tang, and Ting Ting Chang. "Environment Research with Progress of Bioremediations for Aquaculture Effluent." Advanced Materials Research 977 (June 2014): 264–69. http://dx.doi.org/10.4028/www.scientific.net/amr.977.264.

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Aquatic environment influences the quantity and quality of aquatic livings directly. In China, aquatic environment has been contaminated seriously as the rapid development of aquaculture industry. Bioremediation, mainly including efficient microbial agent method, immobilized microbe method, aquatic plant method, aquatic animal method and constructed wetlands method, can absorb and assimilate the organic and inorganic pollutants even toxic heavy metals in effluent, degrade them to innocuous substances through metabolism of microorganisms, aquatic plants or aquatic animals. Researches and demonstration showed that bioremediation could effectively decrease NH+4-N, NO−X-N, COD, SS generated by excess bait, fish manure, biological excrements and sediments, increase aquatic transparency, DO and stable pH value in aquaculture water. In future, theoretical researches should be enhanced on improvements of individual as well as integrated bioremediations which will contribute to sustainable development of aquaculture.
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2

Lu, Jie, and Meng Hong Li. "Removal of Chloroform in Groundwater by Bioremediation." Advanced Materials Research 113-116 (June 2010): 142–45. http://dx.doi.org/10.4028/www.scientific.net/amr.113-116.142.

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Anaerobic sludge were cultured and acclimated by adding different co-metabolism substrates under six operating conditions, using chloroform as model contaminant in an anaerobic environment. The microorganisms obtained with chloroform biodegradability were concentrated and cultured before adding into the simulated decontaminating apparatus. The results showed that the chloroform could be degraded by the microorganisms under the anaerobic condition, and the addition of co-metabolism substrates could improve the biodegradation efficiency. Moreover, the biodegradation efficiency varied with different co-metabolism matrix. The removal efficiency of pollutants could reach 75% using the microorganisms acclimated with glucose and methanol as co-metabolism substrates.
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3

Ostrem Loss, Erin M., and Jae-Hyuk Yu. "Bioremediation and microbial metabolism of benzo(a)pyrene." Molecular Microbiology 109, no. 4 (August 2018): 433–44. http://dx.doi.org/10.1111/mmi.14062.

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4

Yamamura, Shigeki, and Seigo Amachi. "Microbiology of inorganic arsenic: From metabolism to bioremediation." Journal of Bioscience and Bioengineering 118, no. 1 (July 2014): 1–9. http://dx.doi.org/10.1016/j.jbiosc.2013.12.011.

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5

Chen, Jun Jie, Xu Hui Gao, Long Fei Yan, and De Guang Xu. "Recent Progress in Monoaromatic Pollutants Removal from Groundwater through Bioremediation." International Letters of Natural Sciences 34 (February 2015): 62–69. http://dx.doi.org/10.18052/www.scipress.com/ilns.34.62.

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Monoaromatic pollutants such as benzene, toluene, ethylbenzene and mixture of xylenes are now considered as widespread contaminants of groundwater. In situ bioremediation under natural attenuation or enhanced remediation has been successfully used for removal of organic pollutants, including monoaromatic compounds, from groundwater. Results published indicate that in some sites, intrinsic bioremediation can reduce the monoaromatic compounds content of contaminated water to reach standard levels of potable water. However, engineering bioremediation is faster and more efficient. Also, studies have shown that enhanced anaerobic bioremediation can be applied for many BTEX contaminated groundwaters, as it is simple, applicable and economical. This paper reviews microbiology and metabolism of monoaromatic biodegradation and in situ bioremediation for BTEX removal from groundwater under aerobic and anaerobic conditions. It also discusses the factors affecting and limiting bioremediation processes and interactions between monoaromatic pollutants and other compounds during the remediation processes.
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6

Miazek, Krystian, and Beata Brozek-Pluska. "Effect of PHRs and PCPs on Microalgal Growth, Metabolism and Microalgae-Based Bioremediation Processes: A Review." International Journal of Molecular Sciences 20, no. 10 (May 20, 2019): 2492. http://dx.doi.org/10.3390/ijms20102492.

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In this review, the effect of pharmaceuticals (PHRs) and personal care products (PCPs) on microalgal growth and metabolism is reported. Concentrations of various PHRs and PCPs that cause inhibition and toxicity to growths of different microalgal strains are summarized and compared. The effect of PHRs and PCPs on microalgal metabolism (oxidative stress, enzyme activity, pigments, proteins, lipids, carbohydrates, toxins), as well as on the cellular morphology, is discussed. Literature data concerning the removal of PHRs and PCPs from wastewaters by living microalgal cultures, with the emphasis on microalgal growth, are gathered and discussed. The potential of simultaneously bioremediating PHRs/PCPs-containing wastewaters and cultivating microalgae for biomass production in a single process is considered. In the light of reviewed data, the feasibility of post-bioremediation microalgal biomass is discussed in terms of its contamination, biosafety and further usage for production of value-added biomolecules (pigments, lipids, proteins) and biomass as a whole.
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7

BOUWER, E. "Bioremediation of organic compounds ? putting microbial metabolism to work." Trends in Biotechnology 11, no. 8 (August 1993): 360–67. http://dx.doi.org/10.1016/0167-7799(93)90159-7.

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8

Chauhan, Archana, Fazlurrahman, John G. Oakeshott, and Rakesh K. Jain. "Bacterial metabolism of polycyclic aromatic hydrocarbons: strategies for bioremediation." Indian Journal of Microbiology 48, no. 1 (March 2008): 95–113. http://dx.doi.org/10.1007/s12088-008-0010-9.

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9

Verma, Shikha, Pankaj Kumar Verma, Alok Kumar Meher, Sanjay Dwivedi, Amit Kumar Bansiwal, Veena Pande, Pankaj Kumar Srivastava, Praveen Chandra Verma, Rudra Deo Tripathi, and Debasis Chakrabarty. "A novel arsenic methyltransferase gene of Westerdykella aurantiaca isolated from arsenic contaminated soil: phylogenetic, physiological, and biochemical studies and its role in arsenic bioremediation." Metallomics 8, no. 3 (2016): 344–53. http://dx.doi.org/10.1039/c5mt00277j.

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10

Yun, Jiae, Toshiyuki Ueki, Marzia Miletto, and Derek R. Lovley. "Monitoring the Metabolic Status of Geobacter Species in Contaminated Groundwater by Quantifying Key Metabolic Proteins with Geobacter-Specific Antibodies." Applied and Environmental Microbiology 77, no. 13 (May 6, 2011): 4597–602. http://dx.doi.org/10.1128/aem.00114-11.

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ABSTRACTSimple and inexpensive methods for assessing the metabolic status and bioremediation activities of subsurface microorganisms are required before bioremediation practitioners will adopt molecular diagnosis of the bioremediation community as a routine practice for guiding the development of bioremediation strategies. Quantifying gene transcripts can diagnose important aspects of microbial physiology during bioremediation but is technically challenging and does not account for the impact of translational modifications on protein abundance. An alternative strategy is to directly quantify the abundance of key proteins that might be diagnostic of physiological state. To evaluate this strategy, an antibody-based quantification approach was developed to investigate subsurfaceGeobactercommunities. The abundance of citrate synthase corresponded with rates of metabolism ofGeobacter bemidjiensisin chemostat cultures. Duringin situbioremediation of uranium-contaminated groundwater the quantity ofGeobactercitrate synthase increased with the addition of acetate to the groundwater and decreased when acetate amendments stopped. The abundance of the nitrogen-fixation protein, NifD, increased as ammonium became less available in the groundwater and then declined when ammonium concentrations increased. In a petroleum-contaminated aquifer, the abundance of BamB, an enzyme subunit involved in the anaerobic degradation of mono-aromatic compounds byGeobacterspecies, increased in zones in whichGeobacterwere expected to play an important role in aromatic hydrocarbon degradation. These results suggest that antibody-based detection of key metabolic proteins, which should be readily adaptable to standardized kits, may be a feasible method for diagnosing the metabolic state of microbial communities responsible for bioremediation, aiding in the rational design of bioremediation strategies.
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11

Dundek, Peter, Ladislav Holík, Ladislav Hromádko, Tomáš Rohlík, Valerie Vranová, Klement Rejšek, and Pavel Formánek. "Action of plant root exudates in bioremediations: a review." Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis 59, no. 1 (2011): 303–8. http://dx.doi.org/10.11118/actaun201159010303.

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This work presents a summary of literature dealing with the use of plant root exudates in bioremediations. Bioremediation using plants (phytoremediation or rhizoremediation) and associate rhizosphere to decontaminate polluted soil is a method based on the catabolic potential of root-associated microorganisms, which are supported by the organic substrates released from roots. These substrates are called “root exudates”. Root exudates support metabolism of pollutants-decomposing microorganisms in the rhizosphere, and affect sorption / desorption of pollutants. Awareness of exudation rates is necessary for testing soil decontamination. Commonly, water-soluble root exudates of different plants are studied for their qualitative composition which should be related to total carbon of exuded water-soluble compounds. This paper presents the determined rate of plant root exudation and the amount of root exudates carbon used to form artificial rhizosphere.
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12

Wang, Bin, Dan Zhang, Shaohua Chu, Yuee Zhi, Xiaorui Liu, and Pei Zhou. "Genomic Analysis of Bacillus megaterium NCT-2 Reveals Its Genetic Basis for the Bioremediation of Secondary Salinization Soil." International Journal of Genomics 2020 (February 29, 2020): 1–11. http://dx.doi.org/10.1155/2020/4109186.

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Bacillus megaterium NCT-2 is a nitrate-uptake bacterial, which shows high bioremediation capacity in secondary salinization soil, including nitrate-reducing capacity, phosphate solubilization, and salinity adaptation. To gain insights into the bioremediation capacity at the genetic level, the complete genome sequence was obtained by using a multiplatform strategy involving HiSeq and PacBio sequencing. The NCT-2 genome consists of a circular chromosome of 5.19 Mbp and ten indigenous plasmids, totaling 5.88 Mbp with an average GC content of 37.87%. The chromosome encodes 5,606 genes, 142 tRNAs, and 53 rRNAs. Genes involved in the features of the bioremediation in secondary salinization soil and plant growth promotion were identified in the genome, such as nitrogen metabolism, phosphate uptake, the synthesis of organic acids and phosphatase for phosphate-solubilizing ability, and Trp-dependent IAA synthetic system. Furthermore, strain NCT-2 has great ability of adaption to environments due to the genes involved in cation transporters, osmotic stress, and oxidative stress. This study sheds light on understanding the molecular basis of using B. megaterium NCT-2 in bioremediation of the secondary salinization soils.
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13

Keasling, J. D., Stephen J. Van Dien, and Jaya Pramanik. "Engineering polyphosphate metabolism inEscherichia coli: Implications for bioremediation of inorganic contaminants." Biotechnology and Bioengineering 58, no. 2-3 (April 20, 1998): 231–39. http://dx.doi.org/10.1002/(sici)1097-0290(19980420)58:2/3<231::aid-bit16>3.0.co;2-f.

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14

Mathew, Riya Ann, and Marykutty Abraham. "Bioremediation of diesel oil in marine environment." Oil & Gas Science and Technology – Revue d’IFP Energies nouvelles 75 (2020): 60. http://dx.doi.org/10.2516/ogst/2020053.

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Natural gas emissions from oil spill ensue changes to microbial consortia in oceans which might cause ecotoxicological impacts on marine life. Gas flaring, a technique in the clean-up of oil spill, is a major source of greenhouse gas emission and possess high risk of fire hazard. It is of utmost importance to avoid flaring and resort to cleaner techniques such as bioremediation. The study focuses on bioremediation of marine oil spill by indigenous bacterial consortia using beeswax as a biostimulant which supplements the limiting nutrients such as nitrate and phosphate. The experimental study was conducted by adding diesel oil in marine water with beeswax for bioremediation. The vital parameters such as dissolved oxygen, pH, diesel range organics, total microbial count, nitrate and phosphate contents were measured at intervals of 5 days. The indigenous bacteria utilized oil as carbon source and beeswax as nutrient source for growth and metabolism. The results showed 87% removal of oil content in treatment sample while only 59% reduction was achieved in the corresponding control sample. Evaporation of oil results in formation of aerosols and black carbon which can lead to climate change. The study proves that bioremediation of marine oil spill is an environmentally benign clean-up technique for oil spill which can reduce carbon emission.
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15

Li, Qianwei, Jicheng Liu, and Geoffrey Michael Gadd. "Fungal bioremediation of soil co-contaminated with petroleum hydrocarbons and toxic metals." Applied Microbiology and Biotechnology 104, no. 21 (September 17, 2020): 8999–9008. http://dx.doi.org/10.1007/s00253-020-10854-y.

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Abstract Much research has been carried out on the bacterial bioremediation of soil contaminated with petroleum hydrocarbons and toxic metals but much less is known about the potential of fungi in sites that are co-contaminated with both classes of pollutants. This article documents the roles of fungi in soil polluted with both petroleum hydrocarbons and toxic metals as well as the mechanisms involved in the biotransformation of such substances. Soil characteristics (e.g., structural components, pH, and temperature) and intracellular or excreted extracellular enzymes and metabolites are crucial factors which affect the efficiency of combined pollutant transformations. At present, bioremediation of soil co-contaminated with petroleum hydrocarbons and toxic metals is mostly focused on the removal, detoxification, or degradation efficiency of single or composite pollutants of each type. Little research has been carried out on the metabolism of fungi in response to complex pollutant stress. To overcome current bottlenecks in understanding fungal bioremediation, the potential of new approaches, e.g., gradient diffusion film technology (DGT) and metabolomics, is also discussed. Key points • Fungi play important roles in soil co-contaminated with TPH and toxic metals. • Soil characteristics, enzymes, and metabolites are major factors in bioremediation. • DGT and metabolomics can be applied to overcome current bottlenecks.
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16

Beller, Harry R., Wang-Hsien Ding, and Martin Reinhard. "Byproducts of Anaerobic Alkylbenzene Metabolism Useful as Indicators of in Situ Bioremediation." Environmental Science & Technology 29, no. 11 (November 1995): 2864–70. http://dx.doi.org/10.1021/es00011a024.

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17

Kirillova, Anna V., Anna A. Danilushkina, Denis S. Irisov, Nataliya L. Bruslik, Rawil F. Fakhrullin, Yuri A. Zakharov, Vladimir S. Bukhmin, and Dina R. Yarullina. "Assessment of Resistance and Bioremediation Ability ofLactobacillusStrains to Lead and Cadmium." International Journal of Microbiology 2017 (2017): 1–7. http://dx.doi.org/10.1155/2017/9869145.

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Cadmium (Cd) and lead (Pb) are heavy metals, important environmental pollutants, and potent toxicants to organism. Lactic acid bacteria (LAB) have been reported to remove Cd and Pb from solutions and therefore represent a useful tool for decontamination of food and beverages from heavy metals. Heavy metal ion binding by LAB was reported as metabolism-independent surface process. In this work tenLactobacillusstrains were investigated with respect to hydrophobicity, Lewis acid-base, and electrostatic properties of their outer cell surface in order to characterize their Cd and Pb removal capacity. SevenL. plantarumandL. fermentumstrains were shown to remove Cd from culture medium. The metabolism-dependent accumulation mechanism of Cd removal was proposed based on extended character of Cd binding and lack of correlation between any of the surface characteristics and Cd removal. The results of this study should be considered when selecting probiotic strains for people at risk of Cd exposure.
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18

Kuyukina, Maria, Anastasiya Krivoruchko, and Irina Ivshina. "Hydrocarbon- and metal-polluted soil bioremediation: progress and challenges." Microbiology Australia 39, no. 3 (2018): 133. http://dx.doi.org/10.1071/ma18041.

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The problem of soil contamination with petroleum hydrocarbons and heavy metals is becoming particularly acute for large oil-producing countries, like the Russian Federation. Both hydrocarbon and metal contaminants impact negatively the soil biota and human health, thus requiring efficient methods for their detoxification and elimination. Bioremediation of soil co-contaminated with hydrocarbon and metal pollutants is complicated by the fact that, although the two components must be treated differently, they mutually affect the overall removal efficiency. Heavy metals are reported to inhibit biodegradation of hydrocarbons by interfering with microbial enzymes directly involved in biodegradation or through the interaction with enzymes involved in general metabolism. Here we discuss recent progress and challenges in bioremediation of soils co-contaminated with hydrocarbons and heavy metals, focusing on selecting metal-resistant biodegrading strains and biosurfactant amendments.
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19

Cerniglia, C. E. "Fungal metabolism of polycyclic aromatic hydrocarbons: past, present and future applications in bioremediation." Journal of Industrial Microbiology and Biotechnology 19, no. 5-6 (November 1, 1997): 324–33. http://dx.doi.org/10.1038/sj.jim.2900459.

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20

Abd-Allah, E. F., and S. M. Ezzat. "Role of lipid metabolism through bioremediation of fusaric acid in germinating peanut seedlings." Phytoparasitica 32, no. 1 (February 2004): 38–42. http://dx.doi.org/10.1007/bf02980857.

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21

Celiešiūtė, Raimonda, Saulius Grigiškis, and Vilma Čipinytė. "BIOLOGICAL SURFACE ACTIVE COMPOUNDS APPLICATION POSSIBILITIES AND SELECTION OF STRAIN WITH EMULSIFYING ACTIVITY." Environment. Technology. Resources. Proceedings of the International Scientific and Practical Conference 1 (August 3, 2015): 267. http://dx.doi.org/10.17770/etr2009vol1.1091.

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The biological oil- polluted soil treatment method is used widely; however it is not effective enough because the microorganism‟s metabolism is affected by seasonal temperature fluctuation. Besides, soil remediation processes are very slow because of low solubility of oil and oil products in water. Biological surface active compounds show promising results in oil-polluted soil bioremediation. Three hydrocarbons degrading microorganisms strains, showing high emulsification activity were selected.
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22

Vera-Bernal, Mónica, and Rosa María Martínez-Espinosa. "Insights on Cadmium Removal by Bioremediation: The Case of Haloarchaea." Microbiology Research 12, no. 2 (April 11, 2021): 354–75. http://dx.doi.org/10.3390/microbiolres12020024.

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Although heavy metals are naturally found in the environment as components of the earth’s crust, environmental pollution by these toxic elements has increased since the industrial revolution. Some of them can be considered essential, since they play regulatory roles in different biological processes; but the role of other heavy metals in living tissues is not clear, and once ingested they can accumulate in the organism for long periods of time causing adverse health effects. To mitigate this problem, different methods have been used to remove heavy metals from water and soil, such as chelation-based processes. However, techniques like bioremediation are leaving these conventional methodologies in the background for being more effective and eco-friendlier. Recently, different research lines have been promoted, in which several organisms have been used for bioremediation approaches. Within this context, the extremophilic microorganisms represent one of the best tools for the treatment of contaminated sites due to the biochemical and molecular properties they show. Furthermore, since it is estimated that 5% of industrial effluents are saline and hypersaline, halophilic microorganisms have been suggested as good candidates for bioremediation and treatment of this kind of samples. These microorganisms, and specifically the haloarchaea group, are of interest to design strategies aiming the removal of polluting compounds due to the efficiency of their metabolism under extreme conditions and their significant tolerance to highly toxic compounds such as heavy metals, bromate, nitrite, chlorate, or perchlorate ions. However, there are still few trials that have proven the bioremediation of environments contaminated with heavy metals using these microorganisms. This review analyses scientific literature focused on metabolic capabilities of haloarchaea that may allow these microbes to tolerate and eliminate heavy metals from the media, paying special attention to cadmium. Thus, this work will shed light on potential uses of haloarchaea in bioremediation of soils and waters negatively affected by heavy metals, and more specifically by cadmium.
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23

Wilkins, Michael J., Nathan C. VerBerkmoes, Kenneth H. Williams, Stephen J. Callister, Paula J. Mouser, Hila Elifantz, A. Lucie N′Guessan, et al. "Proteogenomic Monitoring of Geobacter Physiology during Stimulated Uranium Bioremediation." Applied and Environmental Microbiology 75, no. 20 (August 28, 2009): 6591–99. http://dx.doi.org/10.1128/aem.01064-09.

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ABSTRACT Implementation of uranium bioremediation requires methods for monitoring the membership and activities of the subsurface microbial communities that are responsible for reduction of soluble U(VI) to insoluble U(IV). Here, we report a proteomics-based approach for simultaneously documenting the strain membership and microbial physiology of the dominant Geobacter community members during in situ acetate amendment of the U-contaminated Rifle, CO, aquifer. Three planktonic Geobacter-dominated samples were obtained from two wells down-gradient of acetate addition. Over 2,500 proteins from each of these samples were identified by matching liquid chromatography-tandem mass spectrometry spectra to peptides predicted from seven isolate Geobacter genomes. Genome-specific peptides indicate early proliferation of multiple M21 and Geobacter bemidjiensis-like strains and later possible emergence of M21 and G. bemidjiensis-like strains more closely related to Geobacter lovleyi. Throughout biostimulation, the proteome is dominated by enzymes that convert acetate to acetyl-coenzyme A and pyruvate for central metabolism, while abundant peptides matching tricarboxylic acid cycle proteins and ATP synthase subunits were also detected, indicating the importance of energy generation during the period of rapid growth following the start of biostimulation. Evolving Geobacter strain composition may be linked to changes in protein abundance over the course of biostimulation and may reflect changes in metabolic functioning. Thus, metagenomics-independent community proteogenomics can be used to diagnose the status of the subsurface consortia upon which remediation biotechnology relies.
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Samin, Ghufrana, Martina Pavlova, M. Irfan Arif, Christiaan P. Postema, Jiri Damborsky, and Dick B. Janssen. "A Pseudomonas putida Strain Genetically Engineered for 1,2,3-Trichloropropane Bioremediation." Applied and Environmental Microbiology 80, no. 17 (June 27, 2014): 5467–76. http://dx.doi.org/10.1128/aem.01620-14.

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ABSTRACT1,2,3-Trichloropropane (TCP) is a toxic compound that is recalcitrant to biodegradation in the environment. Attempts to isolate TCP-degrading organisms using enrichment cultivation have failed. A potential biodegradation pathway starts with hydrolytic dehalogenation to 2,3-dichloro-1-propanol (DCP), followed by oxidative metabolism. To obtain a practically applicable TCP-degrading organism, we introduced an engineered haloalkane dehalogenase with improved TCP degradation activity into the DCP-degrading bacteriumPseudomonas putidaMC4. For this purpose, the dehalogenase gene (dhaA31) was cloned behind the constitutivedhlApromoter and was introduced into the genome of strain MC4 using a transposon delivery system. The transposon-located antibiotic resistance marker was subsequently removed using a resolvase step. Growth of the resulting engineered bacterium,P. putidaMC4-5222, on TCP was indeed observed, and all organic chlorine was released as chloride. A packed-bed reactor with immobilized cells of strain MC4-5222 degraded >95% of influent TCP (0.33 mM) under continuous-flow conditions, with stoichiometric release of inorganic chloride. The results demonstrate the successful use of a laboratory-evolved dehalogenase and genetic engineering to produce an effective, plasmid-free, and stable whole-cell biocatalyst for the aerobic bioremediation of a recalcitrant chlorinated hydrocarbon.
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Dong, Die, Haoyu Sun, Zhengliang Qi, and Xinli Liu. "Improving microbial bioremediation efficiency of intensive aquacultural wastewater based on bacterial pollutant metabolism kinetics analysis." Chemosphere 265 (February 2021): 129151. http://dx.doi.org/10.1016/j.chemosphere.2020.129151.

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Miyashita, Shin-ichi, Chisato Murota, Keisuke Kondo, Shoko Fujiwara, and Mikio Tsuzuki. "Arsenic metabolism in cyanobacteria." Environmental Chemistry 13, no. 4 (2016): 577. http://dx.doi.org/10.1071/en15071.

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Environmental context Cyanobacteria are ecologically important, photosynthetic organisms that are widely distributed throughout the environment. They play a central role in arsenic transformations in terms of both mineralisation and formation of organoarsenic species as the primary producers in aquatic ecosystems. In this review, arsenic resistance, transport and biotransformation in cyanobacteria are reviewed and compared with those in other organisms. Abstract Arsenic is a toxic element that is widely distributed in the lithosphere, hydrosphere and biosphere. Some species of cyanobacteria can grow in high concentrations of arsenate (pentavalent inorganic arsenic compound) (100mM) and in low-millimolar concentrations of arsenite (trivalent inorganic arsenic compound). Arsenate, which is a molecular analogue of phosphate, is taken up by cells through phosphate transporters, and inhibits oxidative phosphorylation and photophosphorylation. Arsenite, which enters the cell through a concentration gradient, shows higher toxicity than arsenate by binding to sulfhydryl groups and impairing the functions of many proteins. Detoxification mechanisms for arsenic in cyanobacterial cells include efflux of intracellular inorganic arsenic compounds, and biosynthesis of methylarsonic acid and dimethylarsinic acid through methylation of intracellular inorganic arsenic compounds. In some cyanobacteria, ars genes coding for an arsenate reductase (arsC), a membrane-bound protein involved in arsenic efflux (arsB) and an arsenite S-adenosylmethionine methyltransferase (arsM) have been found. Furthermore, cyanobacteria can produce more complex arsenic species such as arsenosugars. In this review, arsenic metabolism in cyanobacteria is reviewed, compared with that in other organisms. Knowledge gaps remain regarding both arsenic transport (e.g. uptake of methylated arsenicals and excretion of arsenate) and biotransformation (especially production of lipid-soluble arsenicals). Further studies in these areas are required, not only for a better understanding of the role of cyanobacteria in the circulation of arsenic in aquatic environments, but also for their application to arsenic bioremediation.
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Antonioli, Paolo, Silvia Lampis, Irene Chesini, Giovanni Vallini, Sara Rinalducci, Lello Zolla, and Pier Giorgio Righetti. "Stenotrophomonas maltophilia SeITE02, a New Bacterial Strain Suitable for Bioremediation of Selenite-Contaminated Environmental Matrices." Applied and Environmental Microbiology 73, no. 21 (September 7, 2007): 6854–63. http://dx.doi.org/10.1128/aem.00957-07.

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ABSTRACT Biochemical and proteomic tools have been utilized for investigating the mechanism of action of a new Stenotrophomonas maltophilia strain (SeITE02), a gammaproteobacterium capable of resistance to high concentrations of selenite [SeO3 2−, Se(IV)], reducing it to nontoxic elemental selenium under aerobic conditions; this strain was previously isolated from a selenite-contaminated mining soil. Biochemical analysis demonstrated that (i) nitrite reductase does not seem to take part in the process of selenite reduction by the bacterial strain SeITE02, although its involvement in this process had been hypothesized in other cases; (ii) nitrite strongly interferes with selenite removal when the two oxyanions (NO2 − and SeO3 2−) are simultaneously present, suggesting that the two reduction/detoxification pathways share a common enzymatic step, probably at the level of cellular transport; (iii) in vitro, selenite reduction does not take place in the membrane or periplasmic fractions but only in the cytoplasm, where maximum activity is exhibited at pH 6.0 in the presence of NADPH; and (iv) glutathione is involved in the selenite reduction mechanism, since inhibition of its synthesis leads to a considerable delay in the onset of reduction. As far as the proteomic findings are concerned, the evidence was reached that 0.2 mM selenite and 16 mM nitrite, when added to the culture medium, caused a significant modulation (ca. 10%, i.e., 96 and 85 protein zones, respectively) of the total proteins visualized in the respective two-dimensional maps. These spots were identified by mass spectrometry analysis and were found to belong to the following functional classes: nucleotide synthesis and metabolism, damaged-protein catabolism, protein and amino acid metabolism, and carbohydrate metabolism along with DNA-related proteins and proteins involved in cell division, oxidative stress, and cell wall synthesis.
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Raffa, Carla Maria, and Fulvia Chiampo. "Bioremediation of Agricultural Soils Polluted with Pesticides: A Review." Bioengineering 8, no. 7 (July 2, 2021): 92. http://dx.doi.org/10.3390/bioengineering8070092.

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Pesticides are chemical compounds used to eliminate pests; among them, herbicides are compounds particularly toxic to weeds, and this property is exploited to protect the crops from unwanted plants. Pesticides are used to protect and maximize the yield and quality of crops. The excessive use of these chemicals and their persistence in the environment have generated serious problems, namely pollution of soil, water, and, to a lower extent, air, causing harmful effects to the ecosystem and along the food chain. About soil pollution, the residual concentration of pesticides is often over the limits allowed by the regulations. Where this occurs, the challenge is to reduce the amount of these chemicals and obtain agricultural soils suitable for growing ecofriendly crops. The microbial metabolism of indigenous microorganisms can be exploited for degradation since bioremediation is an ecofriendly, cost-effective, rather efficient method compared to the physical and chemical ones. Several biodegradation techniques are available, based on bacterial, fungal, or enzymatic degradation. The removal efficiencies of these processes depend on the type of pollutant and the chemical and physical conditions of the soil. The regulation on the use of pesticides is strictly connected to their environmental impacts. Nowadays, every country can adopt regulations to restrict the consumption of pesticides, prohibit the most harmful ones, and define the admissible concentrations in the soil. However, this variability implies that each country has a different perception of the toxicology of these compounds, inducing different market values of the grown crops. This review aims to give a picture of the bioremediation of soils polluted with commercial pesticides, considering the features that characterize the main and most used ones, namely their classification and their toxicity, together with some elements of legislation into force around the world.
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Achibat, Hanane, Nohad A. AlOmari, Federica Messina, Luca Sancineto, Mostafa Khouili, and Claudio Santi. "Organoselenium Compounds as Phytochemicals from the Natural Kingdom." Natural Product Communications 10, no. 11 (November 2015): 1934578X1501001. http://dx.doi.org/10.1177/1934578x1501001119.

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Selenium is naturally present in soils but it is also produced by pollution from human activities into the environment. Its incorporation into plants affords organoselenium metabolites that, depending on the nature of the molecules and the plant species, can be incorporated into proteins, stored or eliminated by volatilization. The possibility to use the selenium metabolism of some plants as a method for bioremediation and, at the main time, as a source of selenated phytochemicals is here discussed taking into consideration the growing interest in organic selenium derivatives as new potential therapeutic agents.
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Wang, Xia, Lingui Xue, Sijing Chang, Xiaoyan He, Taotao Fan, Juanli Wu, Junbo Niu, and Brown Emaneghemi. "Bioremediation and metabolism of clothianidin by mixed bacterial consortia enriched from contaminated soils in Chinese greenhouse." Process Biochemistry 78 (March 2019): 114–22. http://dx.doi.org/10.1016/j.procbio.2018.12.031.

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31

Caldwell, Matthew E., Ralph S. Tanner, and Joseph M. Suflita. "Microbial Metabolism of Benzene and the Oxidation of Ferrous Iron under Anaerobic Conditions: Implications for Bioremediation." Anaerobe 5, no. 6 (December 1999): 595–603. http://dx.doi.org/10.1006/anae.1999.0193.

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32

Zablotowicz, R. M., K. T. Leung, T. Alber, M. B. Cassidy, J. T. Trevors, H. Lee, L. Veldhuis, and J. C. Hall. "Degradation of 2,4-dinitrophenol and selected nitroaromatic compounds bySphingomonassp. UG30." Canadian Journal of Microbiology 45, no. 10 (October 1, 1999): 840–48. http://dx.doi.org/10.1139/w99-083.

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Sphingomonas strain UG30 mineralizes both p-nitrophenol (PNP) and pentachlorophenol (PCP). Our current studies showed that UG30 oxidatively metabolized certain other p-substituted nitrophenols, i.e., p-nitrocatechol, 2,4-dinitrophenol (2,4-DNP), and 4,6-dinitrocresol with liberation of nitrite. 2,6-DNP, o- or m-nitrophenol, picric acid, or the herbicide dinoseb were not metabolized. Studies using14C-labelled 2,4-DNP indicated that in glucose-glutamate broth cultures of UG30, greater than 90% of 103 µM 2,4-DNP was transformed to other compounds, while 8-19% of the 2,4-DNP was mineralized within 5 days. A significant portion (20-50%) of the 2,4-DNP was metabolized to highly polar metabolite(s) with one major unidentified metabolite accumulating from 5 to 25% of the initial radioactivity. The amounts of 2,4-DNP mineralized and converted to polar metabolites was affected by glutamate concentration in the medium. Nitrophenolic compounds metabolized by UG30 were also suitable substrates for the UG30 PCP-4-monooxygenase (pcpB gene expressed in Escherichia coli) which is likely central to degradation of these compounds. The wide substrate range of UG30 could render this strain useful in bioremediation of some chemically contaminated soils.Key words: bioremediation, dinitrophenol, metabolism, nitroaromatic, pentachlorophenol, Sphingomonas.
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Gaonkar, Teja, Pramoda Kumar Nayak, Sandeep Garg, and Saroj Bhosle. "Siderophore-Producing Bacteria from a Sand Dune Ecosystem and the Effect of Sodium Benzoate on Siderophore Production by a Potential Isolate." Scientific World Journal 2012 (2012): 1–8. http://dx.doi.org/10.1100/2012/857249.

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Bioremediation in natural ecosystems is dependent upon the availability of micronutrients and cofactors, of which iron is one of the essential elements. Under aerobic and alkaline conditions, iron oxidizes to Fe+3creating iron deficiency. To acquire this essential growth-limiting nutrient, bacteria produce low-molecular-weight, high-affinity iron chelators termed siderophores. In this study, siderophore-producing bacteria from rhizosphere and nonrhizosphere areas of coastal sand dunes were isolated using a culture-dependent approach and were assigned to 8 different genera with the predominance ofBacillussp. Studies on the ability of these isolates to grow on sodium benzoate revealed that a pigmented bacterial culture TMR2.13 identified asPseudomonas aeruginosashowed growth on mineral salts medium (MSM) with 2% of sodium benzoate and produced a yellowish fluorescent siderophore identified as pyoverdine. This was inhibited above 54 μM of added iron in MSM with glucose without affecting growth, while, in presence of sodium benzoate, siderophore was produced even up to the presence of 108 μM of added iron. Increase in the requirement of iron for metabolism of aromatic compounds in ecosystems where the nutrient deficiencies occur naturally would be one of the regulating factors for the bioremediation process.
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Bernabeu, Eric, Jose María Miralles-Robledillo, Micaela Giani, Elena Valdés, Rosa María Martínez-Espinosa, and Carmen Pire. "In Silico Analysis of the Enzymes Involved in Haloarchaeal Denitrification." Biomolecules 11, no. 7 (July 16, 2021): 1043. http://dx.doi.org/10.3390/biom11071043.

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During the last century, anthropogenic activities such as fertilization have led to an increase in pollution in many ecosystems by nitrogen compounds. Consequently, researchers aim to reduce nitrogen pollutants following different strategies. Some haloarchaea, owing to their denitrifier metabolism, have been proposed as good model organisms for the removal of not only nitrate, nitrite, and ammonium, but also (per)chlorates and bromate in brines and saline wastewater. Bacterial denitrification has been extensively described at the physiological, biochemical, and genetic levels. However, their haloarchaea counterparts remain poorly described. In previous work the model structure of nitric oxide reductase was analysed. In this study, a bioinformatic analysis of the sequences and the structural models of the nitrate, nitrite and nitrous oxide reductases has been described for the first time in the haloarchaeon model Haloferax mediterranei. The main residues involved in the catalytic mechanism and in the coordination of the metal centres have been explored to shed light on their structural characterization and classification. These results set the basis for understanding the molecular mechanism for haloarchaeal denitrification, necessary for the use and optimization of these microorganisms in bioremediation of saline environments among other potential applications including bioremediation of industrial waters.
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Ramirez, Miguel, Jennifer Obrzydowski, Mary Ayers, Sonia Virparia, Meijing Wang, Kurtis Stefan, Richard Linchangco, and Domenic Castignetti. "Pyruvic Oxime Nitrification and Copper and Nickel Resistance by aCupriavidus pauculus, an Active Heterotrophic Nitrifier-Denitrifier." Scientific World Journal 2014 (2014): 1–11. http://dx.doi.org/10.1155/2014/901702.

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Heterotrophic nitrifiers synthesize nitrogenous gasses when nitrifying ammonium ion. ACupriavidus pauculus, previously thought anAlcaligenessp. and noted as an active heterotrophic nitrifier-denitrifier, was examined for its ability to produce nitrogen gas (N2) and nitrous oxide (N2O) while heterotrophically nitrifying the organic substrate pyruvic oxime [CH3–C(NOH)–COOH]. Neither N2nor N2O were produced. Nucleotide and phylogenetic analyses indicated that the organism is a member of a genus (Cupriavidus) known for its resistance to metals and its metabolism of xenobiotics. The microbe (aCupriavidus pauculusdesignated asC. pauculusstrain UM1) was examined for its ability to perform heterotrophic nitrification in the presence of Cu2+and Ni2+and to metabolize the xenobiotic phenol. The bacterium heterotrophically nitrified well when either 1 mM Cu2+or 0.5 mM Ni2+was present in either enriched or minimal medium. The organism also used phenol as a sole carbon source in either the presence or absence of 1 mM Cu2+or 0.5 mM Ni2+. The ability of this isolate to perform a number of different metabolisms, its noteworthy resistance to copper and nickel, and its potential use as a bioremediation agent are discussed.
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36

Baron, Noemi Carla, Fernando Carlos Pagnocca, Ayumi Aquino Otsuka, Francesc Xavier Prenafeta-Boldú, Vânia Aparecida Vicente, and Derlene Attili de Angelis. "Black Fungi and Hydrocarbons: An Environmental Survey for Alkylbenzene Assimilation." Microorganisms 9, no. 5 (May 7, 2021): 1008. http://dx.doi.org/10.3390/microorganisms9051008.

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Environmental pollution with alkylbenzene hydrocarbons such as toluene is a recurring phenomenon. Their toxicity and harmful effect on people and the environment drive the search for sustainable removal techniques such as bioremediation, which is based on the microbial metabolism of xenobiotic compounds. Melanized fungi present extremophilic characteristics, which allow their survival in inhospitable habitats such as those contaminated with hydrocarbons. Screening methodologies for testing the microbial assimilation of volatile organic compounds (VOC) are scarce despite their importance for the bioremediation of hydrocarbon associated areas. In this study, 200 strains of melanized fungi were isolated from four different hydrocarbon-related environments by using selective methods, and their biodiversity was assessed by molecular and ecological analyses. Seventeen genera and 27 species from three main orders, namely Chaetothyriales, Cladosporiales, and Pleosporales, were identified. The ecological analysis showed a particular species distribution according to their original substrate. The isolated strains were also screened for their toluene assimilation potential using a simple and inexpensive methodology based on miniaturized incubations under controlled atmospheres. The biomass produced by the 200 strains with toluene as the sole carbon source was compared against positive and negative controls, with glucose and with only mineral medium, respectively. Nineteen strains were selected as the most promising for further investigation on the biodegradation of alkylbenzenes.
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Mohanakrishna, Gunda, Riyadh I. Al-Raoush, and Ibrahim M. Abu-Reesh. "Induced bioelectrochemical metabolism for bioremediation of petroleum refinery wastewater: Optimization of applied potential and flow of wastewater." Bioresource Technology 260 (July 2018): 227–32. http://dx.doi.org/10.1016/j.biortech.2018.03.122.

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38

Zhang, Kai, Sa Wang, Penghong Guo, and Shuhai Guo. "Characteristics of organic carbon metabolism and bioremediation of petroleum-contaminated soil by a mesophilic aerobic biopile system." Chemosphere 264 (February 2021): 128521. http://dx.doi.org/10.1016/j.chemosphere.2020.128521.

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39

Tsezos, Marios. "Metal - Microbes Interactions: beyond Environmental Protection." Advanced Materials Research 71-73 (May 2009): 527–32. http://dx.doi.org/10.4028/www.scientific.net/amr.71-73.527.

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Bioremediation can be applied for the treatment of metal/metalloid and radionuclide bearing water streams in order to immobilize the targeted species. Interactions of microbial cells with soluble targeted species may occur during the microbial metabolism and result to the reduction of their mobility and toxicity. The most important metabolically mediated immobilization processes for metal/metalloid and radionuclide species are bioprecipitation and bioreduction. Bioprecipitation includes the transformation of soluble species to insoluble hydroxides, carbonates, phosphates and sulfides as a result of the microbial metabolism. In the case of biological reduction, the cells use the species as terminal electron acceptors in anoxic environments to produce energy and/or reduce the toxicity of the cells microenvironment. These processes can be the basis of technologies for the rehabilitation of contaminated sites both for surface and groundwater aquifers, soils and industrial water streams. Such technologies are recently developed and applied both in pilot and full scale, although the related mechanisms are complicated and not always fully understood.
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40

Drendel, Gene, Elizabeth R. Mathews, Lucie Semenec, and Ashley E. Franks. "Microbial Fuel Cells, Related Technologies, and Their Applications." Applied Sciences 8, no. 12 (November 25, 2018): 2384. http://dx.doi.org/10.3390/app8122384.

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Microbial fuel cells present an emerging technology for utilizing the metabolism of microbes to fuel processes including biofuel, energy production, and the bioremediation of environments. The application and design of microbial fuel cells are of interest to a range of disciplines including engineering, material sciences, and microbiology. In addition, these devices present numerous opportunities to improve sustainable practices in different settings, ranging from industrial to domestic. Current research is continuing to further our understanding of how the engineering, design, and microbial aspects of microbial fuel cell systems impact upon their function. As a result, researchers are continuing to expand the range of processes microbial fuel cells can be used for, as well as the efficiency of those applications.
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41

Holland, Sophie I., Richard J. Edwards, Haluk Ertan, Yie Kuan Wong, Tonia L. Russell, Nandan P. Deshpande, Michael J. Manefield, and Matthew Lee. "Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture." PeerJ 7 (October 2, 2019): e7775. http://dx.doi.org/10.7717/peerj.7775.

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Bacteria capable of dechlorinating the toxic environmental contaminant dichloromethane (DCM, CH2Cl2) are of great interest for potential bioremediation applications. A novel, strictly anaerobic, DCM-fermenting bacterium, “DCMF”, was enriched from organochlorine-contaminated groundwater near Botany Bay, Australia. The enrichment culture was maintained in minimal, mineral salt medium amended with dichloromethane as the sole energy source. PacBio whole genome SMRTTM sequencing of DCMF allowed de novo, gap-free assembly despite the presence of cohabiting organisms in the culture. Illumina sequencing reads were utilised to correct minor indels. The single, circularised 6.44 Mb chromosome was annotated with the IMG pipeline and contains 5,773 predicted protein-coding genes. Based on 16S rRNA gene and predicted proteome phylogeny, the organism appears to be a novel member of the Peptococcaceae family. The DCMF genome is large in comparison to known DCM-fermenting bacteria. It includes an abundance of methyltransferases, which may provide clues to the basis of its DCM metabolism, as well as potential to metabolise additional methylated substrates such as quaternary amines. Full annotation has been provided in a custom genome browser and search tool, in addition to multiple sequence alignments and phylogenetic trees for every predicted protein, http://www.slimsuite.unsw.edu.au/research/dcmf/.
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42

Bews, Emily, Leslie Booher, Torre Polizzi, Christopher Long, Ju-Hyoung Kim, and Matthew S. Edwards. "Effects of salinity and nutrients on metabolism and growth of Ulva lactuca: Implications for bioremediation of coastal watersheds." Marine Pollution Bulletin 166 (May 2021): 112199. http://dx.doi.org/10.1016/j.marpolbul.2021.112199.

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43

Gallo, Giovanni, Rosanna Puopolo, Miriam Carbonaro, Emanuela Maresca, and Gabriella Fiorentino. "Extremophiles, a Nifty Tool to Face Environmental Pollution: From Exploitation of Metabolism to Genome Engineering." International Journal of Environmental Research and Public Health 18, no. 10 (May 14, 2021): 5228. http://dx.doi.org/10.3390/ijerph18105228.

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Extremophiles are microorganisms that populate habitats considered inhospitable from an anthropocentric point of view and are able to tolerate harsh conditions such as high temperatures, extreme pHs, high concentrations of salts, toxic organic substances, and/or heavy metals. These microorganisms have been broadly studied in the last 30 years and represent precious sources of biomolecules and bioprocesses for many biotechnological applications; in this context, scientific efforts have been focused on the employment of extremophilic microbes and their metabolic pathways to develop biomonitoring and bioremediation strategies to face environmental pollution, as well as to improve biorefineries for the conversion of biomasses into various chemical compounds. This review gives an overview on the peculiar metabolic features of certain extremophilic microorganisms, with a main focus on thermophiles, which make them attractive for biotechnological applications in the field of environmental remediation; moreover, it sheds light on updated genetic systems (also those based on the CRISPR-Cas tool), which expand the potentialities of these microorganisms to be genetically manipulated for various biotechnological purposes.
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44

Lawton, L. A., A. Welgamage, P. M. Manage, and C. Edwards. "Novel bacterial strains for the removal of microcystins from drinking water." Water Science and Technology 63, no. 6 (March 1, 2011): 1137–42. http://dx.doi.org/10.2166/wst.2011.352.

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Microcystins (MC) and nodularin (NOD) are common contaminants of drinking water around the world and due to their significant health impact it is important to explore suitable approaches for their removal. Unfortunately, these toxins are not always removed by conventional water treatments. One of the most exciting areas that hold promise for a successful and cost effective solution is bioremediation of microcystins. Recent work resulted in successful isolation and characterisation of 10 novel bacterial strains (Rhodococcus sp., Arthrobacter spp. and Brevibacterium sp.) capable of metabolizing microcystin-LR (MC-LR) in a Biolog MT2 assay. The work presented here aims to further investigate and evaluate the metabolism and the degradation of multiple microcystins (MC-LR, MC-LF, MC-LY, MC-LW and MC-RR) and nodularin by the bacterial isolates. A total of five bacterial isolates representing the three genera were evaluated using Biolog MT2 assay with a range of MCs where they all demonstrated an overall metabolism on all MCs and NOD. Subsequently, the results were confirmed by observing the degradation of the range of toxins in a separate batch experiment.
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45

Bailey, V. L., and W. B. McGill. "Carbon transformations by indigenous microbes in four hydrocarbon-contaminated soils under static remediation conditions." Canadian Journal of Soil Science 81, no. 2 (May 1, 2001): 193–204. http://dx.doi.org/10.4141/s00-051.

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We sought to learn about the transformations of hydrocarbons and limitations to bioremediation in four hydrocarbon-contaminated soils. Two soils were contaminated with creosote and two with petroleum. We incubated them either with or without added N, P, K and S. We monitored CO2 evolution, and residual dichloromethane-extractable organic C (DEO-C) after 10 wk. Indigenous populations were active in all soils. A single-component first-order model fit the CO2 respiration rate data, yielding estimates of potentially mineralizable C (Co), and specific decay rate, k. The ratio C: DEO was lower in heavier textured and strongly aggregated soils compared with the more poorly aggregated sandy soils. Low respiration rates in the more clayey soils were related to low Co rather than to k for the available C. In the highly amended soils the loss of total C approximated the production of CO2-C while the loss of DEO-C was greater than the evolution of CO2-C. We conclude: 1) Under circumstances such as hydrocarbon contaminants with long exposure to the soil, static systems may be sufficient for metabolism of available contaminants by indigenous microorganisms. 2) Increases in clay content and stability of aggregates, together with biotreatment to remove hydrocarbons may reduce bioavailability of residual contamination. 3) In soils with high clay content, contaminant transformations or attenuation without production of CO2 may be substantial. Key words: Bioremediation, bioaugmentation, soil, hydrocarbons, contaminant, kinetic models, bioavailability, respiration
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46

Cardenas, Erick, Wei-Min Wu, Mary Beth Leigh, Jack Carley, Sue Carroll, Terry Gentry, Jian Luo, et al. "Microbial Communities in Contaminated Sediments, Associated with Bioremediation of Uranium to Submicromolar Levels." Applied and Environmental Microbiology 74, no. 12 (May 2, 2008): 3718–29. http://dx.doi.org/10.1128/aem.02308-07.

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ABSTRACT Microbial enumeration, 16S rRNA gene clone libraries, and chemical analysis were used to evaluate the in situ biological reduction and immobilization of uranium(VI) in a long-term experiment (more than 2 years) conducted at a highly uranium-contaminated site (up to 60 mg/liter and 800 mg/kg solids) of the U.S. Department of Energy in Oak Ridge, TN. Bioreduction was achieved by conditioning groundwater above ground and then stimulating growth of denitrifying, Fe(III)-reducing, and sulfate-reducing bacteria in situ through weekly injection of ethanol into the subsurface. After nearly 2 years of intermittent injection of ethanol, aqueous U levels fell below the U.S. Environmental Protection Agency maximum contaminant level for drinking water and groundwater (<30 μg/liter or 0.126 μM). Sediment microbial communities from the treatment zone were compared with those from a control well without biostimulation. Most-probable-number estimations indicated that microorganisms implicated in bioremediation accumulated in the sediments of the treatment zone but were either absent or in very low numbers in an untreated control area. Organisms belonging to genera known to include U(VI) reducers were detected, including Desulfovibrio, Geobacter, Anaeromyxobacter, Desulfosporosinus, and Acidovorax spp. The predominant sulfate-reducing bacterial species were Desulfovibrio spp., while the iron reducers were represented by Ferribacterium spp. and Geothrix spp. Diversity-based clustering revealed differences between treated and untreated zones and also within samples of the treated area. Spatial differences in community structure within the treatment zone were likely related to the hydraulic pathway and to electron donor metabolism during biostimulation.
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47

Boopathy, R., and J. F. Manning. "Characterization of partial anaerobic metabolic pathway for 2,4,6-trinitrotoluene degradation by a sulfate-reducing bacterial consortium." Canadian Journal of Microbiology 42, no. 12 (December 1, 1996): 1203–8. http://dx.doi.org/10.1139/m96-155.

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The anaerobic degradative pathway for metabolism of 2,4,6-trinitrotoluene (TNT) by a consortium of Desulfovibrio spp. isolated from a creek sediment was studied. This consortium has the metabolic capability to degrade TNT to fatty acids. The growth of the consortium and the metabolism of TNT were greatly enhanced in the presence of an additional carbon source like pyruvate. The optimal concentration of pyruvate for the maximum rate of TNT degradation was 15–20 mM. Various intermediates of TNT metabolism were identified. The first step in the pathway was reduction of TNT to 4-amino-2,6-dinitrotoluene and 2-amino-4,6-dinitrotoluene, which were further reduced to 2,4-diamino,6-nitrotoluene. The next intermediate to appear in the culture medium was nitrobenzoic acid, followed by cyclohexanone, 2-methyl pentanoic acid, butyric acid, and acetic acid. A study using radiolabeled TNT showed that no CO2was produced from TNT during metabolism. The mass balance of the radiolabeled study showed that 49.6% of the TNT was converted to acetic acid, 28% was assimilated into biomass as trichloroacetic acid precipitable materials, and the rest was distributed as various TNT intermediates. Most Desulfovibrio spp. are incomplete oxidizers that are unable to carry out the terminal oxidation of organic substrates. The major end product of TNT metabolism was acetic acid. The bacteria grew on all the TNT intermediates tested as sole source of carbon, except on acetic acid, confirming that the Desulfovibrio spp. have the enzymes necessary for complete degradation of TNT to acetate.Key words: TNT, bioremediation, sulfate reducers, anaerobic process, butyric acid, Desulfovibrio, spp.
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48

Popesku, Jason T., Ajay Singh, Jian-Shen Zhao, Jalal Hawari, and Owen P. Ward. "High TNT-transforming activity by a mixed culture acclimated and maintained on crude-oil-containing media." Canadian Journal of Microbiology 49, no. 5 (May 1, 2003): 362–66. http://dx.doi.org/10.1139/w03-049.

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A mixed microbial culture originating from a petroleum-contaminated site and maintained on crude oil exhibited high 2,4,6-trinitrotoluene (TNT) transformation activity. Cultivation of the mixed culture in glucose-containing medium for 29 h resulted in almost complete transformation of 100 ppm TNT. TNT transformation was observed with both growing and resting cells. With subculturing, it was found that TNT could support growth of the mixed culture when supplied as sole carbon source, sole nitrogen source, or sole carbon and nitrogen source. The finding that a mixed microbial culture maintained on crude oil exhibited high TNT transformation activity without prior subculture on TNT-containing media is novel and may have potential practical applications in the bioremediation of munitions-contaminated soil and wastewater.Key words: 2,4,6-trinitrotoluene, mixed culture, transformation, co-metabolism, surfactant.
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49

Cai, Pingping, Zhuo Ning, Ningning Zhang, Min Zhang, Caijuan Guo, Manlan Niu, and Jiansheng Shi. "Insights into Biodegradation Related Metabolism in an Abnormally Low Dissolved Inorganic Carbon (DIC) Petroleum-Contaminated Aquifer by Metagenomics Analysis." Microorganisms 7, no. 10 (October 1, 2019): 412. http://dx.doi.org/10.3390/microorganisms7100412.

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In petroleum-contaminated aquifers, biodegradation is always associated with various types of microbial metabolism. It can be classified as autotrophic (such as methanogenic and other carbon fixation) and heterotrophic (such as nitrate/sulfate reduction and hydrocarbon consumption) metabolism. For each metabolic type, there are several key genes encoding the reaction enzymes, which can be identified by metagenomics analysis. Based on this principle, in an abnormally low dissolved inorganic carbon (DIC) petroleum-contaminated aquifer in North China, nine groundwater samples were collected along the groundwater flow, and metagenomics analysis was used to discover biodegradation related metabolism by key genes. The major new finding is that autotrophic metabolism was revealed, and, more usefully, we attempt to explain the reasons for abnormally low DIC. The results show that the methanogenesis gene, Mcr, was undetected but more carbon fixation genes than nitrate reduction and sulfate genes were found. This suggests that there may be a considerable number of autotrophic microorganisms that cause the phenomenon of low concentration of dissolved inorganic carbon in contaminated areas. The metagenomics data also revealed that most heterotrophic, sulfate, and nitrate reduction genes in the aquifer were assimilatory sulfate and dissimilatory nitrate reduction genes. Although there was limited dissolved oxygen, aerobic degrading genes AlkB and Cdo were more abundant than anaerobic degrading genes AssA and BssA. The metagenomics information can enrich our microorganic knowledge about petroleum-contaminated aquifers and provide basic data for further bioremediation.
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He, Qiang, Katherine H. Huang, Zhili He, Eric J. Alm, Matthew W. Fields, Terry C. Hazen, Adam P. Arkin, Judy D. Wall, and Jizhong Zhou. "Energetic Consequences of Nitrite Stress in Desulfovibrio vulgaris Hildenborough, Inferred from Global Transcriptional Analysis." Applied and Environmental Microbiology 72, no. 6 (June 2006): 4370–81. http://dx.doi.org/10.1128/aem.02609-05.

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ABSTRACT Many of the proteins that are candidates for bioenergetic pathways involved with sulfate respiration in Desulfovibrio spp. have been studied, but complete pathways and overall cell physiology remain to be resolved for many environmentally relevant conditions. In order to understand the metabolism of these microorganisms under adverse environmental conditions for improved bioremediation efforts, Desulfovibrio vulgaris Hildenborough was used as a model organism to study stress response to nitrite, an important intermediate in the nitrogen cycle. Previous physiological studies demonstrated that growth was inhibited by nitrite and that nitrite reduction was observed to be the primary mechanism of detoxification. Global transcriptional profiling with whole-genome microarrays revealed coordinated cascades of responses to nitrite in pathways of energy metabolism, nitrogen metabolism, oxidative stress response, and iron homeostasis. In agreement with previous observations, nitrite-stressed cells showed a decrease in the expression of genes encoding sulfate reduction functions in addition to respiratory oxidative phosphorylation and ATP synthase activity. Consequently, the stressed cells had decreased expression of the genes encoding ATP-dependent amino acid transporters and proteins involved in translation. Other genes up-regulated in response to nitrite include the genes in the Fur regulon, which is suggested to be involved in iron homeostasis, and genes in the Per regulon, which is predicted to be responsible for oxidative stress response.
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