Applications of metagenomics in microbial bioremediation of pollutants: from genomics to environmental cleanup

Book chapter

Bharagava, R., Purchase, D., Saxena, G. and Mulla, S. 2018. Applications of metagenomics in microbial bioremediation of pollutants: from genomics to environmental cleanup. in: Das, S. and Dash, H. (ed.) Microbial Diversity in the Genomic Era Oxford, UK Elsevier, Academic Press. pp. 459-477
Chapter titleApplications of metagenomics in microbial bioremediation of pollutants: from genomics to environmental cleanup
AuthorsBharagava, R., Purchase, D., Saxena, G. and Mulla, S.
Abstract

Environmental pollutants are of serious ecotoxicological and health concern worldwide. To cope with these, bioremediation technologies utilizing microorganisms is currently viewed as an excellent cost-effective and ecofriendly strategy for the environmental management. However, a strategic execution of the bioremediation technology requires the knowledge of microbial metabolism, key enzymes, and genes involved and nature, dynamics, and composition of microbial communities, which can be easily understood by applying molecular techniques. Conventional or culture-dependent molecular techniques are currently being applied to characterize the potential pollutants degrading/detoxifying microbes, but these techniques are sometimes biased and do not actually provide the accurate information. However, the currently emerging metagenomic approaches including next-generation sequencing technologies can provide the reliable information and reveal very useful information about the metagenome of environmental microorganisms, which play an important role in the biogeochemical cycles and degradation and detoxification of environmental pollutants using culture-independent molecular techniques. Therefore, this chapter provides an overview of the metagenomic approaches and their applications in microbial ecology and bioremediation.

Page range459-477
Book titleMicrobial Diversity in the Genomic Era
EditorsDas, S. and Dash, H.
PublisherElsevier, Academic Press
Place of publicationOxford, UK
ISBN
Hardcover9780128148495
Publication dates
Online28 Sep 2018
Print17 Oct 2018
Publication process dates
Deposited12 Oct 2018
Output statusPublished
Additional information

Copyright © 2019 Elsevier Inc

Digital Object Identifier (DOI)https://doi.org/10.1016/B978-0-12-814849-5.00026-5
Scopus EID2-s2.0-85089757846
2-s2.0-85068780676
LanguageEnglish
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Chemistry and the environment
Purchase, D., Obare, S., Unsworth, J. and Garelick, H. 2018. Chemistry and the environment. Chemistry International. 40 (2), pp. 46-51. https://doi.org/10.1515/ci-2018-0230
Oxidative and monoxygenase enzymatic response in Eisenia hortensis and Lumbricus terrestiris exposed to 3-, 4- and 5-ring hydrocarbons amended with biosurfactant
Popoola, S., Purchase, D. and Jones, H. 2018. Oxidative and monoxygenase enzymatic response in Eisenia hortensis and Lumbricus terrestiris exposed to 3-, 4- and 5-ring hydrocarbons amended with biosurfactant. SETAC AP 2018: 11th Society of Environmental Toxicology and Chemistry – Asia Pacific 2018. Daegu, Korea 16 - 19 Sep 2018
Competition of As and other Group 15 elements for surface binding sites of an extremophilic Acidomyces acidophilus isolated from a historical tin mining site
Chan, W., Wildeboer, D., Garelick, H. and Purchase, D. 2018. Competition of As and other Group 15 elements for surface binding sites of an extremophilic Acidomyces acidophilus isolated from a historical tin mining site. Extremophiles. 22 (5), pp. 795-809. https://doi.org/10.1007/s00792-018-1039-2
To safeguard microgreens from contamination form Salmonella species
Selvam, S., Marvasi, M. and Purchase, D. 2017. To safeguard microgreens from contamination form Salmonella species. University Research Students Summer Conference 2017. London
Electronic waste – an emerging global environmental and health challenge in the 21st century
Purchase, D. 2017. Electronic waste – an emerging global environmental and health challenge in the 21st century. SmART Cities and Waste Research Workshop. London, United Kingdom 06 Apr 2017
Enhanced vermiremediation of hydrocarbon contamination using biosurfactant
Popoola, S., Jones, H. and Purchase, D. 2017. Enhanced vermiremediation of hydrocarbon contamination using biosurfactant. SETAC Europe 27th Annual Meeting. Brussels, Belgium 07 - 11 May 2017
A study of the inhibition of biofilm formation on multiple surfaces by a biosurfactant containing four discrete lipopeptides
Khonsari, S., Gonzalez Baez, A., Nguyen, H., Pantoja Munoz, L. and Purchase, D. 2017. A study of the inhibition of biofilm formation on multiple surfaces by a biosurfactant containing four discrete lipopeptides. Microbiology Society Annual Conference. Edinburgh, United Kingdom 03 - 06 Apr 2017
Coming of age
Purchase, D. 2011. Coming of age. Environmental Scientist. 20 (2), pp. 30-33.
A proteomic study on the responses to arsenate stress by an acidophilic fungal strain Acidomyces acidophilus WKC1
Chan, W., Wildeboer, D., Garelick, H. and Purchase, D. 2016. A proteomic study on the responses to arsenate stress by an acidophilic fungal strain Acidomyces acidophilus WKC1. Biotechnology World Convention. Sao Paulo, Brazil 15 - 17 Aug 2016 OMICS International. pp. 35-35 https://doi.org/10.4172/2155-952X.C1.058
Informal recycling of electronic wastes in developing countries: challenges and solutions
Purchase, D. 2017. Informal recycling of electronic wastes in developing countries: challenges and solutions. 16th International Chemistry and the Environment (ICCE) Conference. Oslo, Norway 18 - 22 Jun 2017
Can metals be used as tracers for organic contaminants in potentially e-waste-polluted environmental media?
Rüdel, H., Abbasi, G., Popoola, O. and Purchase, D. 2017. Can metals be used as tracers for organic contaminants in potentially e-waste-polluted environmental media? 16th International Conference on Chemistry and the Environment (ICCE 2017). Oslo, Norway 18 - 22 Jun 2017
Heavy metals distribution and risk assessment in soil from an informal e-waste recycling site in Lagos State, Nigeria
Isimekhai, K., Garelick, H., Watt, J. and Purchase, D. 2017. Heavy metals distribution and risk assessment in soil from an informal e-waste recycling site in Lagos State, Nigeria. Environmental Science and Pollution Research. 24 (20), pp. 17206-17219. https://doi.org/10.1007/s11356-017-8877-9
Mycoremediation of heavy metal/metalloid-contaminated soil: current understanding and future prospects
Chan, W., Wildeboer, D., Garelick, H. and Purchase, D. 2016. Mycoremediation of heavy metal/metalloid-contaminated soil: current understanding and future prospects. in: Purchase, D. (ed.) Fungal Applications in Sustainable Environmental Biotechnology Cham, Switzerland Springer. pp. 249-272
Application of microalgae and fungal-microalgal associations for wastewater treatment
Egede, E., Jones, H., Cook, B., Purchase, D. and Mouradov, A. 2016. Application of microalgae and fungal-microalgal associations for wastewater treatment. in: Purchase, D. (ed.) Fungal Applications in Sustainable Environmental Biotechnology Cham Springer. pp. 143-181
The mechanisms of detoxification of As(III), dimethylarsinic acid (DMA) and As(V) in the microalga Chlorella vulgaris
Pantoja Munoz, L., Purchase, D., Jones, H., Raab, A., Urgast, D., Feldmann, J. and Garelick, H. 2016. The mechanisms of detoxification of As(III), dimethylarsinic acid (DMA) and As(V) in the microalga Chlorella vulgaris. Aquatic Toxicology. 175, pp. 56-72. https://doi.org/10.1016/j.aquatox.2016.02.020
Microbial keratinases: characteristics, biotechnological applications and potential
Purchase, D. 2016. Microbial keratinases: characteristics, biotechnological applications and potential. in: Gupta, V., Sharma, G., Tuohy, M. and Gaur, R. (ed.) The Handbook of Microbial Bioresources Wallingford, UK CAB International. pp. 634-674
Investigating arsenic resistance in fungi from tin-mining soil and the possible interaction between arsenic and tin/antimony
Chan, W., Wildeboer, D., Garelick, H. and Purchase, D. 2014. Investigating arsenic resistance in fungi from tin-mining soil and the possible interaction between arsenic and tin/antimony. 10th International Mycological Congress. Bangkok, Thailand 03 - 08 Aug 2014
Risk assessment at an informal e-waste recycling site in Lagos state, Nigeria
Isimekhai, K., Watt, J., Garelick, H. and Purchase, D. 2014. Risk assessment at an informal e-waste recycling site in Lagos state, Nigeria. Society for Risk Analysis Europe Conference. Istanbul, Turkey 16 - 18 Jun 2014
Consideration of the bioavailability of metal/metalloid species in freshwaters: experiences regarding the implementation of biotic ligand model-based approaches in risk assessment frameworks
Rüdel, H., Diaz Muñiz, C., Garelick, H., Kandile, N., Miller, B., Pantoja Munoz, L., Peijnenburg, W., Purchase, D., Shevah, Y., Van Sprang, P., Vijer, M. and Vink, J. 2015. Consideration of the bioavailability of metal/metalloid species in freshwaters: experiences regarding the implementation of biotic ligand model-based approaches in risk assessment frameworks. Environmental Science and Pollution Research. 22 (10), pp. 7405-7421. https://doi.org/10.1007/s11356-015-4257-5
The mechanisms of arsenic bioremediation from water by the green microalgae Chlorella vulgaris
Pantoja Munoz, L., Purchase, D., Jones, H., Feldmann, J. and Garelick, H. 2014. The mechanisms of arsenic bioremediation from water by the green microalgae Chlorella vulgaris. THE BNASS / TraceSpec Tandem Conference. Aberdeen, Scotland, UK 31 Aug - 04 Sep 2014
Enhanced determination of As-phytochelatin complexes in Chlorella vulgaris using focused sonication for extraction of water-soluble species
Pantoja Munoz, L., Purchase, D., Jones, H., Feldmann, J. and Garelick, H. 2014. Enhanced determination of As-phytochelatin complexes in Chlorella vulgaris using focused sonication for extraction of water-soluble species. Analytical Methods. 6 (3), pp. 791-797. https://doi.org/10.1039/C3AY41629A
Enzymatic formulation capable of degrading scrapie prion under mild digestion conditions
Okoroma, E., Purchase, D., Garelick, H., Morris, R., Neale, M., Windl, O. and Abiola, O. 2013. Enzymatic formulation capable of degrading scrapie prion under mild digestion conditions. PLoS ONE. 8 (7), pp. 1-7. https://doi.org/10.1371/journal.pone.0068099
Identification and characterisation of a Bacillus licheniformis strain with profound keratinase activity for degradation of melanised feather
Okoroma, E., Garelick, H., Abiola, O. and Purchase, D. 2012. Identification and characterisation of a Bacillus licheniformis strain with profound keratinase activity for degradation of melanised feather. International Biodeterioration and Biodegradation. 74, pp. 54-60. https://doi.org/10.1016/j.ibiod.2012.07.013
Mathematical models to predict soil heavy metal toxicity in the 2012 Olympic site
Radiar, A. and Purchase, D. 2012. Mathematical models to predict soil heavy metal toxicity in the 2012 Olympic site. International Journal of Environmental Science and Technology. 9 (2), pp. 219-226. https://doi.org/10.1007/s13762-012-0027-9
Technical note: effects of arsenate (AS5+) on growth and production of glutathione (GSH) and phytochelatins (PCS) in Chlorella Vulgaris
Jiang, Y., Purchase, D., Jones, H. and Garelick, H. 2011. Technical note: effects of arsenate (AS5+) on growth and production of glutathione (GSH) and phytochelatins (PCS) in Chlorella Vulgaris. International Journal of Phytoremediation. 13 (8), pp. 834-844. https://doi.org/10.1080/15226514.2010.525560
A novel enzymatic composition effective for prion degradation
Okoroma, E., Purchase, D., Garelick, H. and Abiola, O. 2011. A novel enzymatic composition effective for prion degradation. Society for General Microbiology Spring Conference. Harrogate, UK 11 - 14 Apr 2011
Keratin degradation by proteolytic microorganisms isolated from activated sludge and farmyard manure: possible application in decontamination of prion protein
Purchase, D., Garelick, H., Okoroma, E., Christen, H. and Abiola, O. 2007. Keratin degradation by proteolytic microorganisms isolated from activated sludge and farmyard manure: possible application in decontamination of prion protein. BAGECO 9: 9th Symposium on Bacterial Genetics and Ecology. Wernigerode, Germany
Keratinase production by proteolytic micro-organisms in activated sludge and farmyard waste.
Okoroma, E., Purchase, D., Garelick, H. and Abiola, O. 2008. Keratinase production by proteolytic micro-organisms in activated sludge and farmyard waste. Society for General Microbiology, Autumn Meeting. Trinity College, Dublin, Ireland 08 - 11 Sep 2008
Bacterial keratinase: prospects for prion degradation.
Okoroma, E., Purchase, D., Garelick, H. and Abiola, O. 2009. Bacterial keratinase: prospects for prion degradation. Society for General Microbiology, Spring Meeting. Harrogate, UK 30 Mar - 02 Apr 2009
Degradation of scrapie infected brain homogenateby a novel bacterial keratinase
Okoroma, E., Purchase, D., Garelick, H., Jen, A., Morris, R. and Abiola, O. 2009. Degradation of scrapie infected brain homogenateby a novel bacterial keratinase. Prion 2009. Chalkidiki, Greece 23 - 25 Sep 2009
Effects of temperature on metal tolerance and the accumulation of Zn and Pb by metal-tolerant fungi isolated from urban runoff treatment wetlands
Purchase, D., Lundy, L., Revitt, D. and Shutes, B. 2009. Effects of temperature on metal tolerance and the accumulation of Zn and Pb by metal-tolerant fungi isolated from urban runoff treatment wetlands. Journal of Applied Microbiology. 106 (4), pp. 1163-1174. https://doi.org/10.1111/j.1365-2672.2008.04082.x
Effectiveness of domestic antibacterial products in decontaminating food contact surfaces
De Vere, E. and Purchase, D. 2007. Effectiveness of domestic antibacterial products in decontaminating food contact surfaces. Food Microbiology. 24 (4), pp. 425-430. https://doi.org/10.1016/j.fm.2006.07.013
Survival and nodulating ability of indigenous and inoculated rhizobium leguminosarum biovar trifolii in sterilized and unsterilized soil treated with sewage sludge
Purchase, D. and Miles, R. 2001. Survival and nodulating ability of indigenous and inoculated rhizobium leguminosarum biovar trifolii in sterilized and unsterilized soil treated with sewage sludge. Current Microbiology. 42 (1), pp. 59-64. https://doi.org/10.1007/s002840010179
Use of sequential extraction procedures for the analysis of cadmium and lead in sediment samples from a constructed wetland
Carapeto, C. and Purchase, D. 2000. Use of sequential extraction procedures for the analysis of cadmium and lead in sediment samples from a constructed wetland. Bulletin of Environmental Contamination and Toxicology. 64 (1), pp. 51-58. https://doi.org/10.1007/s001289910009
Distribution and removal of cadmium and lead in a constructed wetland receiving urban runoff
Carapeto, C. and Purchase, D. 2000. Distribution and removal of cadmium and lead in a constructed wetland receiving urban runoff. Bulletin of Environmental Contamination and Toxicology. 65 (3), pp. 322-329. https://doi.org/10.1007/s0012800131
The removal of urban pollutants by constructed wetlands during wet weather
Scholes, L., Shutes, R., Revitt, D., Purchase, D. and Forshaw, M. 1999. The removal of urban pollutants by constructed wetlands during wet weather. Water Science & Technology. 40 (3), pp. 333-340. https://doi.org/10.1016/S0273-1223(99)00467-9
The treatment of metals in urban runoff by constructed wetlands
Scholes, L., Shutes, R., Revitt, D., Forshaw, M. and Purchase, D. 1998. The treatment of metals in urban runoff by constructed wetlands. Science of the Total Environment. 214 (1-3), pp. 211-219. https://doi.org/10.1016/S0048-9697(98)00072-2
Expression and content of terminal oxidases in Azotobacter vinelandii grown with excess NH4+ are modulated by O-2 supply
Dmello, R., Purchase, D., Poole, R. and Hill, S. 1997. Expression and content of terminal oxidases in Azotobacter vinelandii grown with excess NH4+ are modulated by O-2 supply. Microbiology. 143 (1), pp. 231-237. https://doi.org/10.1099/00221287-143-1-231
Cadmium uptake and nitrogen fixing ability in heavy-metal-resistant laboratory and field strains of Rhizobium leguminosarum biovar trifolii
Purchase, D., Miles, R. and Young, T. 1997. Cadmium uptake and nitrogen fixing ability in heavy-metal-resistant laboratory and field strains of Rhizobium leguminosarum biovar trifolii. FEMS Microbiology Ecology. 22 (1), pp. 85-93. https://doi.org/10.1111/j.1574-6941.1997.tb00359.x