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Bioremediation of Toxic Metals for Protecting Human Health and the Ecosystem

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Bioremediation of Toxic Metals for Protecting Human Health and the Ecosystem Bioremediation of Toxic Metals for Protecting Human Health and the Ecosystem Dedicated To My parents We won't have a society if we destroy the environment. ―Margaret Mead (1901-1978) Örebro Studies in Life Science 15 AMINUR RAHMAN Bioremediation of Toxic Metals for Protecting Human Health and the Ecosystem © Aminur Rahman, (2016) Title: Bioremediation of Toxic Metals for Protecting Human Health and the Ecosystem Publisher: Örebro University (2016) www.publications.oru.se Print: Örebro University, Repro 08/2016 ISSN 1653-3100 ISBN 978-91-7529-146-8 Abstract Aminur Rahman (2016): Bioremediation of Toxic Metals for Protecting Human Health and the Ecosystem. Örebro Studies in Life Science 15. Heavy metal pollutants, discharged into the ecosystem as waste by anthro- pogenic activities, contaminate drinking water for millions of people and animals in many regions of the world. Long term exposure to these metals, leads to several lethal diseases like cancer, keratosis, gangrene, diabetes, car- dio-vascular disorders, etc. Therefore, removal of these pollutants from soil, water and environment is of great importance for human welfare. One of the possible eco-friendly solutions to this problem is the use of microorgan- isms that can accumulate the heavy metals from the contaminated sources, hence reducing the pollutant contents to a safe level. In this thesis an arsenic resistant bacterium Lysinibacillus sphaericus B1- CDA, a chromium resistant bacterium Enterobacter cloacae B2-DHA and a nickel resistant bacterium Lysinibacillus sp. BA2 were isolated and stud- ied. The minimum inhibitory concentration values of these isolates are 500 mM sodium arsenate, 5.5 mM potassium chromate and 9 mM nickel chlo- ride, respectively. The time of flight-secondary ion mass spectrometry and inductively coupled plasma-mass spectroscopy analyses revealed that after 120 h of exposure, the intracellular accumulation of arsenic in B1-CDA and chromium in B2-DHA were 5.0 mg/g dwt and 320 μg/g dwt of cell biomass, respectively. However, the arsenic and chromium contents in the liquid me- dium were reduced to 50% and 81%, respectively. The adsorption values of BA2 when exposed to nickel for 6 h were 238.04 mg of Ni(II) per gram of dead biomass indicating BA2 can reduce nickel content in the solution to 53.89%. Scanning electron micrograph depicted the effect of these metals on cellular morphology of the isolates. The genetic composition of B1-CDA and B2-DHA were studied in detail by sequencing of whole genomes. All genes of B1-CDA and B2-DHA predicted to be associated with resistance to heavy metals were annotated. The findings in this study accentuate the significance of these bacteria in removing toxic metals from the contaminated sources. The genetic mecha- nisms of these isolates in absorbing and thus removing toxic metals could be used as vehicles to cope with metal toxicity of the contaminated effluents discharged to the nature by industries and other human activities. Keywords: Heavy Metals, Pollution, Accumulation, Remediation, Human Health, Bacteria, Genome Sequencing, de novo Assembly, Gene Prediction. Aminur Rahman, School of Science and Technology, Örebro University, SE-701 82 Örebro, Sweden, e-mail: [email protected] LIST OF PAPERS Paper I Rahman A, Nahar N, Nawani NN, Jass J, Desale P, Kapadnis BP, Hossain K, Saha AK, Ghosh S, Olsson B, Mandal A (2014) Isolation of a Lysini- bacillus strain B1-CDA showing potentials for arsenic bioremediation. J. Environ. Sci. and Health, Part A: Hazardous Substances and Environmental Engineering. 49:12, 1349-1360. doi: 10.1080/10934529.2014.928247 Paper II Rahman A, Nahar N, Nawani NN, Jass J, Hossain K, Saha AK, Ghosh S, Olsson B, Mandal A (2015) Bioremediation of hexavalent chromium (VI) by a soil borne bacterium, Enterobacter cloacae B2-DHA. J. Environ. Sci. and Health, Part A: Hazardous Substances and Environmental Engineering. 50:11, 1136-1147. doi: 10.1080/10934529.2015.1047670 Paper III Desale P., Kashyap D., Nawani N., Nahar N., Rahman A., Kapadnis B. and Mandal A. (2014) Biosorption of Nickel by Lysinibacillus sp. BA2 native to bauxite mine. Ecotoxicology and Environmental Safety. 107, 260-268. doi: 10.1016/j.ecoenv.2014.06.009 Paper IV Rahman A, Nahar N, Nawani NN, Jass J, Ghosh S, Olsson B, Mandal A (2015) Comparative genome analysis of Lysinibacillus B1-CDA, a bacte- rium that accumulates arsenics. Genomics. 106: 384-392. doi: http://dx.doi.org/10.1016/j.ygeno.2015.09.006 Paper V Rahman A, Nahar N, Olsson B, Jass J, Nawani NN, Ghosh S, Saha AK, Hossain K, Mandal A (2016) Genome analysis of Enterobacter cloacae B2- DHA – A bacterium resistant to chromium and/or other heavy metals. Ge- nomics, (Submitted). PAPERS NOT INCLUDED IN THIS THESIS 1. Rahman A, Nahar N, Nawani N, Mandal A (2016) Investigation on arsenic accumulating and transforming bacteria for potential use in bioremediation. Handbook of Metal-microbe interactions and bioremediation: Eds. Surajit Das, Hirak R. Dash. CRC Press, Tay- lor & Francis. 2. Yewale P., Rahman A., Nahar N., Saha A., Jass J., Mandal A. and Nawani N. (2016) Sources of metal pollution, global status and conventional bioremediation practices. Handbook of Metal-mi- crobe interactions and bioremediation: Eds. Surajit Das, Hirak R. Dash. CRC Press, Taylor & Francis. 3. Nawani N, Rahman A, Nahar N, Saha A, Kapadnis B, Mandal A (2016) Status of metal pollution in rivers flowing through urban settlements at Pune and its effect on resident microflora. Biologia. 71 (5): doi: 10.1515/biolog-2016-0074. 4. Rahman A, Nahar N, Olsson B, Mandal A (2016) Complete ge- nome sequence of Enterobacter cloacae B2-DHA, a chromium re- sistant bacterium. Genome Announce. 4(3): e00483-16. doi:10.1128/genomeA.00483-16. 5. Rahman A, Nahar N, Jass J, Olsson B, Mandal A (2016) Complete genome sequence of Lysinibacillus sphaericus B1-CDA, a bacte- rium that accumulates arsenic. Genome Announc 4(1):e00999-15. doi: 10.1128/genomeA.00999-15. 6. Rahman A, Nahar N, Nawani NN, Jass J, Ghosh S, Olsson B, Man- dal A (2015) Data in support of the comparative genome analysis of Lysinibacillus B1-CDA, a bacterium that accumulates arsenics. Data in Brief. 5: 579–585. doi: http://dx.doi.org/10.1016/j.yg- eno.2015.09.006 7. Islam MS, Mohanto NC, Karim MR, Aktar S, Hoque MM, Rah- man A, Jahan M , Khatun R, Aziz A , Salam KA, Saud ZA, Hossain M, Rahman A, Mandal A, Haque A, Miyataka H, Himeno S, Hoss- ain K (2015) Arsenic exposure-related elevation of serum matrix metllaoproteinases- and -9 levels and their associations with circu- lating markers of cardiovascular diseases. Environmental Health 14:92. doi: 10.1186/s12940-015-0079-7 8. Nahar N, Rahman A, Moś M, Warzecha T, Ghosh S, Hossain K, Nawani NN, Mandal A (2014) In silico and in vivo studies of mo- lecular structures and mechanisms of AtPCS1 protein involved in binding arsenite and/or cadmium in plant cells. J Mo. Model 20: 2104. doi: 10.1007/s00894-014-2104-0. 9. Nahar N., Rahman A., Moś M, Warzecha T., Algerin M, Ghosh S., Johnson-Brousseau S. and Mandal A. (2012) In silico and in vivo studies of an Arabidopsis thaliana gene ACR2 putatively in- volved in arsenic accumulation in plants. J. Mol. Model18:4249– 4262, doi: 10.1007/s00894-012-1419-y. LIST OF PATENTS 1. Nawani N, Desale P, Rahman A, Nahar N, Kapadnis B, Mandal A (2015) A novel technology for the removal of metals from aqueous so- lutions. Indian patent 17/MUM/2015 dated 03/01/2015. 2. Nawani N, Desale P, Rahman A, Nahar N, Kapadnis B, Mandal A (2015) A method for removal of metals from aqueous solutions. PCT/IB2016/050358 dated 25/01/2016. ABBREVIATIONS ACR2 Arsenic reductase genes AgNO3 Silver nitrate As Arsenic AsIII Arsenite - AsO2 Meta-arsenite 3- AsO3 Ortho-arsenite - AsO4H2 Arsenate AsV Arsenate Cd Cadmium CFU Colony forming unit Cr Chromium Cr(III) Trivalent chromium Cr(VI) Hexavalent chromium CrO- Chromium oxide - CrO2 Chromium dioxide dwt Dry weight DC Direct current ddH2O Double deionized water DMAA Dimethyl arsenic acid dNTPs Deoxy nucleotide triphosphates E. coli Escherichia coli EDS Energy dispersive system ESEM Environmental scanning electron microscope FAO Food and agricultural organization FeCl3 Ferric chloride FIA Flow injection analysis GO Gene ontology ICP-AES Inductively coupled plasma atomic emission spectroscopy ICP-MS Inductively coupled plasma-mass spectroscopy LB Luria-Bertani LSD Least significant difference MIC Minimum inhibitory concentration MMAA Monomethyl arsenic acid MnCl2 Manganese chloride Na2HAsO4 Sodium arsenate ND Nano drop NEB New England Bio lab Ni Nickel NiCl2 Nickel chloride Pb Lead PBS Phosphate buffered saline RAST Rapid annotations using subsystems technology RFW Reconstructed field water SEM Scanning electron microscope TE Tris EDTA TOF-SIMS Time of flight-secondary ion mass spectrometry ZnCl2 Zinc chloride Table of Contents INTRODUCTION .................................................................................. 15 Heavy metal and metalloid contaminants ............................................... 18 Forms of arsenic ...................................................................................... 20 Forms of chromium ................................................................................. 23 Forms of nickel ....................................................................................... 25 Removal of heavy metals ......................................................................... 27 Genes involved in metal bioremediation ................................................. 30 AIMS ......................................................................................................
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