Evaluating Microbial Community Potential for Environmental Cleanup and Pollutant Biodegradation

Mahfoudh A.M. Abdulghani ^1*, Fouad Saleh AL Suede ^1*

Bacterial degradation plays a vital role in environmental remediation, breaking down pollutants like hydrocarbons and heavy metals through diverse mechanisms.

Abstract

Microbial biodegradation is a crucial method for reducing environmental pollution. These communities, composed of diverse microorganisms, adeptly decompose various pollutants, showcasing remarkable adaptability. From pesticides to petroleum hydrocarbons, they play a vital role in cleaning contaminated areas. Enzymatic processes like hydrolases, oxidases, and dehydrogenases facilitate the transformation of contaminants into less harmful forms. Advancements in genomics and molecular biology deepen our understanding of microbial biodegradation's genetic basis. Techniques like biostimulation and bioaugmentation enhance microbial community performance. By adjusting factors such as temperature, nutrient availability, and pH, we optimize biodegradation efficacy tailored to specific pollutants and habitats. Microbial biodegradation stands out as an environmentally acceptable and cost-effective method for environmental cleanup, offering solutions to pressing pollution challenges while preserving ecosystems. This abstract underscores the importance of further research and practical implementation of microbial communities for a cleaner Earth.

Keywords: Microbial biodegradation, Environmental cleanup,  Pollutant biodegradation, Microbial communities, Biostimulation

References

Alexander M. Biodegradation and Bioremediation, San Diego CA 1994. Academic Press.

Army US. Interim army policy on natural attenuation for environmental restoration: Washington, DC, Department of the Army, Assistant Chief of Staff for Installation Management, DAIM-ED-R (200-1c), September 12, 1995.

Baelum, J., Jacobsen, C. S., Holben, W. E., & Al-Soud, W. A. (2012). Comparison of 16S rRNA gene phylogeny and functional tfdA gene in monitoring bioremediation of herbicide-contaminated soil. FEMS Microbiology Ecology, 81(1), 181-190.

 Bennet JW, Wunch KG and Faison B D. Use of fungi biodegradation. Manual of environmental microbiology 2002, 2nd ed., ASM Press: Washington, D.C., 960-971.

Bond DR, Lovley DR. Reduction of Fe(III) oxide by methanogens in the presence and absence of extracellular quinines. Environmental Microbiology 2002; 4 115-124.

Cases I, de Lorenzo V. Genetically modified organisms for the environment: stories of success and failure and what we have learned from them. International microbiology 2005; 8 213-222.

Chaube P, Indurkar H, Moghe S. Biodegradation and decolorisation of dye by mix consortia of bacteria and study of toxicity on Phaseolus mungo and Triticum aestivum. Asiatic Journal of Biotechnology Resources 2010; 01 45-56.

Chen BY., Chen WM. Nd Chang JS. Optimal biostimulation strategy for phenol degradation withindigenous rhizobium Ralstonia taiwanensis. Journal of Hazardous Materials; 2007 B139 232-237.

Chen M., Shih K., Hu M., Li F., Liu C., Wu W. And Tong H. Biostimulation of Indigenous Microbial Communities for Anaerobic transformation of pentachlorophenol in paddy soils of southern China. Journal of Agricultural and Food Chemistry 2012; 60 2967-2975.

Das N and Chandran P. Microbial Degradation of Petroleum Hydrocarbon Contaminants: An Overview SAGE-Hindawi Access to Research Biotechnology. Research International. Volume 2011, Article ID 941810, 13 pages.

Delgado-Baquerizo, M., Oliverio, A. M., Brewer, T. E., Benavent-González, A., Eldridge, D. J., Bardgett, R. D., ... & Singh, B. K. (2018). A global atlas of the dominant bacteria found in soil. Science, 359(6373), 320-325.

Demnerova K, Mackova M, Spevakova, V, Beranova K, Kochankova L, Lovecka P, Ryslava, E, Macek T. Two approaches to biological decontamination of groundwater and soil polluted by aromatics characterization of microbial populations. International Microbiology 2005; 8 205-211.

Diez MC. Biological Aspects involved in the degradation of organic pollutants. Journal of Soil Science and Plant Nutrition. [online] 2010; 10 (3) 244-267. ISSN 0718-9516.

Divya B and Deepak Kumar M. Plant–Microbe Interaction with Enhanced Bioremediation. Research Journal of BioTechnology. 2011; 6 (4).

Dos Santos AB, Cervantes JF, Van Lier BJ. Review paper on current technologies for decolourisation of textile wastewaters: perspectives for anaerobic biotechnology. Bioresource Technology 2007; 98 2369-2385.

Eijsink, V. G. H., Gaseidnes, S., Borchert, T. V., & van den Burg, B. (2010). Directed evolution of enzyme stability. Biomolecular Engineering, 16(1-4), 81-86.

El Fantroussi S and Agathos SN. Is bioaugmentation a feasible strategy for pollutant removal and site remediation? Current Opinion in Microbiology 2005; 8 268-275.

El Fantroussi S, Belkacemi M, Top EM, Mahillon J, Naveau H, Agathos SN. Bioaugmentation of a soil bioreactor designed for pilot-scale anaerobic bioremediation studies. Environmental Science & Technology 1999; 33 2992-3001.

EPA (U.S. Environmental Protection Agency). 2001. A Citizen’s Guide to Monitored Natural Attenuation. EPA 542-F-01-004, U.S. Environmental Protection Agency, Washington, D.C

ERD: Environmental Response Division. 1998. Fundamental principles of bioremediation (An aid to the development of bioremediation proposals).

Fatima M. Bento, Fla´vio A.O. Camargo, Benedict C. Okeke, William T. Frankenberger. Comparative bioremediation of soils contaminated with diesel oil by natural attenuation, biostimulation and bioaugmentation. Bioresource Technology 2005; 96 1049-1055.

Fern´andez PM, Martorell MM, Fari˜na JI, and Figueroa LIC., Removal Efficiency of Cr6+ by Indigenous Pichia sp. Isolated from Textile Factory Effluent. The Scientific World Journal. 2012, Article ID 708213, 6 pages doi:10.1100/2012/708213.

Floodgate G. The fate of petroleum in marine ecosystems. In Petroleum Microbiology, R. M. Atlas, Ed., pp. 355–398, Macmillion, New York, NY, USA, 1984.

Fritsche W and Hofrichter M. Aerobic Degradation by Microorganisms 2008 in Biotechnology Set, Second Edition (eds H.-J. Rehm and G. Reed), Wiley-VCH Verlag GmbH, Weinheim, Germany.

Fritsche W and Hofrichter M. Aerobic degradation of recalcitrant organic compounds by microorganisms, in environmental biotechnology: Concepts and applications (eds H.-J. Jördening and J. Winter), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, FRG. 2005

Gan, S., Lau, E. V., & Ng, H. K. (2018). Remediation of soils contaminated with polycyclic aromatic hydrocarbons (PAHs). Journal of Hazardous Materials, 172(2-3), 532-549.

Glick BR. Using soil bacteria to facilitate phytoremediation. Biotechnology Advances. 2010; 28 367-374.

Grishchenkov VG, Townsend RT, McDonald TJ, Autenrieth RL, Bonner JS, Boronin AM Degradation of petroleum hydrocarbons by facultative anaerobic bacteria under aerobic and anaerobic conditions. Process Biochemistry 2000; 35(9) 889-896.

Harwood WS and Herring FG, General Chemistry (8th ed., Prentice-Hall 2002), p.1025-26

Hong Y, Xu M, Guo J et al. Respiration and growth of Shewanella decolorations S12 with an azo compound as the sole electron acceptor. Applied and Environmental Microbiology 2007; 73 64-72.

Hontzeas N, Zoidakis J and Glick BR. Expression and characterization of 1-aminocyclopropane-1-carboxylate deaminase from the rhizobacterium Pseudomonas putida UW4: A key enzyme in bacterial plant growth promotion. Biochimica et Biophysica Acta 2004; 1703 11-19

Jing Y, He Z, Yang X. Role of soil rhizobacteria in phytoremediation of heavy metal contaminated soils. Journal of Zhejiang University Sciences 2007; 8 192-207.

Kafilzadeh F, Sahragard P, Jamali H and Tahery Y. Isolation and identification of hydrocarbons degrading bacteria in soil around Shiraz Refinery. African Journal of Microbiology Research 2011; 4(19) 3084-3089.

Kanade SN, Ade1 AB and Khilare VC. Malathion Degradation by Azospirillum lipoferum Beijerinck. Science Research Reporter 2012; 2(1) 94-103.

Kaplan CW, Kitts CL. Bacterial succession in a petroleum land treatment unit. Applied and Environmental Microbiology 2004; 70 1777-1786

Khalid A, Arshad M, and Crowley D. Bioaugmentation of Azo Dyes. The Handbook of Environmental Chemistry 2010; 9.

Leitão AL. Potential of Penicillium Species in the Bioremediation Field. International Journal of Environmental Resarch. Public Health 2009; 6 1393-1417.

Lesley A. Ogilvie and Penny R. Hirsch. 2012. Microbial ecological theory: Current perspectives

Li CH, Wong YS, Tam NF. Anaerobic biodegradation of polycyclic aromatic hydrocarbons with amendment of iron(III) in mangrove sediment slurry. Bioresource Technology 2010; 101 8083−8092.

Liliane RR, Meneghetti, AntônioThomé, Fernando Schnaid, Pedro D.M. Prietto and Gabriel Cavelhão. Natural Attenuation and Biostimulation of Biodiesel Contaminated Soils from Southern Brazil with Different Particle Sizes. Journal of Environmental Science and Engineering 2012; B1 155-162.

Lloyd JR and Lovley DR. Microbial detoxification of metals and radionuclides. Current Opinion in Biotechnology 2001; 12 248–253.

Lodato A, Alfieri F, Olivieri G, Di Donato, Marzocchella A, Salatino A, P. Azo-dye conversion by means of Pseudomonas sp. OX1. Enzyme and Microbial Technology 2007; 41 646-652

Ma B, Chen HH, He YandXu JM. Isolations and consortia of PAH-degrading bacteria from the rhizosphere of four crops in PAH-contaminated field. 2010 19th World Congress of Soil Science, Soil Solutions for a Changing World.

Marinescu M, Dumitru M and Lacatusu A. Biodegradation of Petroleum Hydrocarbons in an Artificial Polluted Soil. Research Journal of Agricultural Science 2009; 41(2).

Mason, O. U., Scott, N. M., Gonzalez, A., Robbins-Pianka, A., Bælum, J., Kimbrel, J., ... & Knight, R. (2019). Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. The ISME Journal, 8(7), 1464-1475.

McMurry J (2000). In Aromatic hydrocarbons. Organic Chmistry.5th ed brooks/cole: Thomas learning. New York, pp. 120-180.

Menn FM, Easter JP and Sayler GS. Genetically Engineered Microorganisms and Bioremediation, in Biotechnology: Environmental Processes II 2008; 11b, Second Edition (eds H.-J. Rehm and G. Reed), Wiley-VCH Verlag GmbH, Weinheim, German

Mrozik A, Piotrowska-Seget Z and Labuzek S. Bacterial degradation and bioremediation of Polycyclic Aromatic Hydrocarbons. Polish Journal of Environmental Studies 2003; 12 (1) 15-25.

Mrozik A, Piotrowska-Seget Z. Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbial Research 2006; (2009),

Okere UV and Semple KT. Biodegradation of PAHs in ‘Pristine’ Soils from Different Climatic Regions. Okere and Semple. J BioremedBiodegrad 2011

Olaniran AO, Pillay D, Pillay B. Biostimulation and bioaugmentation enhances aerobic biodegradation of dichloroethenes. Chemosphere 2006; 63 600-608.

Petric I, Hrak D, Fingler S, Vonina E, Cetkovic H, Begonja A Kolar and UdikoviKoli N. Enrichment and characterization of PCB-Degrading bacteria as potential seed cultures for bioremediation of contaminated soil. Food Technology and Biotechnology 2007; 45(1)11-20.

Pramila R., Padmavathy K, Ramesh KV and Mahalakshmi K. Brevibacillus parabrevis, Acinetobacter baumannii and Pseudomonas citronellolis – Potential candidates for biodegradation of low density polyethylene (LDPE). Journal of Bacteriology Research 2012; 4(1) 9-14.

Raffi F, Hall JD and Cernigila, CE. Mutagenicity of azo dyes used in foods, drugs and cosmetics before and after reduction by Clostridium species from the human intestinal tract. Food and chemical Toxicology 1997; 35 897-901.

Riser-Roberts E. Remediation of petroleum contaminated soils. Biological, physical, and chemical process. Lewis Publishers Inc (ed). CRC Press LLC. USA. 1998 1-542.

Saharan BS, Nehra V. Plant Growth Promoting Rhizobacteria: A Critical Review Life Sciences and Medicine Research, Volume 2011: LSMR-21

Sayler GS, Ripp S. Field applications of genetically engineered microorganisms for bioremediation processes. Current Opinion in Biotechnology 2000; 11 286-289.

Schlüter, A., Bekel, T., Diaz, N. N., Dondrup, M., Eichenlaub, R., Gartemann, K. H., ... & Goesmann, A. (2008). The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology. Journal of Biotechnology, 136(1-2), 77-90.

Seeger M, Cámara B, Hofer B. Dehalogenation, denitration, dehydroxylation, and angular attack on substituted biphenyls and related compounds by a biphenyl dioxygenase. Journal of Bacteriology 2001; 183 3548-3555.

Seeger M, Hernández M, Méndez V, Ponce B, Córdova1 M and González M. Bacterial degradation and bioremediation of chlorinated herbicides and biphenyls. Journal of Soil Science and Plant Nutrition 2010; 10 (3) 320-332.

Seo JS, Keum YS and Li QX. Bacterial Degradation of Aromatic Compounds. International Journal of Environmental Resarch. Public Health 2009, 6, 278- 309

Seshan, H., Chow, C. E., & Rappé, M. S. (2017). Metagenomics: challenging the biomass optimization based on community structure. Environmental Microbiology, 19(4), 1114-1118.

Shan HF, Kurtz HD, Freedman D L. Evaluation of strategies for anaerobic bioremediatidon of high concentrations of halomethanes. Water Research 2010; 44 1317-1328.

Steffan, R. J., & Yang, X. (2015). Challenges in microbial bioaugmentation: the case of polycyclic aromatic hydrocarbons. FEMS Microbiology Ecology, 91(3), 1-9.

Struthers JK, Jayachandran K, Moorman TB. Biodegradation of atrazine by Agrobacterium radiobacter J14a and use of this strain in bioremediation of contaminated soil. Applied of Environonmental Microbiology 1998; 64 3368-3375

Surekha Rani M, Lakshmi V, Suvarnalatha Devi KP, Jaya Madhuri R, Aruna S, Jyothi K, Narasimha G and Venkateswarlu K. Isolation and characterization of a chlorpyrifos degrading bacterium from agricultural soil and its growth response. African Journal of Microbiology Research 2008; (2) 026-031.

Taguchi K, Motoyama M and Kudo T. PCB/biphenyl degradation gene cluster in Rhodococcus rhodochrousK37, is different from the well-known bph gene clusters in Rhodococcus sp. P6, RHA1, and TA42. RIKEN Review 2001; 42. Focused on Ecomolecular Science Research.

Thierry L., Armelle B. And Karine J. Performance of bioaugmentation-assisted phytoextraction applied to metal contaminated soils: A review . Environmental Pollution 2008; 153 497-522.

Van der Heul RM. Environmental Degradation of petroleum hydrocarbons. 2009

Vandevivere PC, Bianchi R, Verstraete W. Treatment and reuse of wastewater from the textile wet-processing industry: review of emerging technologies. Journal of Chemical Technology and Biotechnology 1998; 72 289-302.

Vargas, J. M. “Pesticide degradation.” J. Arboriculture 1.12 (1975): 232-233.

Verma P, Madamwar, D. Decolorization of synthetic dyes by a newly isolated strain of Serratia marcescers. World Journal of Microbiology and Biotechnology 2003; 19 615- 618.

Yakimov MM, Timmis KN and Golyshin PN. Obligate oil-degrading marine bacteria. Current Opinion in Biotechnology, 2007; 18(3) 257-266.

Yee N, Ma J, Dalia A, Boonfueng T, and Kobayashi DY. Se(VI) Reduction and the Precipitation of Se(0) by the Facultative Bacterium Enterobacter cloacae SLD1a-1 Are Regulated by FNR. Applied and environmental microbiology 2007; 73(6) 1914-1920.

Yu KSH, Wong AHY, Yau KWY, Wong YS, Tam NFY. Natural attenuation, biostimulation and bioaugmentation on biodegradation of polycyclic aromatic hydrocarbons (PAHs) in mangrove sediments. Marine Pollution Bulletin 2005; 51(8-12)1071-1077.

Zafra, G., Absalón, Á. E., & Bayona, J. M. (2016). Organic micropollutants in coastal waters from NW Mexico. Water Research, 100, 602-611.

Zhu W., Chai L., Ma Z., Wang Y., Xiao H. And Zhao K. Anaerobic reduction of hexavalent chromium by bacterial cells of Achromobacter sp. StrainCh1. Microbiological Research 2008; 163 616-623.