Advances in Anaerobic Benzene Bioremediation: Microbes, Mechanisms, and Biotechnologies
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Detection of a Bacterial Group Within the Phylum Chloroflexi And
Microbes Environ. Vol. 21, No. 3, 154–162, 2006 http://wwwsoc.nii.ac.jp/jsme2/ Detection of a Bacterial Group within the Phylum Chloroflexi and Reductive-Dehalogenase-Homologous Genes in Pentachlorobenzene- Dechlorinating Estuarine Sediment from the Arakawa River, Japan KYOSUKE SANTOH1, ATSUSHI KOUZUMA1, RYOKO ISHIZEKI2, KENICHI IWATA1, MINORU SHIMURA3, TOSHIO HAYAKAWA3, TOSHIHIRO HOAKI4, HIDEAKI NOJIRI1, TOSHIO OMORI2, HISAKAZU YAMANE1 and HIROSHI HABE1*† 1 Biotechnology Research Center, The University of Tokyo, 1–1–1 Yayoi, Bunkyo-ku, Tokyo 113–8657, Japan 2 Department of Industrial Chemistry, Faculty of Engineering, Shibaura Institute of Technology, Minato-ku, Tokyo 108–8548, Japan 3 Environmental Biotechnology Laboratory, Railway Technical Research Institute, 2–8–38 Hikari-cho, Kokubunji-shi, Tokyo 185–8540, Japan 4 Technology Research Center, Taisei Corporation, 344–1 Nase, Totsuka-ku, Yokohama 245–0051, Japan (Received April 21, 2006—Accepted June 12, 2006) We enriched a pentachlorobenzene (pentaCB)-dechlorinating microbial consortium from an estuarine-sedi- ment sample obtained from the mouth of the Arakawa River. The sediment was incubated together with a mix- ture of four electron donors and pentaCB, and after five months of incubation, the microbial community structure was analyzed. Both DGGE and clone library analyses showed that the most expansive phylogenetic group within the consortium was affiliated with the phylum Chloroflexi, which includes Dehalococcoides-like bacteria. PCR using a degenerate primer set targeting conserved regions in reductive-dehalogenase-homologous (rdh) genes from Dehalococcoides species revealed that DNA fragments (approximately 1.5–1.7 kb) of rdh genes were am- plified from genomic DNA of the consortium. The deduced amino acid sequences of the rdh genes shared sever- al characteristics of reductive dehalogenases. -
Bioaugmentation: an Emerging Strategy of Industrial Wastewater Treatment for Reuse and Discharge
International Journal of Environmental Research and Public Health Review Bioaugmentation: An Emerging Strategy of Industrial Wastewater Treatment for Reuse and Discharge Alexis Nzila 1,*, Shaikh Abdur Razzak 2 and Jesse Zhu 3 1 Department of Life Sciences, King Fahd University of Petroleum and Minerals (KFUPM), P.O. Box 468, Dhahran 31261, Saudi Arabia 2 Department of Chemical Engineering, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia; [email protected] 3 Department of Chemical and Biochemical Engineering, University of Western Ontario, London, ON N6A 5B9, Canada; [email protected] * Correspondence: [email protected]; Tel.: +966-13-860-7716; Fax: +966-13-860-4277 Academic Editors: Rao Bhamidiammarri and Kiran Tota-Maharaj Received: 12 May 2016; Accepted: 9 July 2016; Published: 25 August 2016 Abstract: A promising long-term and sustainable solution to the growing scarcity of water worldwide is to recycle and reuse wastewater. In wastewater treatment plants, the biodegradation of contaminants or pollutants by harnessing microorganisms present in activated sludge is one of the most important strategies to remove organic contaminants from wastewater. However, this approach has limitations because many pollutants are not efficiently eliminated. To counterbalance the limitations, bioaugmentation has been developed and consists of adding specific and efficient pollutant-biodegrading microorganisms into a microbial community in an effort to enhance the ability of this microbial community to biodegrade contaminants. This approach has been tested for wastewater cleaning with encouraging results, but failure has also been reported, especially during scale-up. In this review, work on the bioaugmentation in the context of removal of important pollutants from industrial wastewater is summarized, with an emphasis on recalcitrant compounds, and strategies that can be used to improve the efficiency of bioaugmentation are also discussed. -
Bioaugmentation of Chlorinated Solvents
BIOAUGMENTATION FOR REMEDIATION OF CHLORINATED SOLVENTS: TECHNOLOGY DEVELOPMENT, STATUS, AND RESEARCH NEEDS October 2005 GeoSyntec Consultants TABLE OF CONTENTS LIST OF TABLES ...........................................................................................................................................III LIST OF FIGURES .........................................................................................................................................III ACRONYMNS AND ABBREVIATIONS........................................................................................................V FOREWORD...................................................................................................................................................VII EXECUTIVE SUMMARY ............................................................................................................................... IX 1. INTRODUCTION ..........................................................................................................................................1 2. EARLY DEVELOPMENT OF BIOAUGMENTATION.............................................................................5 3. RECENT PROGRESS IN CHLORINATED SOLVENT BIOREMEDIATION .....................................13 4. DEHALORESPIRATION: THE KEY PROCESS UNDERLYING CURRENT BIOAUGMENTATION PRACTICES..............................................................................................................................................................19 4.1 THE UBIQUITY CONCEPT REVISITED -
Biological Methods
Biological Methods Jerry Walsh, Jenna Bishop, Quinn Albertson, Shane Galloway, Carlos Rivera, Tom Devenney, Jeff Green Physical Mechanisms In Situ Methods Permeable Reactive Barriers Biostimulation Bioaugmentation Phytoremediation Permeable Reactive Barriers (Biobarriers) • Semi-permeable reactive media in flow path • Chemically or biologically-mediated reactions transform contaminants into non-toxic or immobile products • Hydrocarbons need to be oxidized • Chlorinated solvents and nitrate need to be reduced • Microorganisms help mediate redox reactions to gain energy and materials for synthesis Reactive Media Reactive Medium Removal Mechanism Contaminants Removed Organic Material Microbial sulfate reduction Acid mine drainage and precipitation Organic Material Microbial nitrate reduction Nitrate Oxygen/Nitrate-Releasing Microbial degradation BTEX Compounds Resting-State Microbial cometabolism Chlorinated aliphatics Microorganisms Oxidative Biodegradation • To respire electrons removed from contaminants, need electron acceptors Aerobic: • Aerobic methods Molecular Oxygen Anaerobic: • Anaerobic methods Nutrients (nitrate, sulfates, CO2, ferric iron, metal oxides, etc) • Aerobic methods are generally preferred to provide more energy to the microbes • Biochemical oxygen demands (BOD’s) often exceed available oxygen, so adding oxygen to the system can stimulate oxidative biodegradation Reductive Biodegradation • Electron donors are required, which anaerobic environments more abundantly produce • Organic matter is a well-suited electron donor for this process • This method works well for TCE, hexavalent chromium, sulfate, and nitrate contamination • Heterotrophic denitrification to remove nitrate Biostimulation • Modification of environment to stimulate existing bacteria capable of bioremediation. • Only works if correct bacteria are present. • Often done through use of phosphorous, nitrogen, carbon, and oxygen. • Chemicals usually added through injection wells. • EPA approved method. Advantages • Low Costs • Can be tailored to the specific site conditions. -
Selecting Bacteria Candidates for the Bioaugmentation of Activated Sludge to Improve the Aerobic Treatment of Landfill Leachate
water Article Selecting Bacteria Candidates for the Bioaugmentation of Activated Sludge to Improve the Aerobic Treatment of Landfill Leachate Justyna Michalska *, Artur Pi ´nski , Joanna Zur˙ and Agnieszka Mrozik Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiello´nska28, 40-032 Katowice, Poland; [email protected] (A.P.); [email protected] (J.Z.);˙ [email protected] (A.M.) * Correspondence: [email protected] Received: 6 November 2019; Accepted: 27 December 2019; Published: 1 January 2020 Abstract: In this study, a multifaceted approach for selecting the suitable candidates for bioaugmentation of activated sludge (AS) that supports leachate treatment was used. To determine the exploitation of 10 bacterial strains isolated from the various matrices for inoculating the AS contaminated with the Kalina pond leachate (KPL), their degradative potential was analyzed along with their aptitude to synthesize compounds improving remediation of pollutants in wastewater and ability to incorporate into the AS flocs. Based on their capability to degrade aromatic compounds (primarily catechol, phenol, and cresols) at a concentration of 1 mg/mL and survive in 12.5% of the KPL, Pseudomonas putida OR45a and P. putida KB3 can be considered to be the best candidates for bioaugmentation of the AS among all of the bacteria tested. Genomic analyses of these two strains revealed the presence of the genes encoding enzymes related to the metabolism of aromatic compounds. Additionally, both microorganisms exhibited a high hydrophobic propensity (above 50%) and an ability to produce biosurfactants as well as high resistance to ammonium (above 600 µg/mL) and heavy metals (especially chromium). -
Bioremediation of Groundwater: an Overview
International Journal of Applied Engineering Research ISSN 0973-4562 Volume 13, Number 24 (2018) pp. 16825-16832 © Research India Publications. http://www.ripublication.com Bioremediation of Groundwater: An Overview Shivam Mani Tripathi 1, Shri Ram2 1 ,2 Civil Engineering Department, MMMUT Gorakhpur, India Abstract can be treated on site, thus reducing exposure risks for clean- In past, we have large open area and abundant land resources up personnel, or potentially wider exposure as a result of and groundwater. But after the industrialization the use of transportation accidents. Methodology of this process is not hazardous chemicals increased due to unmanageable technically difficult, considerable experience and knowledge conditions. The chemical disposed on the ground surface & may require implementing this process, by thoroughly many other anthropogenic activities by humans like use of investigating the site and to know required condition to pesticides and oil spillage contaminated the soil and achieve. groundwater. The different type of contaminant by percolation The usual technique of remediation is to plow up through the ground reach to the aquifer and get affected which contaminated soil and take away to the site, or to cover or cap causes serious problem. We spend lot of money and use many the contaminated area. There are some drawbacks. The first technologies to extract and remediate the contamination. In method simply transport the contaminated materials which spite of different methods, bioremediation is a technology create major risks is excavation, handling, and transport of which is cost efficient and effective by using natural microbes hazardous material. It is very difficult to find the new landfill and degrades the contaminants the conditions and different sites for disposal. -
A Systems-Level Investigation of the Metabolism of Dehalococcoides Mccartyi and the Associated Microbial Community
A Systems-Level Investigation of the Metabolism of Dehalococcoides mccartyi and the Associated Microbial Community by Mohammad Ahsanul Islam A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Chemical Engineering and Applied Chemistry University of Toronto © Copyright by Mohammad Ahsanul Islam 2014 A Systems-Level Investigation of the Metabolism of Dehalococcoides mccartyi and the Associated Microbial Community Mohammad Ahsanul Islam Doctor of Philosophy Department of Chemical Engineering and Applied Chemistry University of Toronto 2014 Abstract Dehalococcoides mccartyi are a group of strictly anaerobic bacteria important for the detoxification of man-made chloro-organic solvents, most of which are ubiquitous, persistent, and often carcinogenic ground water pollutants. These bacteria exclusively conserve energy for growth from a pollutant detoxification reaction through a novel metabolic process termed organohalide respiration. However, this energy harnessing process is not well elucidated at the level of D. mccartyi metabolism. Also, the underlying reasons behind their robust and rapid growth in mixed consortia as compared to their slow and inefficient growth in pure isolates are unknown. To obtain better insight on D. mccartyi physiology and metabolism, a detailed pan- genome-scale constraint-based mathematical model of metabolism was developed. The model highlighted the energy-starved nature of these bacteria, which probably is linked to their slow growth in isolates. The model also provided a useful framework for subsequent analysis and visualization of high-throughput transcriptomic data of D. mccartyi. Apart from confirming expression of the majority genes of these bacteria, this analysis helped review the annotations of ii metabolic genes. -
CENSUS® – Reductive Dechlorination
CENSUS® – Reductive Dechlorination CENSUS Detect and quantify Dehalococcoides and other bacteria capable of reductive dechlorination Under anaerobic conditions, certain bacteria can use chlorinated ethenes Successful reductive dechlorination can be hindered by a few site-specific (PCE, TCE, DCE, and VC) as electron acceptors in a process called reductive factors that cannot be evaluated with chemical and geochemical tests including: dechlorination. The net result is the sequential dechlorination of PCE and • a lack of a key dechlorinating bacteria including Dehalococcoides, the TCE through daughter products DCE and VC to non-toxic ethene, which only known bacteria that completely dechlorinates PCE and TCE to volatilizes or can be further metabolized. non-toxic ethene • reasons for incomplete dechlorination and the accumulation of daughter PCE TCE cis-DCE VC Ethene products (DCE stall) CENSUS® provides the most direct avenue to investigate the potentials and limitations to implementing corrective action plan decisions and to target a variety of organisms involved in the reductive dechlorination pathway. Target Code Contaminants Environmental Relevance / Data Interpretation Dehalococcoides qDHC PCE, TCE, Only known group of bacteria capable of complete dechlorination of PCE and/or TCE to ethene DCE, VC Absence of Dehalococcoides suggests dechlorination of DCE and VC is improbable and accumulation of daughter products is likely The presence of Dehalococcoides even in low copy numbers indicates the potential for complete reductive dechlorination -
Microbial Community Changes in Methyl Tert-Butyl Ether (MTBE)- Contaminated Soils
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Masters Theses Graduate School 8-2004 Microbial Community Changes in Methyl tert-Butyl Ether (MTBE)- Contaminated Soils Bo Yang University of Tennessee - Knoxville Follow this and additional works at: https://trace.tennessee.edu/utk_gradthes Part of the Civil and Environmental Engineering Commons Recommended Citation Yang, Bo, "Microbial Community Changes in Methyl tert-Butyl Ether (MTBE)-Contaminated Soils. " Master's Thesis, University of Tennessee, 2004. https://trace.tennessee.edu/utk_gradthes/2223 This Thesis is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Masters Theses by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a thesis written by Bo Yang entitled "Microbial Community Changes in Methyl tert-Butyl Ether (MTBE)-Contaminated Soils." I have examined the final electronic copy of this thesis for form and content and recommend that it be accepted in partial fulfillment of the requirements for the degree of Master of Science, with a major in Environmental Engineering. Kung-Hui Chu, Major Professor We have read this thesis and recommend its acceptance: Chris D. Cox, Paul D. Frymier Accepted for the Council: Carolyn R. Hodges Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) To the Graduate Council: I am submitting herewith a thesis written by Bo Yang entitled “Microbial Community Changes in Methyl tert-Butyl Ether (MTBE)-Contaminated Soils.” I have examined the final electronic copy of this thesis for form and content and recommend that it be accepted in partial fulfillment of the requirements for the degree of Master of Science, with a major in Environmental Engineering. -
Biochemistry and Physiology of Halorespiration by Desulfitobacterium Dehalogenans
Biochemistry and Physiology of Halorespiration by Desulfitobacterium dehalogenans ..?.^TJ?*LE_ LANDBOUWCATALOGU S 0000 0807 1728 Promotor: Dr.W.M . deVo s hoogleraar in de microbiologie Co-promotoren: Dr.ir .A.J.M .Stam s universitair hoofddocent bij deleerstoelgroe p Microbiologie Dr.ir . G. Schraa universitair docent bij deleerstoelgroe p Microbiologie Stellingen 1. Halorespiratie is een weinig efficiente wijze van ademhalen. Dit proefschrift 2. Halorespiratie moet worden opgevat als verbreding en niet als specialisatie van het genus Desulfitobacterium. Dit proefschrift 3. Reductieve dehalogenases zijn geen nieuwe enzymen. 4. 16S-rRNA probes zijn minder geschikt voor het aantonen van specifieke metabole activiteiten in een complex ecosysteem. Loffler etal. (2000) AEM66 : 1369;Gottscha l &Kroonema n (2000)Bode m3 : 102 5. Het "twin-arginine" transportsysteem wordt niet goed genoeg begrepen om op basis van het voorkomen van het "twin-arginine" motief enzymen te lokaliseren. Berks etal. (2000)Mol .Microbiol .35 : 260 6. Asbesthoudende bodem is niet verontreinigd. 7. Biologische groente is een pleonasme. Stellingen behorende bij het proefschrift 'Biochemistry and physiology of halorespiration by Desulfitobacterium dehalogenans' van Bram A. van de Pas Wageningen, 6 december 2000 MJOQ^O \lZ°]0 ^ Biochemistry and Physiology of Halorespiration by Desulfitobacterium dehalogenans BramA. van de Pas Proefschrift ter verkrijging van de graad van doctor op gezag van derecto r magnificus van Wageningen Universiteit, dr. ir. L. Speelman, in het openbaar -
Changes of the Proteome and Acetylome During Transition Into the Stationary Phase in the Organohalide-Respiring Dehalococcoides Mccartyi Strain CBDB1
microorganisms Article Changes of the Proteome and Acetylome during Transition into the Stationary Phase in the Organohalide-Respiring Dehalococcoides mccartyi Strain CBDB1 Franziska Greiner-Haas 1, Martin von Bergen 2, Gary Sawers 1, Ute Lechner 1,* and Dominique Türkowsky 2,* 1 Institute of Biology/Microbiology, Martin-Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; [email protected] (F.G.-H.); [email protected] (G.S.) 2 Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research–UFZ, 04318 Leipzig, Germany; [email protected] * Correspondence: [email protected] (U.L.); [email protected] (D.T.) Abstract: The strictly anaerobic bactGIerium Dehalococcoides mccartyi obligatorily depends on organohalide respiration for energy conservation and growth. The bacterium also plays an important role in bioremediation. Since there is no guarantee of a continuous supply of halogenated substrates in its natural environment, the question arises of how D. mccartyi maintains the synthesis and activity of dehalogenating enzymes under these conditions. Acetylation is a means by which energy- restricted microorganisms can modulate and maintain protein levels and their functionality. Here, we analyzed the proteome and N"-lysine acetylome of D. mccartyi strain CBDB1 during growth with 1,2,3-trichlorobenzene as an electron acceptor. The high abundance of the membrane-localized organohalide respiration complex, consisting of the reductive dehalogenases CbrA and CbdbA80, the Citation: Greiner-Haas, F.; Bergen, uptake hydrogenase HupLS, and the organohalide respiration-associated molybdoenzyme OmeA, M.v.; Sawers, G.; Lechner, U.; was shown throughout growth. In addition, the number of acetylated proteins increased from Türkowsky, D. -
Microbial Dechlorinating Consortia & Brief Introduction to Metagenomics
Microbial Dechlorinating Consortia & Brief Introduction to Metagenomics Elizabeth A. Edwards Department of Chemical Engineering and Applied Chemistry And Cell and Systems Biology University of Toronto Centre for Applied Bioscience and Bioengineering Co-Authors and Acknowledgments Edwards lab Ivy Yang, Courtney Toth, Katherine Picott, Olivia Bulka, Fei Luo, Nadia Morson, Olivia Molenda, Mahbod Sandra Dworatzek Hajighasemi, Laura Hug, Shuiquan Tang, Marie Phil Dennis Manchester, Luz Puentes, Camilla Nesbo, Xioaming Jeff Roberts & Jen Webb Liang, Line Lomheim, Kai Wei, Jine Jine Li, Cleo Ho, Ahsan Islam, Cheryl Devine, Alfredo Perez de Mora, Anna Zila, Sarah McRae, Laurent Laquitaine, Winnie Chan, Ariel Grostern, Melanie Duhamel, Alison Waller… Dr. David Major, Evan Cox And many more Michaye McMaster & others Collaborators Frank Löffler (U. Tenn) Krishna Mahadevan (U of Toronto) Barb Sherwood Lollar, Brent Sleep (U of Toronto) Alfred Spormann (Stanford) Ruth Richardson & Stephen Zinder (Cornell) Lorenz Adrian (UFZ); Craig Criddle (Stanford) 1 Fate of contaminants in the environment: role of Biology CF TCE spill Typically Dissolved plume of oxygen contaminant Clay lens becomes depleted Groundwater Flow Impermeable layer Bioremediation Bioremediation: the remediation (clean up) of contaminated sites (soil, sediment, groundwater) using microorganisms in an engineered system • ex situ (on-site): in above-ground bioreactors • in situ (in-place): the subsurface is the bioreactor • Biostimulation vs. Bioaugmentation Three challenges: 1) Mixing