DOCSLIB.ORG

Data Driven Hypothesis Modelling of Dehalococcoides Mccartyi

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Data Driven Hypothesis Modelling of Dehalococcoides Mccartyi DATA DRIVEN HYPOTHESIS MODELLING OF DEHALOCOCCOIDES MCCARTYI : PREDICTED BIOLOGY AND BIOMARKERS OF STRESS IN TWO MIXED MICROBIAL COMMUNITIES A Dissertation Presented to the Faculty of the Graduate School of Cornell University in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Cresten Brant Mansfeldt January 2013 © 2013 Cresten Brant Mansfeldt DATA DRIVEN HYPOTHESIS MODELLING OF DEHALOCOCCOIDES MCCARTYI : PREDICTED BIOLOGY AND BIOMARKERS OF STRESS IN TWO MIXED MICROBIAL COMMUNITIES Cresten Brant Mansfeldt, Ph. D. Cornell University, 2013 Transcriptomic and proteomic expression levels were examined in two Dehalococcoides mccartyi (DMC)-containing mixed community cultures (D2 and the commercially available KB- 1®). These reductively organodehalorespiring communities were subjected to a wide range of feeding conditions in regards to electron acceptor type, electron donor type, feeding rate, and additions of known stressors. The electron acceptors included chloroethenes, chlorophenols, and chlorobenzenes. D2- specific and genus-wide (pangenome) microarrays monitored the transcriptional response. Clustering of D2’s transcriptome formed distinct groupings of genes responding either positively, negatively, or indifferently to increased chloroethene respiration rate. The transcripts responding positively to respiration potentially participate in DMC’s incompletely described electron transport chain. Correlation analysis inferred putative relationships in the regulation of reductive dehalogenases (RDases) and small electron carriers such as glutaredoxin and thioredoxin. Differential expression comparisons across electron acceptor types also highlighted the potential role of the RDases DET1559 and pceA (DET0318) in chloro-aromatic respiration. To comprehend more fully the transcriptomic data, the Reverse Engineering/Forward SimulationTM Bayesian network inference platform predicted a sparse set of confident gene-to- gene and gene-to-condition relationships. Conditions included metabolite levels, phenotypic respiration rates, or the existence of stressors. Strong interactions were noted across the D2 and KB-1® mixed communities for a positive relationship between the S-Layer cell wall protein and a major RDase (tceA in D2 and vcrA in KB-1®) as well as a positive interaction between the hydrogenase hup and the formate dehydrogenase. Applying a network inference algorithm to the D2 and KB-1® communities’ transcriptome behavior created a data-driven predictive tool. This tool allows for hypothesis generation for hundreds of genes in the inferred network. Combining the transcriptomic with proteomic data for stress conditions allowed a targeted detection of diagnostic biomarkers. Across the stressful conditions investigated for DMC (electron donor limitation as well as solvent, oxygen, and pH stress) DnaJ and HspR (DET1411-1412) appeared up-regulated. Due to their centrality in the cell and high background noise, they may prove to be difficult in situ biomarkers. Instead, the linking of a methylglyoxal synthase (DET0146) to solvent and the superoxide dismutase operon (DET0954-0965) to oxidative stress should be pursued as potential diagnostic field site indicators. BIOGRAPHICAL SKETCH Cresten grew up in the alternatingly frozen and burning state of Minnesota. He stayed transfixed for undergrad and attended the University of Minnesota where he graduated in 2007 with a Bachelors in Civil Engineering. Following the allure of the East Coast, Cresten ended up in the hills of upstate New York, mostly because of his crazy tour guides. Ever since, science and eccentricity have suited him quite well. iii “If he was half as good as he thought he was, He would be twice as good as he was.” - Phyllis Mansfeldt (a.k.a. Grandma) About Frank Lloyd Wright. In a museum. Very loudly. (…I dedicate this to my mom, for having me). iv ACKNOWLEDGEMENTS: The stoplight outside of my lab window has kept me company through most of the writing process of this thesis. The simple controlled rhythm, the red, the green, the little blinky hand, reminds me of the pace of my graduate career and all of those I have to thank for being here and assisting me along the way. Green. Go. I am eternally in debt to those who launched me into this world. My parents serve as a great inspiration of how to approach being a human. They sacrificed substantially to ensure that my sister and I were able to lead a comfortable and productive life. Dad, the man of ink, of bass and steel, of electricity and fictional birds, thank you for teaching me how to humbly push against a world set to embarrass and cause harm. Mom, the woman in the yellow shirt, in the car and classroom, in the armor and fiery rage, thank you for teaching me compassion, rebellion, and individuality. My sister, Giliane, my comrade in-arms, my best and oldest friend, thank you for teaching me how to imagine and hope. Blinking hand. Transition’s ahead, plan. I was steered into the world of environmental engineering by numerous incredible teachers. Thank you, Mr. Enderton, for teaching the beauty surrounding mathematics. Newton sits on my shelf to this day. Thank you, Dr. Bill Arnold, for teaching such a great introduction to environmental engineering course that I end up as a dishwasher. Seriously. Thank you, Dr. Tim LaPara, for continuously challenging me and encouraging me to go to grad school. And finally, thank you Dr. Paige Novak. I would not be here without you. Yellow. Let’s be honest, speed up to make it through. I would have mentally crashed years ago were it not for the professional and personal relationships I have here at Cornell University. Often, they blur. To Dr. Ruth Richardson, thank you for taking on a young 21 year- v old. As an advisor, your mentorship and guidance have not only made me (hopefully) a better researcher, but also a better person. I can never thank you enough. To Dr. James Gossett and Dr. Stephen Zinder, thank you for always finding the time to assist me with my small to major research problems. The incredible expertise, talent, and inquisitives both of you display in all areas of life is truly stunning. To Dr. Lorenz Adrian, thank you for the incredible experience and showing me the German side of science. To Dr. Elizabeth Edwards, thank you for always providing input and generally being supportive of our lab. To Boris and Bruce at GNS Healthcare and Mike at EMSL, you guys have continuously saved me. To the PSS Posse, Annie and Gretchen, to make the complex simple, thank you. You both provided an unmatched collaborator and second family. To Ben Logsdon for his help on the networks, running long distances, and finishing the scotch; to Brian Rahm for coining PSS, mad board game and DJ skills; Laura Hug, without your continued assistance, I would have gone mad; to Jenny Nelson for chlorobenzenes and softball; to Heather Fullerton for trading shop stories of DMC and snarky comments about bands; to Annie O. and the high pitched whining machine; to Garrett, the culturing king; to Ju Khuan and Sage; to all of you, thank you for your help and input on my research. To my friends, my family away from home, to detail how much you’ve meant to me would fill far more pages than my thesis. So, in brief as this yellow is about to change, to Ben Heavner, my political ally, thank you for RoboCop. To Mike B, for the hike; Cloe for the walking tour; Sarah Short for always being right; Rick for always being wrong; Pete for the after work beers; Mark J. for the scotch; Howarth for being a pack of flying invisible space bears; Kassie for the Moon; Ross for Mars; Pinshane for space on the couch; Arend for space on the floor; all the micro men and women; the trivia team; the fancy poker crew; the GPSA; and all of vi Stewart Little; thank you. Rendina, you are the only one I am not going to thank. You know why. To Punita, thank you for always having space on your couch, whether it was in Ithaca or England. To Madeline, I take back my previous statement: you get no thanks as well. And to those I forgot, I am writing this at four in the morning, so I thank you for your understanding. The all red. What engineers don’t often tell you is that for a brief moment all traffic stops. Everything halts to let the chaos that remains in the intersection to clear before traffic flows again. I have found that brief peace sitting next to you, Melina. I have no idea where the traffic of life will take me next when this light changes, but I will probably figure it out sitting next to you. vii TABLE OF CONTENTS Page Biographical Sketch iii Dedication iv Acknowledgements v Table of Contents viii List of Tables xii List of Figures xiv CHAPTER 1: Introduction and Research Objectives 1 1.A. History of Chlorinated Organics 1 1.B. Discovery of Reductively Dehalogenating Organisms 3 1.C. Genome Functional Annotation 4 1.D. From Biomolecules to Biomarkers 5 1.E. Insights Gained from Analyzing Omic Datasets 6 1.F. Rationale for Research Initiative 7 1.G. Research Objectives 9 References 10 CHAPTER 2: Dehalococcoides mccartyi strain 195’s Genome-wide 15 Transcriptomic Response to a Range of Respiration Rates and Substrate Types with a Focus on the Expression of Reductive Dehalogenases. 2.A. Abstract 16 2.B. Introduction 17 2.C. Materials and Methods 20 2.C.1. Continous feed setup 20 2.C.2. Culture growth conditions 20 2.C.3. Gas chromatography monitoring 21 2.C.4. Calculation of respiration rates 22 2.C.5. Microarray design 23 2.C.6. RNA-cDNA handling for microarray monitoring 24 2.C.7. Microarray hybridization and scanning 24 2.C.8. Statistical treatment of the data set 25 2.D. Results 25 2.D.1.
Load more

Recommended publications
  • Experimental Validation of in Silico Modelpredicted Isocitrate
    Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Islam, M. Ahsanul, Anatoli Tchigvintsev, Veronica Yim, Alexei Savchenko, Alexander F. Yakunin, Radhakrishnan Mahadevan, and Elizabeth A. Edwards. “Experimental Validation of in Silico Model-Predicted Isocitrate Dehydrogenase and Phosphomannose Isomerase from Dehalococcoides Mccartyi.” Microbial Biotechnology (September 16, 2015): n/a–n/a. As Published http://dx.doi.org/10.1111/1751-7915.12315 Publisher Wiley Blackwell Version Final published version Citable link http://hdl.handle.net/1721.1/99704 Terms of Use Creative Commons Attribution Detailed Terms http://creativecommons.org/licenses/by/4.0/ bs_bs_banner Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi M. Ahsanul Islam,† Anatoli Tchigvintsev, Veronica and confirmed experimentally. Further bioinformatics Yim, Alexei Savchenko, Alexander F. Yakunin, analyses of these two protein sequences suggest Radhakrishnan Mahadevan and Elizabeth A. their affiliation to potentially novel enzyme families Edwards* within their respective larger enzyme super families. Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Introduction Canada As one of the smallest free-living organisms, Dehalococcoides mccartyi are important for their ability to Summary detoxify ubiquitous and stable groundwater pollutants Gene sequences annotated as proteins of unknown such as chlorinated ethenes and benzenes into benign or or non-specific function and hypothetical proteins less toxic compounds (Maymó-Gatell et al., 1997; Adrian account for a large fraction of most genomes. In et al., 2000; 2007a; He et al., 2003; Löffler et al., 2012).
    [Show full text]
  • 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.
    [Show full text]
  • Microbial Community and Geochemical Analyses of Trans-Trench Sediments for Understanding the Roles of Hadal Environments
    The ISME Journal (2020) 14:740–756 https://doi.org/10.1038/s41396-019-0564-z ARTICLE Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments 1 2 3,4,9 2 2,10 2 Satoshi Hiraoka ● Miho Hirai ● Yohei Matsui ● Akiko Makabe ● Hiroaki Minegishi ● Miwako Tsuda ● 3 5 5,6 7 8 2 Juliarni ● Eugenio Rastelli ● Roberto Danovaro ● Cinzia Corinaldesi ● Tomo Kitahashi ● Eiji Tasumi ● 2 2 2 1 Manabu Nishizawa ● Ken Takai ● Hidetaka Nomaki ● Takuro Nunoura Received: 9 August 2019 / Revised: 20 November 2019 / Accepted: 28 November 2019 / Published online: 11 December 2019 © The Author(s) 2019. This article is published with open access Abstract Hadal trench bottom (>6000 m below sea level) sediments harbor higher microbial cell abundance compared with adjacent abyssal plain sediments. This is supported by the accumulation of sedimentary organic matter (OM), facilitated by trench topography. However, the distribution of benthic microbes in different trench systems has not been well explored yet. Here, we carried out small subunit ribosomal RNA gene tag sequencing for 92 sediment subsamples of seven abyssal and seven hadal sediment cores collected from three trench regions in the northwest Pacific Ocean: the Japan, Izu-Ogasawara, and fi 1234567890();,: 1234567890();,: Mariana Trenches. Tag-sequencing analyses showed speci c distribution patterns of several phyla associated with oxygen and nitrate. The community structure was distinct between abyssal and hadal sediments, following geographic locations and factors represented by sediment depth. Co-occurrence network revealed six potential prokaryotic consortia that covaried across regions. Our results further support that the OM cycle is driven by hadal currents and/or rapid burial shapes microbial community structures at trench bottom sites, in addition to vertical deposition from the surface ocean.
    [Show full text]
  • 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.
    [Show full text]
  • 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
    [Show full text]
  • Evolution of the 3-Hydroxypropionate Bicycle and Recent Transfer of Anoxygenic Photosynthesis Into the Chloroflexi
    Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi Patrick M. Shiha,b,1, Lewis M. Wardc, and Woodward W. Fischerc,1 aFeedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608; bEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; and cDivision of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125 Edited by Bob B. Buchanan, University of California, Berkeley, CA, and approved August 21, 2017 (received for review June 14, 2017) Various lines of evidence from both comparative biology and the provide a hard geological constraint on these analyses, the timing geologic record make it clear that the biochemical machinery for of these evolutionary events remains relative, thus highlighting anoxygenic photosynthesis was present on early Earth and provided the uncertainty in our understanding of when and how anoxy- the evolutionary stock from which oxygenic photosynthesis evolved genic photosynthesis may have originated. ca. 2.3 billion years ago. However, the taxonomic identity of these A less recognized alternative is that anoxygenic photosynthesis early anoxygenic phototrophs is uncertain, including whether or not might have been acquired in modern bacterial clades relatively they remain extant. Several phototrophic bacterial clades are thought recently. This possibility is supported by the observation that to have evolved before oxygenic photosynthesis emerged, including anoxygenic photosynthesis often sits within a derived position in the Chloroflexi, a phylum common across a wide range of modern the phyla in which it is found (3). Moreover, it is increasingly environments. Although Chloroflexi have traditionally been thought being recognized that horizontal gene transfer (HGT) has likely to be an ancient phototrophic lineage, genomics has revealed a much played a major role in the distribution of phototrophy (8–10).
    [Show full text]
  • Anaerobic Bacteria Confirmed Plenary Speakers
    OFFICIALOFFICIAL JOURNALJOURNAL OFOF THETHE AUSTRALIAN SOCIETY FOR MICROBIOLOGY INC.INC. VolumeVolume 3636 NumberNumber 33 SeptemberSeptember 20152015 Anaerobic bacteria Confirmed Plenary speakers Professor Peter Professor Dan Assoc Prof Susan Lynch Dr Brian Conlon Professor Anna Hawkey Andersson University of California Northeastern Durbin University of Upsalla University San Francisco University, Boston Johns Hopkins Birmingham Environmental pollution Colitis, Crohn's Disease Drug discovery in Dengue and vaccines Nosocomial by antibiotics and its and Microbiome soil bacteria infection control and role in the evolution of Research antibiotic resistance resistance As with previous years, ASM 2016 will be co-run with NOW CONFIRMED! EduCon 2016: Microbiology Educators’ Conference 2016 Rubbo Oration Watch this space for more details on the scientific and Professor Anne Kelso social program, speakers, ASM Public Lecture, workshops, CEO NHMRC ASM awards, student events, travel awards, abstract deadlines and much more.. Perth, WA A vibrant and beautiful city located on the banks of the majestic Swan river. Come stay with us in WA and experience our world class wineries and restaurants, stunning national parks, beaches and much more.. www.theasm.org.au www.westernaustralia.theasm.org.au Annual Scientific Meeting and Trade Exhibition The Australian Society for Microbiology Inc. OFFICIAL JOURNAL OF THE AUSTRALIAN SOCIETY FOR MICROBIOLOGY INC. 9/397 Smith Street Fitzroy, Vic. 3065 Tel: 1300 656 423 Volume 36 Number 3 September 2015 Fax: 03 9329 1777 Email: [email protected] www.theasm.org.au Contents ABN 24 065 463 274 Vertical For Microbiology Australia Transmission 102 correspondence, see address below. Jonathan Iredell Editorial team Guest Prof. Ian Macreadie, Mrs Jo Macreadie Editorial 103 and Mrs Hayley Macreadie Anaerobic bacteria 103 Editorial Board Dena Lyras and Julian I Rood Dr Chris Burke (Chair) Dr Gary Lum Under the Prof.
    [Show full text]
  • Evolution of the 3-Hydroxypropionate Bicycle and Recent Transfer of Anoxygenic Photosynthesis Into the Chloroflexi
    Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi Patrick M. Shiha,b,1, Lewis M. Wardc, and Woodward W. Fischerc,1 aFeedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608; bEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; and cDivision of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125 Edited by Bob B. Buchanan, University of California, Berkeley, CA, and approved August 21, 2017 (received for review June 14, 2017) Various lines of evidence from both comparative biology and the provide a hard geological constraint on these analyses, the timing geologic record make it clear that the biochemical machinery for of these evolutionary events remains relative, thus highlighting anoxygenic photosynthesis was present on early Earth and provided the uncertainty in our understanding of when and how anoxy- the evolutionary stock from which oxygenic photosynthesis evolved genic photosynthesis may have originated. ca. 2.3 billion years ago. However, the taxonomic identity of these A less recognized alternative is that anoxygenic photosynthesis early anoxygenic phototrophs is uncertain, including whether or not might have been acquired in modern bacterial clades relatively they remain extant. Several phototrophic bacterial clades are thought recently. This possibility is supported by the observation that to have evolved before oxygenic photosynthesis emerged, including anoxygenic photosynthesis often sits within a derived position in the Chloroflexi, a phylum common across a wide range of modern the phyla in which it is found (3). Moreover, it is increasingly environments. Although Chloroflexi have traditionally been thought being recognized that horizontal gene transfer (HGT) has likely to be an ancient phototrophic lineage, genomics has revealed a much played a major role in the distribution of phototrophy (8–10).
    [Show full text]
  • Advances in Anaerobic Benzene Bioremediation: Microbes, Mechanisms, and Biotechnologies
    Advances in Anaerobic Benzene Bioremediation: Microbes, Mechanisms, and Biotechnologies Sandra Dworatzek, Phil Dennis and Jeff Roberts RemTech, Virtual October 15, 2020 Introduction and Acknowledgements • Sandra Dworatzek, Jennifer Webb (SiREM, Guelph, ON) • Elizabeth Edwards, Nancy Bawa, Shen Guo and Courtney Toth (University of Toronto, Toronto, ON) • Kris Bradshaw and Rachel Peters (Federated Co-operatives Ltd., Saskatoon, SK) • Krista Stevenson (Imperial Oil, Sarnia, ON) The Landscape of Hydrocarbon Bioremediation: A Lot Has Changed… Microbial bioremediation is currently the most common technology used to remediate petroleum hydrocarbons Microbial Remediation Phytoremediation Chemical Treatment Contain and Excavate Pump and Treat Other Near Cold Lake, Alberta Adapted from Elekwachi et al., 2014 (J Bioremed Biodeg 5) What Sites are Currently Being Targeted for Hydrocarbon Bioremediation? 4 Shallow Soils and Groundwater 1 2 (aerobic) Offshore Spills Ex situ Bioreactors (mostly aerobic) (mostly aerobic) 3 Tailings Ponds 5 Deeper Groundwater (aerobic and anaerobic) (intrinsically anaerobic) Groundwater Bioremediation Technologies Focusing on Anaerobic Microbial Processes Natural Attenuation Biostimulation Bioaugmentation unsaturated zone aquifer 3- PO4 sugars Plume source - 2- NO3 SO4 VFAs GW flow aquitard Bioaugmentation for anaerobic sites works! Dehalococcoides (Dhc) bioaugmentation is widely accepted to improve reductive dehalogenation of chlorinated ethenes 1 Month Post KB-1® Bioaugmentation Dhc TCE Bioaugmentation for anaerobic
    [Show full text]
  • Research Project Summary
    Division of Science, Research and Environmental Health Research Project Summary August 2016 Applying Innovative Diagnostic Tools at New Jersey Publicly Funded Sites Authors Donna E. Fennell, Ph.D.1 and Max Häggblom, Ph.D.2 Prepared By Robert Mueller, M.S. (Project Manager) 3 Abstract This project demonstrated the use of Environmental Molecular Diagnostic Tools (EMDs) for detecting microbial biodegradation of contaminants and identifying bacteria responsible for contaminant biodegradation or biotransformation at three contaminated sites in New Jersey. These sites were unique based on the contamination present, and EMDs were selected to address a particular issue at each site. EMDs is a collective term that describes a group of advanced and emerging techniques used to analyze biological and chemical characteristics of soils, sediments, groundwater, and surface water. Many of these tools were originally developed for applications in medicine, defense, and industry. Over the last decade, great advances have been made in adapting and applying EMDs for site characterization, remediation, monitoring, and closure. EMDs are important and valuable because they can provide key information not available using traditional analytical methods (e.g., groundwater analysis for volatile organic compounds). While they are intended to complement these traditional methods, EMDs can bring a new perspective to all stages in the environmental management decision-making process. As a result of this work, a bio-augmentation/bio-stimulation design was developed for an organic solvent plume at one site. At a second site, Stable Isotope Probing (SIP) was used to confirm the presence of dehalogenating organisms and bio-stimulation demonstrated rapid reductive dechlorination. Finally, aniline degrading organisms were studied using SIP.
    [Show full text]
  • 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
    [Show full text]
  • 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.
    [Show full text]