DOCSLIB.ORG

Final Report Modeling and Decision Support Tools Based on the Effects of Sediment Geochemistry and Microbial Populations on Contaminant Reactions in Sediments

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Final Report Modeling and Decision Support Tools Based on the Effects of Sediment Geochemistry and Microbial Populations on Contaminant Reactions in Sediments Final Report Modeling and Decision Support Tools Based on the Effects of Sediment Geochemistry and Microbial Populations on Contaminant Reactions in Sediments SERDP Project ER-1495 September 2011 Jeanne M. VanBriesen Carnegie Mellon University Todd Bridges U.S. Army Engineer Research and Development Center (ERDC) Table of Contents Abstract ......................................................................................................................................... iii Executive Summary ..................................................................................................................... iv List of Acronyms ......................................................................................................................... vii List of Figures ............................................................................................................................... ix List of Tables ................................................................................................................................ xi Acknowledgments ....................................................................................................................... xii 1 Objectives .................................................................................................................................. 1 2 Background ............................................................................................................................... 2 2.1 Fundamentals of PCBs ........................................................................................................ 3 2.2 Microbial Transformation of PCBs .................................................................................... 5 2.2.1 PCB Dechlorinating Microorganisms ....................................................................... 6 2.2.2 Factors Affecting PCB Dechlorination ..................................................................... 7 2.3 PCB Dechlorination Pathways and Processes .................................................................... 7 3 Materials and Methods .......................................................................................................... 11 3.1 Site Selection and Initial Characterization ........................................................................ 12 3.1.1 The Grasse River ..................................................................................................... 13 3.1.2 The Hudson River ................................................................................................... 13 3.2 Core Characterization ....................................................................................................... 13 3.3 Grab Sample Geochemical Analysis ................................................................................ 14 3.4 Congener-Specific PCB Analysis of Sediments ............................................................... 14 3.4.1 Extraction of PCBs from the Grab and Core 18M Sediment Samples ................... 14 3.4.2 Congener Specific PCB Analysis with the GC-µECD Method .............................. 14 3.5 Molecular Microbiological Analyses ................................................................................ 15 3.5.1 Genomic DNA Extraction....................................................................................... 16 3.5.2 Microbial Community Profiles by PCR-DGGE Analyses ...................................... 16 3.5.3 Clone Library for Bacteria in Core Segments ......................................................... 18 3.5.4 Quantitative Polymerase Chain Reaction (Q-PCR) ................................................ 18 3.6 Computational and Statistical Analyses Methods ............................................................. 19 3.6.1 Molar Dechlorination Product Ratio (MDPR) ........................................................ 19 3.6.2 Identification of Missing Pathways in Eight Processes .......................................... 20 3.6.3 Bayes Monte Carlo (BMC) Method for Process Occurrence ................................. 20 3.6.4 Decision Support Modeling Methods ..................................................................... 22 3.7 Microcosm Study Methods ............................................................................................... 22 3.7.1 Selection of PCB Congeners ................................................................................... 22 3.7.2 Sediment Characterization for Microcosm Preparation .......................................... 23 3.7.3 Preparation of PCB Spiked Sediments ................................................................... 24 3.7.3.1 Prepare the PCB Mixture ................................................................................... 24 3.7.3.2 Prepare the Spiked Sediment .............................................................................. 29 3.7.3.3 Prepare the Microbial Media .............................................................................. 29 3.7.3.4 Assemble the Microcosms ................................................................................. 29 3.7.4 Microcosm Sampling and Analysis ........................................................................ 30 i 3.7.4.1 Iron and Sulfide Analysis ................................................................................... 31 3.7.4.2 PCB Analysis ..................................................................................................... 31 3.7.5 DNA Extraction and Microbial Community Analysis ............................................ 31 4 Results and Discussion ........................................................................................................... 32 4.1 Task A-1. Grab Sample Sediment Characterization ......................................................... 32 4.1.1 Geochemical Characterization ................................................................................ 32 4.1.2 Microbial Analysis of Hudson and Grasse Sediment ............................................. 40 4.2 Task A-2. Characterization of Sediment Cores ................................................................ 51 4.2.1 Cesium Results........................................................................................................ 51 4.2.2 TOC, Geochemical Characteristics and Total PCBs .............................................. 56 4.2.3 Evidence of Reductive Dechlorination in Sediment Cores ..................................... 58 4.2.4 Changes in Congener Distributions in Cores from 1997 to 2006 ........................... 67 4.2.5 Microbiological Analysis of Grasse River Core 18M. ........................................... 71 4.2.5.1 PCR Detection of 6 Microbial Groups from the 8 Segments of Core 18M ....... 73 4.2.5.2 Group-Specific Microbial Community Profiles by DGGE Analyses ................ 74 4.2.5.3 Bacterial Clone Libraries from Two segments of Core 18M and the Grasse River Surficial Sample .................................................................................................... 79 4.2.5.4 Quantitative PCR for Group Specific Enumeration ........................................... 81 4.3 Task B. PCB Model Development.................................................................................... 86 4.3.1 Classification Trees for the Identification of Missing Pathways in Dechlorination Processes ........................................................................................................................... 86 4.3.1.1 Bayes Monte Carlo (BMC) for Process Occurrence .......................................... 96 4.4 Task C. Microcosm Study............................................................................................... 104 4.4.1 PCB Dechlorination in Microcosms Spiked with Two PCB Mixtures ................ 104 4.4.1.1 Shifts of Tracker Pair Ratios in Microcosms Spiked with PCB Mixture 1. ..... 106 4.4.1.2 Pathways Occurred in Microcosms Spiked with PCB Mixture 1 (No Sulfate or Iron Amendment) .......................................................................................................... 107 4.4.1.2.1 Target Chlorines in Microcosms with Sulfate Amendments .................... 108 4.4.1.2.2 Altered Dechlorination Preference in the Grasse Microcosms with Iron Amendments ............................................................................................................... 108 4.4.1.2.3 Evidence of Ferric Iron Reduction in Microcosms Spiked with PCBs ..... 108 4.4.1.2.4 Evidence of Methanogenesis ..................................................................... 110 4.4.1.2.5 Quantification of Putative Dechlorinating Microorganisms ..................... 113 4.5 Task D. Decision Support Model.................................................................................... 115 5 Conclusions and Implications for Future Research .......................................................... 120 Literature Cited ........................................................................................................................ 123 Appendix A. Raw Data Appendix B. List of Scientific and Technical Publications Appendix C. Modeling and Decion Support Tools White Paper ii Abstract The proper management of polychlorinated biphenyl (PCB)-contaminated sediment has proven to be a wide-spread, complex, and costly issue. PCBs are a primary contaminant driving risk at many Department of Defense facilities. There is a need for sound science and
Load more

Recommended publications
  • Insights Into Archaeal Evolution and Symbiosis from the Genomes of a Nanoarchaeon and Its Inferred Crenarchaeal Host from Obsidian Pool, Yellowstone National Park
    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Microbiology Publications and Other Works Microbiology 4-22-2013 Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar University of Tennessee - Knoxville, [email protected] Kira S. Makarova National Institutes of Health David E. Graham University of Tennessee - Knoxville, [email protected] Yuri I. Wolf National Institutes of Health Eugene V. Koonin National Institutes of Health See next page for additional authors Follow this and additional works at: https://trace.tennessee.edu/utk_micrpubs Part of the Microbiology Commons Recommended Citation Biology Direct 2013, 8:9 doi:10.1186/1745-6150-8-9 This Article is brought to you for free and open access by the Microbiology at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Microbiology Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Authors Mircea Podar, Kira S. Makarova, David E. Graham, Yuri I. Wolf, Eugene V. Koonin, and Anna-Louise Reysenbach This article is available at TRACE: Tennessee Research and Creative Exchange: https://trace.tennessee.edu/ utk_micrpubs/44 Podar et al. Biology Direct 2013, 8:9 http://www.biology-direct.com/content/8/1/9 RESEARCH Open Access Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar1,2*, Kira S Makarova3, David E Graham1,2, Yuri I Wolf3, Eugene V Koonin3 and Anna-Louise Reysenbach4 Abstract Background: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes.
    [Show full text]
  • Nitrate Decreases Ruminal Methane Production with Slight Changes To
    Zhao et al. BMC Microbiology (2018) 18:21 https://doi.org/10.1186/s12866-018-1164-1 RESEARCH ARTICLE Open Access Nitrate decreases ruminal methane production with slight changes to ruminal methanogen composition of nitrate- adapted steers Liping Zhao, Qingxiang Meng, Yan Li, Hao Wu, Yunlong Huo, Xinzhuang Zhang and Zhenming Zhou* Abstract Background: This study was conducted to examine effects of nitrate on ruminal methane production, methanogen abundance, and composition. Six rumen-fistulated Limousin×Jinnan steers were fed diets supplemented with either 0% (0NR), 1% (1NR), or 2% (2NR) nitrate (dry matter basis) regimens in succession. Rumen fluid was taken after two-week adaptation for evaluation of in vitro methane production, methanogen abundance, and composition measurements. Results: Results showed that nitrate significantly decreased in vitro ruminal methane production at 6 h, 12 h, and 24 h (P < 0.01; P < 0.01; P = 0.01). The 1NR and 2NR regimens numerically reduced the methanogen population by 4.47% and 25.82% respectively. However, there was no significant difference observed between treatments. The alpha and beta diversity of the methanogen community was not significantly changed by nitrate either. However, the relative abundance of the methanogen genera was greatly changed. Methanosphaera (PL = 0.0033) and Methanimicrococcus (PL = 0.0113) abundance increased linearly commensurate with increasing nitration levels, while Methanoplanus abundance was significantly decreased (PL = 0.0013). The population of Methanoculleus, the least frequently identified genus in this study, exhibited quadratic growth from 0% to 2% when nitrate was added (PQ = 0.0140). Conclusions: Correlation analysis found that methane reduction was significantly related to Methanobrevibacter and Methanoplanus abundance, and negatively correlated with Methanosphaera and Methanimicrococcus abundance.
    [Show full text]
  • Methanogens Diversity During Anaerobic Sewage Sludge Stabilization and the Effect of Temperature
    processes Article Methanogens Diversity during Anaerobic Sewage Sludge Stabilization and the Effect of Temperature Tomáš Vítˇez 1,2, David Novák 3, Jan Lochman 3,* and Monika Vítˇezová 1,* 1 Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; [email protected] 2 Department of Agricultural, Food and Environmental Engineering, Faculty of AgriSciences, Mendel University, 61300 Brno, Czech Republic 3 Department of Biochemistry, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; [email protected] * Correspondence: [email protected] (J.L.); [email protected] (M.V.); Tel.: +420-549-495-602 (J.L.); Tel.: +420-549-497-177 (M.V.) Received: 29 June 2020; Accepted: 10 July 2020; Published: 12 July 2020 Abstract: Anaerobic sludge stabilization is a commonly used technology. Most fermenters are operated at a mesophilic temperature regime. Modern trends in waste management aim to minimize waste generation. One of the strategies can be achieved by anaerobically stabilizing the sludge by raising the temperature. Higher temperatures will allow faster decomposition of organic matter, shortening the retention time, and increasing biogas production. This work is focused on the description of changes in the community of methanogenic microorganisms at different temperatures during the sludge stabilization. At higher temperatures, biogas contained a higher percentage of methane, however, there was an undesirable accumulation of ammonia in the fermenter. Representatives of the hydrogenotrophic genus Methanoliea were described at all temperatures tested. At temperatures up to 50 ◦C, a significant proportion of methanogens were also formed by acetoclastic representatives of Methanosaeta sp. and acetoclastic representatives of the order Methanosarcinales.
    [Show full text]
  • Chlorate Reduction by an Acetogenic Bacterium, Sporomusa Sp., Isolated from an Underground Gas Storage
    Appl Microbiol Biotechnol (2010) 88:595–603 DOI 10.1007/s00253-010-2788-8 ENVIRONMENTAL BIOTECHNOLOGY (Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage Melike Balk & Farrakh Mehboob & Antonie H. van Gelder & W. Irene C. Rijpstra & Jaap S. Sinninghe Damsté & Alfons J. M. Stams Received: 12 March 2010 /Revised: 16 July 2010 /Accepted: 16 July 2010 /Published online: 3 August 2010 # The Author(s) 2010. This article is published with open access at Springerlink.com Abstract A mesophilic bacterium, strain An4, was isolated Keywords Sporomusa sp. Perchlorate . from an underground gas storage reservoir with methanol Underground gas storage as substrate and perchlorate as electron acceptor. Cells were Gram-negative, spore-forming, straight to curved rods, 0.5– 0.8 μm in diameter, and 2–8 μm in length, growing as Introduction single cells or in pairs. The cells grew optimally at 37°C, and the pH optimum was around 7. Strain An4 converted Perchlorate and chlorate are used in a wide range of various alcohols, organic acids, fructose, acetoin, and applications. Chlorate is used as an herbicide or defoliant. H2/CO2 to acetate, usually as the only product. Succinate Perchlorate salts have been manufactured in large quantities was decarboxylated to propionate. The isolate was able to and used as ingredients in solid rocket fuels, highway safety respire with (per)chlorate, nitrate, and CO2. The G+C flares, air bag inflators, fireworks, and matches (Renner content of the DNA was 42.6 mol%. Based on the 16S 1998; Logan 2001; Motzer 2001). Perchlorate is chemically rRNA gene sequence analysis, strain An4 was most closely very stable and has low reactivity even in highly reducing related to Sporomusa ovata (98% similarity).
    [Show full text]
  • Repeated Anaerobic Microbial Redox Cycling of Iron †
    APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Sept. 2011, p. 6036–6042 Vol. 77, No. 17 0099-2240/11/$12.00 doi:10.1128/AEM.00276-11 Copyright © 2011, American Society for Microbiology. All Rights Reserved. Repeated Anaerobic Microbial Redox Cycling of Ironᰔ† Aaron J. Coby,1‡ Flynn Picardal,2 Evgenya Shelobolina,1 Huifang Xu,1 and Eric E. Roden1* Department of Geoscience, University of Wisconsin, Madison, Wisconsin 53706,1 and School of Public and Environmental Affairs, Indiana University, Bloomington, Indiana 474052 Received 7 February 2011/Accepted 28 June 2011 Some nitrate- and Fe(III)-reducing microorganisms are capable of oxidizing Fe(II) with nitrate as the electron acceptor. This enzymatic pathway may facilitate the development of anaerobic microbial communities that take advantage of the energy available during Fe-N redox oscillations. We examined this phenomenon in synthetic Fe(III) oxide (nanocrystalline goethite) suspensions inoculated with microflora from freshwater river floodplain sediments. Nitrate and acetate were added at alternate intervals in order to induce repeated cycles of microbial Fe(III) reduction and nitrate-dependent Fe(II) oxidation. Addition of nitrate to reduced, acetate- depleted suspensions resulted in rapid Fe(II) oxidation and accumulation of ammonium. High-resolution transmission electron microscopic analysis of material from Fe redox cycling reactors showed amorphous coatings on the goethite nanocrystals that were not observed in reactors operated under strictly nitrate- or Fe(III)-reducing conditions. Microbial communities associated with N and Fe redox metabolism were assessed using a combination of most-probable-number enumerations and 16S rRNA gene analysis. The nitrate- reducing and Fe(III)-reducing cultures were dominated by denitrifying Betaproteobacteria (e.g., Dechloromonas) and Fe(III)-reducing Deltaproteobacteria (Geobacter), respectively; these same taxa were dominant in the Fe cycling cultures.
    [Show full text]
  • Bacterial Community Dynamics During the Early Stages of Biofilm Formation
    Bacterial community dynamics during the early stages of biofilm formation in a chlorinated experimental drinking water distribution system: implications for drinking water discolouration DOUTERELO, I., SHARPE, Rebecca <http://orcid.org/0000-0002-2783-9215> and BOXALL, J. Available from Sheffield Hallam University Research Archive (SHURA) at: http://shura.shu.ac.uk/9517/ This document is the author deposited version. You are advised to consult the publisher's version if you wish to cite from it. Published version DOUTERELO, I., SHARPE, Rebecca and BOXALL, J. (2014). Bacterial community dynamics during the early stages of biofilm formation in a chlorinated experimental drinking water distribution system: implications for drinking water discolouration. Journal of applied microbiology, 117 (1), 286-301. Copyright and re-use policy See http://shura.shu.ac.uk/information.html Sheffield Hallam University Research Archive http://shura.shu.ac.uk Journal of Applied Microbiology ISSN 1364-5072 ORIGINAL ARTICLE Bacterial community dynamics during the early stages of biofilm formation in a chlorinated experimental drinking water distribution system: implications for drinking water discolouration I. Douterelo1, R. Sharpe2 and J. Boxall1 1 Pennine Water Group, Department of Civil and Structural Engineering, University of Sheffield, Sheffield, UK 2 School of Civil and Building Engineering, Loughborough University, Loughborough, UK Keywords Abstract 16s rRNA sequencing, bacterial community structure, biofilm development, Aims: To characterize bacterial communities during the early stages of biofilm discolouration, drinking water distribution formation and their role in water discolouration in a fully representative, systems, terminal restriction fragment length chlorinated, experimental drinking water distribution systems (DWDS). polymorphism. Methods and Results: Biofilm development was monitored in an experimental DWDS over 28 days; subsequently the system was disturbed by raising hydraulic Correspondence conditions to simulate pipe burst, cleaning or other system conditions.
    [Show full text]
  • Physiology and Biochemistry of Aromatic Hydrocarbon-Degrading Bacteria That Use Chlorate And/Or Nitrate As Electron Acceptor
    Invitation for the public defense of my thesis Physiology and biochemistry of aromatic hydrocarbon-degrading of aromatic and biochemistry Physiology bacteria that use chlorate and/or nitrate as electron acceptor as electron nitrate and/or use chlorate that bacteria Physiology and biochemistry Physiology and biochemistry of aromatic hydrocarbon-degrading of aromatic hydrocarbon- degrading bacteria that bacteria that use chlorate and/or nitrate as electron acceptor use chlorate and/or nitrate as electron acceptor The public defense of my thesis will take place in the Aula of Wageningen University (Generall Faulkesweg 1, Wageningen) on December 18 2013 at 4:00 pm. This defense is followed by a reception in Café Carré (Vijzelstraat 2, Wageningen). Margreet J. Oosterkamp J. Margreet Paranimphs Ton van Gelder ([email protected]) Aura Widjaja Margreet J. Oosterkamp ([email protected]) Marjet Oosterkamp (911 W Springfield Ave Apt 19, Urbana, IL 61801, USA; [email protected]) Omslag met flap_MJOosterkamp.indd 1 25-11-2013 5:58:31 Physiology and biochemistry of aromatic hydrocarbon-degrading bacteria that use chlorate and/or nitrate as electron acceptor Margreet J. Oosterkamp Thesis-MJOosterkamp.indd 1 25-11-2013 6:42:09 Thesis committee Thesis supervisor Prof. dr. ir. A. J. M. Stams Personal Chair at the Laboratory of Microbiology Wageningen University Thesis co-supervisors Dr. C. M. Plugge Assistant Professor at the Laboratory of Microbiology Wageningen University Dr. P. J. Schaap Assistant Professor at the Laboratory of Systems and Synthetic Biology Wageningen University Other members Prof. dr. L. Dijkhuizen, University of Groningen Prof. dr. H. J. Laanbroek, University of Utrecht Prof.
    [Show full text]
  • Investigation of a Sulfur-Utilizing Perchlorate-Reducing Bacterial Consortium" (2011)
    University of Massachusetts Amherst ScholarWorks@UMass Amherst Open Access Dissertations 5-13-2011 Investigation of a Sulfur-Utilizing Perchlorate- Reducing Bacterial Consortium Teresa Anne Conneely University of Massachusetts Amherst Follow this and additional works at: https://scholarworks.umass.edu/open_access_dissertations Part of the Bacteriology Commons Recommended Citation Conneely, Teresa Anne, "Investigation of a Sulfur-Utilizing Perchlorate-Reducing Bacterial Consortium" (2011). Open Access Dissertations. 372. https://scholarworks.umass.edu/open_access_dissertations/372 This Open Access Dissertation is brought to you for free and open access by ScholarWorks@UMass Amherst. It has been accepted for inclusion in Open Access Dissertations by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact [email protected]. INVESTIGATION OF A SULFUR-UTILIZING PERCHLORATE-REDUCING BACTERIAL CONSORTIUM A Dissertation Presented by TERESA ANNE CONNEELY Submitted to the Graduate School of the University of Massachusetts Amherst in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY May 2011 Department of Microbiology © Copyright by Teresa Anne Conneely 2011 All Rights Reserved INVESTIGATION OF A SULFUR-UTILIZING PERCHLORATE-REDUCING BACTERIAL CONSORTIUM A Dissertation Presented by TERESA ANNE CONNEELY Approved as to style and content by: ____________________________________ Klaus Nüsslein, Chair ____________________________________ Jeffery Blanchard, Member ____________________________________ James F. Holden, Member ____________________________________ Sarina Ergas, Member __________________________________________ John Lopes, Department Head Department of Microbiology DEDICATION Lé grá dó mo chlann ACKNOWLEDGMENTS I would like to thank my advisor Klaus Nüsslein for inviting me to join his lab, introducing me to microbial ecology and guiding me on my research path and goal of providing clean water through microbiology. Thank you to all my committee members throughout my Ph.D.
    [Show full text]
  • The Genome Sequence of Methanohalophilus Mahii SLPT
    Hindawi Publishing Corporation Archaea Volume 2010, Article ID 690737, 16 pages doi:10.1155/2010/690737 Research Article TheGenomeSequenceofMethanohalophilus mahii SLPT Reveals Differences in the Energy Metabolism among Members of the Methanosarcinaceae Inhabiting Freshwater and Saline Environments Stefan Spring,1 Carmen Scheuner,1 Alla Lapidus,2 Susan Lucas,2 Tijana Glavina Del Rio,2 Hope Tice,2 Alex Copeland,2 Jan-Fang Cheng,2 Feng Chen,2 Matt Nolan,2 Elizabeth Saunders,2, 3 Sam Pitluck,2 Konstantinos Liolios,2 Natalia Ivanova,2 Konstantinos Mavromatis,2 Athanasios Lykidis,2 Amrita Pati,2 Amy Chen,4 Krishna Palaniappan,4 Miriam Land,2, 5 Loren Hauser,2, 5 Yun-Juan Chang,2, 5 Cynthia D. Jeffries,2, 5 Lynne Goodwin,2, 3 John C. Detter,3 Thomas Brettin,3 Manfred Rohde,6 Markus Goker,¨ 1 Tanja Woyke, 2 Jim Bristow,2 Jonathan A. Eisen,2, 7 Victor Markowitz,4 Philip Hugenholtz,2 Nikos C. Kyrpides,2 and Hans-Peter Klenk1 1 DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545-001, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA 5 Oak Ridge National Laboratory, Oak Ridge, TN 37830-8026, USA 6 HZI—Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany 7 Davis Genome Center, University of California, Davis, CA 95817, USA Correspondence should be addressed to Stefan Spring, [email protected] and Hans-Peter Klenk, [email protected] Received 24 August 2010; Accepted 9 November 2010 Academic Editor: Valerie´ de Crecy-Lagard´ Copyright © 2010 Stefan Spring et al.
    [Show full text]
  • Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes
    GBE Different Ways of Doing the Same: Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes Dennifier Costa Brandao~ Cruz1, Lenon Lima Santana1, Alexandre Siqueira Guedes2, Jorge Teodoro de Souza3,*, and Phellippe Arthur Santos Marbach1,* 1CCAAB, Biological Sciences, Recoˆ ncavo da Bahia Federal University, Cruz das Almas, Bahia, Brazil 2Agronomy School, Federal University of Goias, Goiania,^ Goias, Brazil 3 Department of Phytopathology, Federal University of Lavras, Minas Gerais, Brazil Downloaded from https://academic.oup.com/gbe/article/11/4/1235/5345563 by guest on 27 September 2021 *Corresponding authors: E-mails: [email protected]fla.br; [email protected]. Accepted: February 16, 2019 Abstract The last two steps of the purine biosynthetic pathway may be catalyzed by different enzymes in prokaryotes. The genes that encode these enzymes include homologs of purH, purP, purO and those encoding the AICARFT and IMPCH domains of PurH, here named purV and purJ, respectively. In Bacteria, these reactions are mainly catalyzed by the domains AICARFT and IMPCH of PurH. In Archaea, these reactions may be carried out by PurH and also by PurP and PurO, both considered signatures of this domain and analogous to the AICARFT and IMPCH domains of PurH, respectively. These genes were searched for in 1,403 completely sequenced prokaryotic genomes publicly available. Our analyses revealed taxonomic patterns for the distribution of these genes and anticorrelations in their occurrence. The analyses of bacterial genomes revealed the existence of genes coding for PurV, PurJ, and PurO, which may no longer be considered signatures of the domain Archaea. Although highly divergent, the PurOs of Archaea and Bacteria show a high level of conservation in the amino acids of the active sites of the protein, allowing us to infer that these enzymes are analogs.
    [Show full text]
  • Microbial Community Analysis of the University of Wisconsin Oshkosh Dry Biodigester
    UNIVERSITY OF WISCONSIN SYSTEM SOLID WASTE RESEARCH PROGRAM Student Project Report Microbial Community Analysis of the University of Wisconsin Oshkosh Dry Biodigester May 2015 Student Investigator: Jessi Zimmerman Advisor: Dr. Eric Matson University of Wisconsin-Oshkosh 1 Abstract In natural environments, heterotrophic bacteria and methanogenic Archaea assist in the degradation of organic waste, which results in the production of a mixture of carbon dioxide and methane gas, together known as biogas. In the UW-Oshkosh dry anaerobic biodigester, these same naturally occurring microbial processes are utilized to benefit the University and surrounding community. Organic waste produced by local farms, grocery stores, and residential households are collected and delivered to the biodigester facility rather than being added to landfills. These waste products serve as the feedstock for biogas production. The combustible biogas is captured and used as fuel for a combined heat and power generator, which meets about 10% of the campus electricity demand and helps to heat the digester and other nearby campus facilities. The process reduces the University’s operating costs while diverting some forms of municipal waste away from landfills and provides a cleaner alternative to fossil fuels. The composition of the incoming feedstock is closely monitored as are the physicochemical conditions such as temperature, pH and hydration. These are measured at the beginning and throughout the cycle, because they can influence methane output. What is not measured (and not currently known) is how the growth of microbial species changes throughout the course of the digestion cycle. In particular, changes that may occur in methanogenic species richness and relative abundance are likely to influence biogas quality and output.
    [Show full text]
  • Enrichment and Diversity Analysis of the Thermophilic Microbes in a High Temperature Petroleum Reservoir
    African Journal of Microbiology Research Vol. 5(14), pp. 1850-1857, 18 July, 2011 Available online http://www.academicjournals.org/ajmr DOI: 10.5897/AJMR11.354 ISSN 1996-0808 ©2011 Academic Journals Full Length Research Paper Enrichment and diversity analysis of the thermophilic microbes in a high temperature petroleum reservoir Guihong Lan1,2, Zengting Li1, Hui zhang3, Changjun Zou2, Dairong Qiao1 and Yi Cao1* 1School of Life Science, Sichuan University, Chengdu 610065, China. 2School of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu 610500, China. 3Biogas Institute of Ministry of Agriculture P. R. China, Chengdu 610041, China. Accepted 1 June, 2011 Thermophilic microbial diversity in production water from a high temperature, water-flooded petroleum reservoir of an offshore oilfield in China was characterized by enrichment and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis. Six different function enrichment cultures were cultivated one year, at 75°C DGGE and sequence analyses of 16S rRNA gene fragments were used to assess the thermophilic microbial diversity. A total of 27 bacterial and 9 archaeal DGGE bands were excised and sequenced. Phylogenetic analysis of these sequences indicated that 21 bacterial and 7 archaeal phylotypes were affiliated with thermophilic microbe. The bacterial sequences were mainly bonged to the genera Fervidobacterium, Thermotoga, Dictyoglomus, Symbiobacterium, Moorella, Thermoanaerobacter, Desulfotomaculum, Thermosyntropha, Coprothermobacter, Caloramator, Thermacetogenium, and the archaeal phylogypes were represented in the genera Geoglobus and Thermococcus, Methanomethylovorans, Methanothermobacter Methanoculleus and Methanosaeta. So many thermophiles were detected suggesting that they might be common habitants in high-temperature petroleum reservoirs. The results of this work provide further insight into the thermophilic composition of microbial communities in high temperature petroleum reservoirs.
    [Show full text]