DOCSLIB.ORG

Virus Inactivation Utilising Naturally Occurring Enzymes in Wastewater

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Virus Inactivation Utilising Naturally Occurring Enzymes in Wastewater Virus inactivation utilising naturally occurring enzymes in wastewater Amanda Rachel Inglis School of Physical and Chemical Sciences University of Canterbury This dissertation is submitted for the degree of Doctor of Philosophy 2018 For Mum and Dad ii I would like to acknowledge my supervisors, Dr. Louise Weaver, Matthew Ashworth and Professor Emily Parker. Without all of your encouragement, input and advice I would not have made it to this point! I would also like to thank the whole groundwater team at ESR, especially Judith, Bronwyn, Phil, and Lee for their day to day support and distractions. Thanks also go to Dr. Sarah Masters in the Chemistry Department at UC for all of the sage advice and support she supplied me with. This project would not have been possible if it was not for the funding supplied by ESR and Scholarships awarded by ESR, the Chemistry Department at UC and the Biomolecular Interaction Centre at UC. Abstract Adequate sewage treatment is vital for maintaining New Zealand’s economy as well as offering economic and sustainable methods of treating wastewater globally. Effective treatment is required to protect both public health and the environment from anthropogenic activities. Pathogen removal mechanisms are largely unknown and are likely to be complex due to the diverse environment. The purpose of this study was the investigation of natural virus inactivation in waste stabilisation ponds. By investigating these complex mechanisms, particularly the enzymatic virus removal, we can develop models of pathogen removal and increase the knowledge of these processes to enable the efficient, low-cost, running of waste stabilisation ponds. A laboratory-scale waste stabilisation pond system was developed in order to investigate pathogen behaviour in the wastewater matrix. The laboratory-scale WSP system was combined with enzyme assays, viral enumeration, and genomic sequencing to investigate the bacterial communities present in wastewater and their potential production of enzymes involved in virus inactivation. It was determined that the bacterial communities in laboratory-scale and full-scale WSPs were compositionally similar, with a shared core microbiome. The bacterial abundance and functions associated with the bacteria varied in response to pond properties, while enzyme activity leads to reduced viral concentrations. Sequencing, physiochemical properties, and microbial pathogen reduction indicated a successful laboratory-scale WSP was developed. Human enteric virus concentration was reduced in the presence of extracellular enzymes present in wastewater, indicating a possible alternative for virus removal than expensive chlorination or UV. Contents Contents iv List of Figures xi List of Tables xiv 1 Introduction 17 1.1 Research Gaps . 19 1.2 Research objectives . 20 2 Literature review 21 2.1 Wastewater . 22 2.2 Managing the spread of disease . 23 2.3 Waste stabilisation ponds . 25 2.3.1 Treatment aims . 26 2.3.1.1 Pre-treatment . 28 2.3.1.2 Primary treatment . 28 2.3.1.3 Secondary treatment . 31 Contents v 2.3.1.4 Tertiary treatment . 32 2.3.2 Disinfection potential . 34 2.3.3 Effluent fate . 37 2.3.4 WSP biological community . 39 2.3.4.1 Bacteria in WSPs . 39 2.3.4.2 Algae in WSPs . 43 2.3.4.3 Protozoa and Metazoa in WSPs . 44 2.3.5 Pathogenic community . 47 2.3.5.1 Protozoan pathogens in WSPs . 47 2.3.5.2 Microbial pathogens in WSPs . 49 2.3.5.3 Viruses in WSPs . 51 2.3.6 Pathogen detection . 55 2.3.6.1 Indicator organisms . 56 2.3.6.2 Use of MS2 for enteric virus monitoring . 59 2.4 Monitoring wastewater treatment . 61 2.4.1 Parameters for defining successful treatment . 66 2.4.2 Design manuals . 68 2.5 Model wastewater systems . 69 3 Methods 76 3.1 Full-scale sample site and sampling methods . 76 3.2 Physicochemical parameters . 78 Contents vi 3.3 Total solids . 78 3.4 Bacterial plating . 79 3.5 Bacteriophage plaque assay . 82 3.6 Enzyme assays . 83 3.6.1 Enzyme inhibition . 87 3.6.2 Heat inactivation . 88 3.7 Protein determination . 88 3.7.1 Lowry protein assay . 88 3.8 Enterovirus end-point titration assay . 89 3.8.1 Preparation of stock echovirus . 91 3.9 Viral spike . 91 3.10 Sample preparation . 91 3.10.1 Filtration . 92 3.10.2 Protein concentration . 93 3.10.3 Chloroform extraction . 93 3.10.4 Solid phase extraction . 93 3.11 Mass spectrometry . 94 3.12 Bacterial and enzyme culture . 95 3.13 Pond design . 97 3.14 Sequencing . 97 3.14.1 Data analysis and storage . 98 3.15 Statistics . 101 Contents vii 4 Laboratory-scale waste stabilisation pond development 102 4.1 Introduction . 102 4.2 Methods . 104 4.2.1 Pond construction . 104 4.2.1.1 Pond set-up . 106 4.2.2 Monitoring and sample collection . 107 4.2.3 Bacterial plating . 108 4.2.4 Viral spike and enumeration . 108 4.2.5 Statistical analysis . 108 4.3 Results and Discussion . 109 4.3.1 Physicochemical fluctuations . 109 4.3.2 Microbial behaviour and survival . 114 4.3.3 Virus behaviour and survival . 117 4.4 Summary . 120 5 Enzyme activity in waste stabilisation pond wastewater and virus survival 122 5.1 Introduction . 122 5.2 Methods . 123 5.2.1 Sample collection . 124 5.2.2 Enzyme assays . 124 5.2.3 Viral spike and detection . 124 5.2.4 Enzyme inhibition . 125 Contents viii 5.2.5 Filtration . 125 5.2.6 Statistics . 125 5.3 Results and Discussion . 126 5.3.1 Enzyme activity in laboratory-scale WSP . 126 5.3.2 Enzyme activity in full-scale WSP fractions . 127 5.3.3 Enzymatic inactivation of viruses . 133 5.3.4 Enzyme activity in presence of virus . 138 5.4 Summary . 140 6 Enzyme production capabilities of bacterial communities in WSPs 142 6.1 Introduction . 142 6.2 Methods . 145 6.2.1 Sample sites . 145 6.2.2 Sequencing . 146 6.2.3 Mass spectrometry . 147 6.2.4 Statistics . 147 6.3 Results and Discussion . 148 6.3.1 Targeted sequencing . 148 6.3.2 Shotgun sequencing . 153 6.3.3 Pathogenic bacteria in WSPs . 155 6.3.4 Metadata correlation . 157 6.3.5 Functional categorisation . 159 Contents ix 6.3.5.1 Targeted sequence analysis . 159 6.3.5.2 Shotgun sequence analysis . 161 6.3.6 Potential enzymes produced . 163 6.4 Summary . 167 7 Conclusions and future work considerations 168 7.1 Development of a laboratory-scale WSP system for the investigation of virus survival and inactivation . 168 7.2 Enzyme activity and virus survival . 169 7.3 Microbial diversity and enzyme production in WSPs . 169 7.4 Future work . 170 References 173 A Pond design equations 232 A.1 Laboratory-scale design . 232 A.2 Design process . 236 A.3 Design results . ..
Load more

Recommended publications
  • Denitrification Process Enhancement and Diversity of the Denitrifying
    energies Article Denitrification Process Enhancement and Diversity of the Denitrifying Community in the Full Scale Activated Sludge System after Adaptation to Fusel Oil Przemysław Kowal 1 , Sławomir Ciesielski 2,* , Jeremiah Otieno 1, Joanna Barbara Majtacz 1, Krzysztof Czerwionka 1 and Jacek M ˛akinia 1 1 Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland; [email protected] (P.K.); [email protected] (J.O.); [email protected] (J.B.M.); [email protected] (K.C.); [email protected] (J.M.) 2 Department of Environmental Biotechnology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, ul. Słoneczna 45G, 10-709 Olsztyn, Poland * Correspondence: [email protected] Abstract: Implementation of anaerobic digestion of primary sludge in modern wastewater treat- ment plants (WWTPs) limits the availability of organic carbon for denitrification in conventional nitrification-denitrification (N/DN) systems. In order to ensure efficient denitrification, dosage of the external carbon source is commonly undertaken. However, application of commercial products, such us ethanol or acetate, greatly increases operational costs. As such, inexpensive and efficient alternative carbon sources are strongly desirable. In this study, the use of the fusel oil, a by-product from the distillery industry, was validated in terms of the denitrification process enhancement and Citation: Kowal, P.; Ciesielski, S.; impact on the activated sludge bacterial community structure. The experiment was conducted at a Otieno, J.; Majtacz, J.B.; Czerwionka, full scale biological nutrient removal facility (210,000 PE), in the set of the two technological lines: the K.; M ˛akinia,J.
    [Show full text]
  • Identification of N2-Fixing Plant-And Fungus-Associated Azoarcus
    APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Nov. 1997, p. 4331–4339 Vol. 63, No. 11 0099-2240/97/$04.0010 Copyright © 1997, American Society for Microbiology Identification of N2-Fixing Plant- and Fungus-Associated Azoarcus Species by PCR-Based Genomic Fingerprints THOMAS HUREK, BIANCA WAGNER, AND BARBARA REINHOLD-HUREK* Max-Planck-Institut fu¨r Terrestrische Mikrobiologie, Arbeitsgruppe Symbioseforschung, D-35043 Marburg, Germany Received 14 February 1997/Accepted 30 August 1997 Most species of the diazotrophic Proteobacteria Azoarcus spp. occur in association with grass roots, while A. tolulyticus and A. evansii are soil bacteria not associated with a plant host. To facilitate species identification and strain comparison, we developed a protocol for PCR-generated genomic fingerprints, using an automated sequencer for fragment analysis. Commonly used primers targeted to REP (repetitive extragenic palindromic) and ERIC (enterobacterial repetitive intergenic consensus) sequence elements failed to amplify fragments from the two species tested. In contrast, the BOX-PCR assay (targeted to repetitive intergenic sequence elements of Streptococcus) yielded species-specific genomic fingerprints with some strain-specific differences. PCR profiles of an additional PCR assay using primers targeted to tRNA genes (tDNA-PCR, for tRNAIle) were more discriminative, allowing differentiation at species-specific (for two species) or infraspecies-specific level. Our protocol of several consecutive PCR assays consisted of 16S ribosomal DNA (rDNA)-targeted, genus- specific
    [Show full text]
  • Copyright © 2018 by Boryoung Shin
    HYDROCARBON DEGRADATION UNDER CONTRASTING REDOX CONDITIONS IN SHALLOW COASTAL SEDIMENTS OF THE NORTHERN GULF OF MEXICO A Dissertation Presented to The Academic Faculty by Boryoung Shin In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Georgia Institute of Technology Georgia Institute of Technology May 2018 COPYRIGHT © 2018 BY BORYOUNG SHIN HYDROCARBON DEGRADATION UNDER CONTRASTING REDOX CONDITIONS IN SHALLOW COASTAL SEDIMENTS OF THE NORTHERN GULF OF MEXICO Approved by: Dr. Joel E. Kostka, Advisor Dr. Kuk-Jeong Chin School of Biologial Sciences Department of Biology Georgia Institute of Technology Georgia State University Dr. Martial Taillefert Dr. Karsten Zengler School of Earth and Atmospheric Sciences Department of Pediatrics Georgia Institute of Technology University of California, San Diego Dr. Thomas DiChristina School of Biological Sciences Georgia Institute of Technology Date Approved: 03/15/2018 ACKNOWLEDGEMENTS I would like to express my sincere gratitude to my advisor Prof. Joel E Kostka for the continuous support of my Ph.D studies and related research, for his patience, and immense knowledge. His guidance greatly helped me during the research and writing of this thesis. Besides my advisor, I would like to thank the rest of my thesis committee: Prof. Martial Taillefert, Prof. Thomas DiChristina, Prof. Kuk-Jeong Chin, and Prof. Karsten Zengler for their insightful comments and encouragement, but also for the hard questions which provided me with incentive to widen my research perspectives. I thank my fellow labmates for the stimulating discussions and for all of the fun we had in the last six years. Last but not the least, I would like to greatly thank my family: my parents and to my brother for supporting me spiritually throughout my whole Ph.D period and my life in general.
    [Show full text]
  • Microbial Community of a Gasworks Aquifer and Identification of Nitrate
    Water Research 132 (2018) 146e157 Contents lists available at ScienceDirect Water Research journal homepage: www.elsevier.com/locate/watres Microbial community of a gasworks aquifer and identification of nitrate-reducing Azoarcus and Georgfuchsia as key players in BTEX degradation * Martin Sperfeld a, Charlotte Rauschenbach b, Gabriele Diekert a, Sandra Studenik a, a Institute of Microbiology, Friedrich Schiller University Jena, Department of Applied and Ecological Microbiology, Philosophenweg 12, 07743 Jena, Germany ® b JENA-GEOS -Ingenieurbüro GmbH, Saalbahnhofstraße 25c, 07743 Jena, Germany article info abstract Article history: We analyzed a coal tar polluted aquifer of a former gasworks site in Thuringia (Germany) for the Received 9 August 2017 presence and function of aromatic compound-degrading bacteria (ACDB) by 16S rRNA Illumina Received in revised form sequencing, bamA clone library sequencing and cultivation attempts. The relative abundance of ACDB 18 December 2017 was highest close to the source of contamination. Up to 44% of total 16S rRNA sequences were affiliated Accepted 18 December 2017 to ACDB including genera such as Azoarcus, Georgfuchsia, Rhodoferax, Sulfuritalea (all Betaproteobacteria) Available online 20 December 2017 and Pelotomaculum (Firmicutes). Sequencing of bamA, a functional gene marker for the anaerobic benzoyl-CoA pathway, allowed further insights into electron-accepting processes in the aquifer: bamA Keywords: Environmental pollutions sequences of mainly nitrate-reducing Betaproteobacteria were abundant in all groundwater samples, Microbial communities whereas an additional sulfate-reducing and/or fermenting microbial community (Deltaproteobacteria, Bioremediation Firmicutes) was restricted to a highly contaminated, sulfate-depleted groundwater sampling well. By Box pathway conducting growth experiments with groundwater as inoculum and nitrate as electron acceptor, or- Functional gene marker ganisms related to Azoarcus spp.
    [Show full text]
  • Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota
    University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln US Department of Energy Publications U.S. Department of Energy 2010 Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota Gurdeep Rastogi South Dakota School of Mines and Technology Shariff Osman Lawrence Berkeley National Laboratory Ravi K. Kukkadapu Pacific Northwest National Laboratory, [email protected] Mark Engelhard Pacific Northwest National Laboratory Parag A. Vaishampayan California Institute of Technology See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/usdoepub Part of the Bioresource and Agricultural Engineering Commons Rastogi, Gurdeep; Osman, Shariff; Kukkadapu, Ravi K.; Engelhard, Mark; Vaishampayan, Parag A.; Andersen, Gary L.; and Sani, Rajesh K., "Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota" (2010). US Department of Energy Publications. 170. https://digitalcommons.unl.edu/usdoepub/170 This Article is brought to you for free and open access by the U.S. Department of Energy at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in US Department of Energy Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Gurdeep Rastogi, Shariff Osman, Ravi K. Kukkadapu, Mark Engelhard, Parag A. Vaishampayan, Gary L. Andersen, and Rajesh K. Sani This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/ usdoepub/170 Microb Ecol (2010) 60:539–550 DOI 10.1007/s00248-010-9657-y SOIL MICROBIOLOGY Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota Gurdeep Rastogi & Shariff Osman & Ravi Kukkadapu & Mark Engelhard & Parag A.
    [Show full text]
  • Comparative Genomics Provides Insights Into the Taxonomy of Azoarcus and Reveals Separate Origins of Nif Genes in the Proposed Azoarcus and Aromatoleum Genera
    G C A T T A C G G C A T genes Article Comparative Genomics Provides Insights into the Taxonomy of Azoarcus and Reveals Separate Origins of Nif Genes in the Proposed Azoarcus and Aromatoleum Genera Roberto Tadeu Raittz 1,*,† , Camilla Reginatto De Pierri 2,† , Marta Maluk 3 , Marcelo Bueno Batista 4, Manuel Carmona 5 , Madan Junghare 6, Helisson Faoro 7, Leonardo M. Cruz 2 , Federico Battistoni 8, Emanuel de Souza 2,Fábio de Oliveira Pedrosa 2, Wen-Ming Chen 9, Philip S. Poole 10, Ray A. Dixon 4,* and Euan K. James 3,* 1 Laboratory of Artificial Intelligence Applied to Bioinformatics, Professional and Technical Education Sector—SEPT, UFPR, Curitiba, PR 81520-260, Brazil 2 Department of Biochemistry and Molecular Biology, UFPR, Curitiba, PR 81531-980, Brazil; [email protected] (C.R.D.P.); [email protected] (L.M.C.); [email protected] (E.d.S.); [email protected] (F.d.O.P.) 3 The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK; [email protected] 4 John Innes Centre, Department of Molecular Microbiology, Norwich NR4 7UH, UK; [email protected] 5 Centro de Investigaciones Biológicas Margarita Salas-CSIC, Department of Biotechnology of Microbes and Plants, Ramiro de Maeztu 9, 28040 Madrid, Spain; [email protected] 6 Faculty of Chemistry, Biotechnology and Food Science, NMBU—Norwegian University of Life Sciences, 1430 Ås, Norway; [email protected] 7 Laboratory for Science and Technology Applied in Health, Carlos Chagas Institute, Fiocruz, Curitiba, PR 81310-020, Brazil; helisson.faoro@fiocruz.br 8 Department of Microbial Biochemistry and Genomics, IIBCE, Montevideo 11600, Uruguay; [email protected] Citation: Raittz, R.T.; Reginatto De 9 Laboratory of Microbiology, Department of Seafood Science, NKMU, Kaohsiung City 811, Taiwan; Pierri, C.; Maluk, M.; Bueno Batista, [email protected] M.; Carmona, M.; Junghare, M.; Faoro, 10 Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; H.; Cruz, L.M.; Battistoni, F.; Souza, [email protected] E.d.; et al.
    [Show full text]
  • DNA-SIP Identifies Sulfate-Reducing Clostridia As Important Toluene Degraders in Tar-Oil-Contaminated Aquifer Sediment
    The ISME Journal (2010) 4, 1314–1325 & 2010 International Society for Microbial Ecology All rights reserved 1751-7362/10 www.nature.com/ismej ORIGINAL ARTICLE DNA-SIP identifies sulfate-reducing Clostridia as important toluene degraders in tar-oil-contaminated aquifer sediment Christian Winderl, Holger Penning, Frederick von Netzer, Rainer U Meckenstock and Tillmann Lueders Institute of Groundwater Ecology, Helmholtz Zentrum Mu¨nchen—German Research Centre for Environmental Health, Neuherberg, Germany Global groundwater resources are constantly challenged by a multitude of contaminants such as aromatic hydrocarbons. Especially in anaerobic habitats, a large diversity of unrecognized microbial populations may be responsible for their degradation. Still, our present understanding of the respective microbiota and their ecophysiology is almost exclusively based on a small number of cultured organisms, mostly within the Proteobacteria. Here, by DNA-based stable isotope probing (SIP), we directly identified the most active sulfate-reducing toluene degraders in a diverse sedimentary microbial community originating from a tar-oil-contaminated aquifer at a former coal gasification plant. 13 13 On incubation of fresh sediments with C7-toluene, the production of both sulfide and CO2 was clearly coupled to the 13C-labeling of DNA of microbes related to Desulfosporosinus spp. within the Peptococcaceae (Clostridia). The screening of labeled DNA fractions also suggested a novel benzylsuccinate synthase alpha-subunit (bssA) sequence type previously only detected in the environment to be tentatively affiliated with these degraders. However, carbon flow from the contaminant into degrader DNA was only B50%, pointing toward high ratios of heterotrophic CO2-fixation during assimilation of acetyl-CoA originating from the contaminant by these degraders.
    [Show full text]
  • Diversidad De Genes Bacterianos Relacionados Con Promoción Del Crecimiento Vegetal
    Diversidad de genes bacterianos relacionados con promoción del crecimiento vegetal Miguel García Hidalgo Máster de Bioinformática y Bioestadística Microbiología, biotecnología y biología molecular Paloma Pizarro Tobías Profesora Consultora David Merino Arranz Carles Ventura Rojo Profesores responsables de la asignatura 02 de enero de 2018 Esta obra está sujeta a una licencia de Reconocimiento-NoComercial- SinObraDerivada 3.0 España de Creative Commons FICHA DEL TRABAJO FINAL Diversidad de genes bacterianos Título del trabajo: relacionados con promoción del crecimiento vegetal Nombre del autor: Miguel García Hidalgo Nombre del consultor/a: Paloma Pizarro-Tobías Nombre del PRA: David Merino Arranz y Carles Ventura Rojo Fecha de entrega (mm/aaaa): 01/2018 Titulación: Máster en Bioestadística y Bioinformática Microbiología, biotecnología y biología Área del Trabajo Final: molecular Idioma del trabajo: Castellano Phylogeny, Plant Growth Promoting Palabras clave Rhizobacteria (PGPR), Rhizosphere. Resumen del Trabajo (máximo 250 palabras): Con la finalidad, contexto de aplicación, metodología, resultados i conclusiones del trabajo. El estudio de las propiedades de las bacterias promotoras del crecimiento vegetal (Plant Growth Promoting Rhizobacteria, PGPR) ha conseguido tal avance en los últimos años que ya son consideradas como una herramienta verosímil para la mejora de suelos y la biofertilización. No obstante, para una correcta administración de bacterias en un suelo o cultivo, se deben conocer los diferentes efectos beneficiosos de cada
    [Show full text]
  • Phylogenetic Analyses of a New Group of Denitrifiers Capable of Anaerobic Growth on Toluene and Description of Azoarcus Tolulyticus Sp
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1995, p. 500-506 Vol. 45, No. 3 0020-7713/95/$04.00 + 0 Copyright 0 1995, International Union of Microbiological Societies Phylogenetic Analyses of a New Group of Denitrifiers Capable of Anaerobic Growth on Toluene and Description of Azoarcus tolulyticus sp. nov. JIZHONG ZHOU,1,2 MARCOS R. FRIES,1.2 JOANNE C. CHEE-SANFORD,3 AND JAMES M. TIEDJE17273* Center For Microbial Ecology, Department of Crop and Soil Sciences, and Department of Microbiology, Michigan State University, East Lansing, Michigan 48824-1325 To understand the phylogeny and taxonomy of eight new toluene-degrading denitrifying isolates, we per- formed a 16s rRNA sequence analysis and a gas chromatographic analysis of their cellular fatty acids and examined some of their biochemical and physiological features. These isolates had 165 rRNA sequence signatures identical to those of members of the beta subclass of the Proteobacteria.The levels of similarity were as follows: 97.9 to 99.9% among the new isolates; 91.2 to 92.4%between the new isolates and Azoarcus sp. strain S5b2; 95.3 to 96.2% between the new isolates and Azoarcus sp. strain BH72; and 94.8 to 95.3% between the new isolates and Azoarcus indigens VB32T (T = type strain). Phylogenetic trees constructed by using the distance matrix, maximum-parsimony, and maximum-likelihood methods showed that our eight denitrifying isolates form a phylogenetically coherent cluster which represents a sister lineage of the previously described Azoarcus species. Furthermore, the fatty acid profiles, the cell morphology, and several physiological and nutritional characteristics of the eight isolates and the previously described members of the genus Azoarcus were also similar.
    [Show full text]
  • Identification and Isolation of a Castellaniella Species Important During Biostimulation of an Acidic Nitrate
    APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Aug. 2007, p. 4892–4904 Vol. 73, No. 15 0099-2240/07/$08.00ϩ0 doi:10.1128/AEM.00331-07 Copyright © 2007, American Society for Microbiology. All Rights Reserved. Identification and Isolation of a Castellaniella Species Important during Biostimulation of an Acidic Nitrate- and Uranium-Contaminated Aquiferᰔ Anne M. Spain,1 Aaron D. Peacock,2 Jonathan D. Istok,3 Mostafa S. Elshahed,1† Fares Z. Najar,4 Bruce A. Roe,4 David C. White,2 and Lee R. Krumholz1* Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma1; Center for Biomarker Analysis, University of Tennessee, Knoxville, Tennessee2; Department of Civil Engineering, Oregon State University, Corvallis, Oregon3; and Advanced Center for Genome Technology, University of Oklahoma, Norman, Oklahoma4 Received 9 February 2007/Accepted 30 May 2007 Immobilization of uranium in groundwater can be achieved through microbial reduction of U(VI) to U(IV) upon electron donor addition. Microbial community structure was analyzed in ethanol-biostimulated and control sediments from a high-nitrate (>130 mM), low-pH, uranium-contaminated site in Oak Ridge, TN. Analysis of small subunit (SSU) rRNA gene clone libraries and polar lipid fatty acids from sediments revealed that biostimulation resulted in a general decrease in bacterial diversity. Specifically, biostimulation resulted in an increase in the proportion of Betaproteobacteria (10% of total clones in the control sediment versus 50 and 79% in biostimulated sediments) and a decrease in the proportion of Gammaproteobacteria and Acidobacteria. Clone libraries derived from dissimilatory nitrite reductase genes (nirK and nirS) were also dominated by clones related to Betaproteobacteria (98% and 85% of total nirK and nirS clones, respectively).
    [Show full text]
  • Ucalgary 2017 Toth Courtney.Pdf
    University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2017 Characterizing and Accelerating Methanogenic Hydrocarbon Biodegradation Toth, Courtney Toth, C. (2017). Characterizing and Accelerating Methanogenic Hydrocarbon Biodegradation (Unpublished doctoral thesis). University of Calgary, Calgary, AB. doi:10.11575/PRISM/25297 http://hdl.handle.net/11023/3980 doctoral thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca UNIVERSITY OF CALGARY Characterizing and Accelerating Methanogenic Hydrocarbon Biodegradation by Courtney Rose Afton Toth A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY GRADUATE PROGRAM IN BIOLOGICAL SCIENCES CALGARY, ALBERTA JULY, 2017 © Courtney Rose Afton Toth 2017 Abstract Microbial transformation of hydrocarbons to methane is an environmentally relevant but slow process taking place in a wide variety of electron acceptor-depleted environments, from oil reservoirs and coal deposits, to contaminated groundwater and deep sediments. Despite the prevalence of chemical evidence demonstrating methanogenic hydrocarbon
    [Show full text]
  • Expression of Extracellular Multiheme Cytochromes Discovered in A
    bioRxiv preprint doi: https://doi.org/10.1101/695007; this version posted July 8, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Expression of extracellular multiheme cytochromes discovered in a 2 betaproteobacterium during Mn(III) reduction 3 Nadia Szeinbaum1,2,5*, Brook L. Nunn3, Amanda R. Cavazos2, Sean A. Crowe3, Frank J. 4 Stewart1, Thomas J. DiChristina1, Christopher T. Reinhard2,5, and Jennifer B. Glass2,5* 5 6 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA 7 2School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA 8 3Department of Genome Sciences, University of Washington, Seattle, WA, USA 9 4Department of Microbiology & Immunology and Department of Earth, Ocean, & Atmospheric 10 Sciences, University of British Columbia, Vancouver, Canada 11 5NASA Astrobiology Institute, Alternative Earths Team, Mountain View, CA 12 13 *Corresponding author: [email protected] 14 Running title: Novel undecaheme in Betaproteobacteria 15 1 bioRxiv preprint doi: https://doi.org/10.1101/695007; this version posted July 8, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 16 Abstract: Soluble ligand-bound Mn(III) can support anaerobic microbial respiration in diverse 17 aquatic environments. Thus far, Mn(III) reduction has only been associated with certain 18 Gammaproteobacteria. Here, we characterized microbial communities enriched from Mn-replete 19 sediments of Lake Matano, Indonesia. Our results provide the first evidence for biological 20 reduction of soluble Mn(III) outside of the Gammaproteobacteria.
    [Show full text]