DOCSLIB.ORG

Universidad Autónoma De Aguascalientes. Centro De Ciencias Básicas. Doctorado En Ciencias Biológicas. “Pathogens in Biofilm

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Universidad Autónoma De Aguascalientes. Centro De Ciencias Básicas. Doctorado En Ciencias Biológicas. “Pathogens in Biofilm UNIVERSIDAD AUTÓNOMA DE AGUASCALIENTES. CENTRO DE CIENCIAS BÁSICAS. DOCTORADO EN CIENCIAS BIOLÓGICAS. “PATHOGENS IN BIOFILMS IN FARM DRINKING WATER IN AGUASCALIENTES”. Thesis submitted for obtaining the degree of "Ph.D. in Biological Sciences" for the student Abraham Loera Muro. Advisors: Ph.D. Alma Lilián Guerrero Barrera. Ph.D. Francisco Javier Avelar González. Universidad Autónoma de Aguascalientes. Ph.D. Mario Jacques. Université de Montréal. Aguascalientes, Ags., June, 2014. UNIVERSIDAD AUTÓNOMA DE AGUASCALIENTES. CENTRO DE CIENCIAS BÁSICAS. DOCTORADO EN CIENCIAS BIOLÓGICAS. TESIS. PATÓGENOS ASOCIADOS A BIOPELÍCULAS EN AGUA DE CONSUMO EN GRANJAS PORCÍCOLAS EN EL ESTADO DE AGUASCALIENTES. PRESENTA. Abraham Loera Muro. PARA OBTENER EL GRADO DE DOCTORADO EN CIENCIAS BIOLÓGICAS. TUTOR(ES). Dra. Alma Lilián Guerrero Barrera. Dr. Francisco Javier Avelar González. COMITÉ TUTORAL. Dr. Mario Jacques. Université de Montréal. Aguascalientes, Ags., Junio, 2014. ACKNOWLEDGEMENTS. To Ph.D. Alma Lilián Guerrero Barrera, for her time, supervision, encouragement and support throughout all these years. As well as, for teaching the importance of teamwork and collaboration, because as she says, "is more important to have friends than money." To Ph.D. Francisco Javier Avelar González, for his supervision, encouragement and support throughout all these years. As well as, by the confidence since we started this adventure. To Ph.D. Mario Jacques, for the fruitful supervision, discussions and his helpful suggestions during all these years. As well as, for all the support received during all the thesis and when I stayed in his laboratory in Canda. To Ph.D. Ricardo Oropeza Navarro, for the fruitful collaboration and critical comments during all these years. As well as, his help in resolving several of the problems encountered during the investigation. All my friends from the “Laboratorio de Biología Celular y Tisular” (Flor, Adriana, Mónica, Guadalupe, Victor, Mónica, Guadalupe, Samanta, Alejandra, Romi and Laurita), from “Laboratoire de Microbiologie-Pathologie, Université de Montréal” (Josée, Skander, Yannick and Jeremy) and from Ph.D. in Biological Sciences (Carmen, Alondra, Rosalía and Manuel). To UAA, represented by Mr. Rector M. in C. Mario Andrade, for all the support received from all in this institution. To CONACYT, for its financial support through the scholarship for postgraduate studies. DEDICATIONS. Dedicated to Sandra Hernández Camacho, my friend, my wife and my love, for all the support and confidence that she always had me, and because without all the support and unconditionally love, I could have never have finished this Ph.D. My parents Victor Manuel Loera Solís and María Lourdes Muro Lizárraga, for all teaching and support that they have given me throughout my life, and because they have taught me to work with honesty and perseverance to achieve any objetive in life. My brother Victor Manuel Loera Muro, for all the moments of joy that we shared and for being a role model as a brother. "As the richest soil it can not bear fruit unless it is cultivated, the mind without cultivation can not produce." Seneca. “In scientific matters, the authority of a thousand is not merit against the humble reasoning of a single individual. " Galileo Galilei. DEDICATORIA. Dedicada a Sandra Hernández Camacho, mi compañera, mi esposa y mi amor, por todo el apoyo y confianza que siempre me tuvo, y porque sin todo ese apoyo y amor que incondicionalmente me entrega a diario, jamás hubiera podido haber terminado este doctorado. A mis padres Victor Manuel Loera Solís y María Lourdes Muro Lizárraga, por todas las enseñanzas y el apoyo que me han otorgado durante toda mi vida, y porque me han enseñado a trabajar con honestidad y constancia para lograr cualquier objetivo en la vida. A mi hermano Victor Manuel Loera Muro, por todos los momentos de alegría que hemos compartido y por ser un ejemplo a seguir como hermano. “Como el suelo por más rico que sea, no puede dar fruto si no se cultiva; la mente sin cultivo tampoco puede producir”. Séneca. “En cuestiones científicas, la autoridad de un millar no es mérito frente al humilde razonamiento de un solo individuo”. Galileo Galilei. Winner photography of the fourth place in the National Scientific Photography Contest 2013 organized by CONACYT. INDEX. INDEX 1 INDEX TABLES. 5 INDEX FIGURES. 7 ABSTRACT 20 RESUMEN 23 1. ANTECEDENTS. 26 1.1 Bacterial Biofilms. 26 1.2 Development of Biofilms. 27 1.3 Structure of Biofilm. 30 1.4 Interactions in Biofilms. 35 1.5 Associations in Multi-species Biofilms. 38 1.6 Advantages of Biofilms. 39 1.7 Porcine Respiratory Disease Complex (PRDC). 44 1.8 Actinobacillus pleuropneumoniae. 44 1.9 Streptococcus suis. 49 1.10 Pasteurella multocida. 52 1.11 Bordetella bronchiseptica. 54 1.12 Haemophilus parasuis. 56 1.13 Mycoplasma hyopneumoniae. 58 2. JUSTIFICATION. 61 3. HYPHOTESIS. 63 4. OBJECTIVES. 63 4.1 General Objective. 63 4.2 Specific Objectives. 63 5. MATERIALS AND METHODS. 64 5.1 General scheme of work. 64 5.2 Protocol for sampling of swine farms. 66 1 5.2.1 Sampling of swine farms. 67 5.2.2 Statistical calculation for sampling nasal swabs. 67 5.3 Bacterial Viability Live/Dead BacLight Bacterial Viability Kit (Molecular 69 Probes). 5.4 Extraction of DNA (Sambrook & Russell (2001), with modifications). 70 5.5 Bacterial strains used for amplification, CAMP test, and growth conditions. 71 5.6 Protocol for detection of porcine respiratory pathogens by PCR 72 (Polymerase chain reaction). 5.6.1 Protocol for PCR against Actinobacillus pleuropneumoniae apxIV gene. 72 5.6.2 Protocol for PCR against Pasteurella multocida. 72 5.6.3 Protocol for PCR for Streptococcus suis. 73 5.6.4 Protocol for PCR against Bordetella bronchiseptica. 73 5.6.5 Protocol for PCR against Mycoplasma hyopneumoniae. 74 5.6.6 Protocol for PCR against Haemophilus parasuis. 74 5.6.7 Protocol for PCR with universal primers against 16S rDNA. 74 5.6.8 PCRs again 16S rDNA and apx toxin genes. 75 5.7 Protocol for Isolation of different pathogens in drinking water in swine 76 farms. 5.7.1 Isolation of A. pleuropneumoniae. 76 5.7.2 Isolation of S. suis. 77 5.7.3 Isolation of P. multocida. 77 5.7.4 Isolation of E. coli. 78 5.7.4.1 Confirmation of E. coli by PCR. 78 5.8 Antimicrobial Susceptibility Testing. 79 5.8.1 Interpretation of Results. 80 5.9 Biofilms formation. 81 5.9.1 Biofilms formation assay for drinking water samples. 81 5.9.2 Biofilms formation for FISH assay for drinking water samples. 82 5.9.3 FISH assay for drinking water samples. 82 2 5.9.4 Biofilms formation for staining with Crystal Violet for drinking water 83 samples. 5.9.5 Biofilms formation directly in drinkers. 83 5.10 Scanning Electron Microscopy (SEM). 84 5.11 Swine respiratory pathogen A. pleuropneumoniae in multi-species biofilm. 84 5.11.1 Bacterial strain. 84 5.11.2 Multi-specie biofilms assay. 85 5.11.3 Colony Forming Units Assay (CFU). 87 5.11.4 Fluorescent in situ hybridization (FISH). 87 5.11.5 Confocal laser scanning microscopy (CLSM). 88 5.11.6 Enzymatic treatments of multi-species biofilms. 88 5.11.7 Measurement of NAD production by the mono and multi-species 89 biofilms. 5.11.8 A. pleuropneumoniae biofilm formation with crude cell-free 89 supernatants. 5.11.9 Scanning electron microscopy. 90 5.12 Statistical analysis. 90 6. RESULTS. 91 6.1 General screening of swine farms in the state of Aguascalientes. 91 6.2 Viability tests on samples of drinking water from swine farms. 98 6.3 General scanning and isolation of pathogens from drinking water samples 99 from swine farms. 6.4 Positive samples of A. pleuropneumoniae. 101 6.5 16S rDNA and Apx toxin sequencing of isolates of A. pleuropneumoniae 102 ApxIV positive. 6.6 Detection of A. pleuropneumoniae in biofilms in vitro and in vivo. 104 6.7Antimicrobial susceptibility testing. 109 6.8 EM analysis of biofilms formed by isolated from drinking water. 112 6.9 Analysis nonpathogenic or commensal bacteria in drinking water of swine 114 farms. 3 6.10 Multi-species biofilms analysis. 117 6.10.1 Multi-species biofilms formation with NAD supplementation. 117 6.10.2 Multi-species biofilms matrix composition with NAD supplementation. 119 6.10.3 Effect of enzymatic treatment on multi-species biofilms with NAD 120 supplementation. 6.10.4 Multi-species biofilms formation without NAD supplementation. 129 6.10.5 Multi-species biofilms matrix composition without NAD 130 supplementation. 6.10.6 Effect of enzymatic treatment on multi-species biofilms without NAD 137 supplementation. 6.10.7 Confirmation of the presence of A. pleuropneumoniae in multi-species 141 biofilms by FISH. 6.10.8 Scanning electron microscopy. 143 6.10.9 Incorporation of A. pleuropneumoniae in pre-formed biofilms in 145 conditions for S. aureus, S. suis and E. coli. 6.10.10 Measurement of NAD production by the mono and multi-species 149 biofilms. 6.10.11 A. pleuropneumoniae biofilm formation with crude cell-free 151 supernatants. 6.10.12 Multi-species biofilms formed by A. pleuropneumoniae with the E. coli 152 isolated from drinking water of swine farm. 6.11 Mobile device for obtaining biofilms directly from the environment. 154 7. DISCUSION. 156 CONCLUSIONS. 164 GLOSSARY. 166 REFERENCES. 167 APPENDIX. 189 4 TABLES INDEX. Table 1: Farms selected for analysis of associated pathogens in multispecies 66 biofilms in drinking water in the state of Aguascalientes. Table 2: Primers sequences used again apx toxins genes in this study. 75 Table 3: Primers sequences used for E. coli confirmation and phylogroup in 79 this study. Table 4: Interpretation of results for antimicrobial susceptibility testing. 81 Table 5: Total nasal swabs samples obtained in this study, total positive 92 results (per farm and total) by PCR for each pathogen searched and the percentages observed in the same.
Load more

Recommended publications
  • Community and Whole Genome Analysis of Wastewater Bacteria
    Community and Whole Genome Analysis of Wastewater Bacteria By Daniel Rice BSc(Hons) A thesis submitted in total fulfilment of the requirements for the degree of Master of Science School of Life Sciences College of Science, Health and Engineering La Trobe University Victoria Australia February 2020 1 TABLE OF CONTENTS TABLE OF CONTENTS ................................................................................................................ i LIST OF FIGURES ..................................................................................................................... iii LIST OF TABLES ....................................................................................................................... iv LIST OF ABBREVIATIONS .......................................................................................................... v STATEMENT OF AUTHORSHIP ................................................................................................vii ACKNOWLEDGEMENTS ......................................................................................................... viii SUMMARY ..............................................................................................................................ix SECTION 1: INTRODUCTION 1.1 Activated sludge process ................................................................................................... 2 1.2 Community profiling of activated sludge bacterial communities ....................................... 7 1.2.1 Phosphorous removal ..........................................................................................
    [Show full text]
  • Bioflocculation of Wastewater Organic Matter at Short Retention Times
    Bioflocculation of Wastewater Organic Matter at Short Retention Times Lena Faust Thesis committee Promotor Prof. dr. ir. H.H.M. Rijnaarts Professor, Chair Environmental Technology Wageningen University Co-promotor Dr. ir. H. Temmink Assistant professor, Sub-department of Environmental Technology Wageningen University Other members Prof. Dr A.J.M. Stams, Wageningen University Prof. Dr. I. Smets, University of Leuven, Belgium Prof. Dr. B.-M. Wilen, Chalmers University of Technology, Sweden Prof. Dr. D.C. Nijmeijer, University of Twente, The Netherlands This research was conducted under the auspices of the Graduate School SENSE (Socio- Economic and Natural Sciences of the Environment) Bioflocculation of Wastewater Organic Matter at Short Retention Times Lena Faust Thesis submitted in fulfillment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. Dr M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Wednesday 3rd of December 2014 at 1.30 p.m. in the Aula. Lena Faust Bioflocculation of Wastewater Organic Matter at Short Retention Times, 163 pages. PhD thesis, Wageningen University, Wageningen, NL (2014) With references, with summaries in English and Dutch ISBN 978-94-6257-171-6 ˮDa steh ich nun, ich armer Tor, und bin so klug als wie zuvor.ˮ Dr. Faust (in Faust I written by Johann Wolgang von Goethe) Contents 1 GENERAL INTRODUCTION ....................................................................................................................1
    [Show full text]
  • 55Th Annual W.W.O.A. Conference October 5-8, 2021 La Crosse Convention Center, La Crosse Inside This Issue… 2021- 2022 W.W.O.A
    VOL. 241, JUNE 2021 WISCONSIN WASTEWATER OPERATORS’ ASSOCIATION, INC. Aerial view of Jefferson Wastewater Treatment Plant, Jefferson, Wisconsin 55th Annual W.W.O.A. Conference October 5-8, 2021 La Crosse Convention Center, La Crosse Inside This Issue… 2021- 2022 W.W.O.A. OFFICIAL DIRECTORY • Presidents message / Page 3 Don Lintner Jenny Pagel President Director (2021) N2511 State Rd 57 Wastewater Foreman • Tribute to Tim Nennig / Page 4 New Holstein, WI 53061 City of Clintonville Cell: 920-418-3869 N9055 Cty Road M [email protected] Shiocton WI 54170 • City of Jefferson Wastewater / Page 6 Work: 715-823-7675 Rick Mealy Cell: 920-606-4634 President Elect [email protected] Independent Contractor Lab • Board meeting minutes & Regulatory Assistance April 2 and 3, 2020 / Page 17 319 Linden Lane Marc Stephanie Delavan WI 53115 Director (2020) Cell: 608-220-9457 Director of Public Works • Collection System seminars / Page 24 [email protected] Village of Valders 1522 Puritan Rd New Holstein WI 53061 Jeremy Cramer Work: 920-629-4970 • Board meeting minutes Vice President Wastewater Treatment Cell: 920-251-8100 March 19, 2020 / Page 25 Director [email protected] City of Sun Prairie Joshua Voigt 300 E Main Street • Reminder: Director (2022) Sun Prairie WI 53590 Direct Sales Representative Awards nominations / Page 26 Work: 608-825-0731 Flygt a Xylem Brand Cell: 608-235-9280 3894 Lake Drive jcramer@ Hartford WI 53027 • Troubleshooting Corner: cityofsunprairie.com Work: 262-506-2343 Zoogloea and Thauera / Page 27 Cell: 414-719-5567 [email protected] Jeff Smudde • Index of advertisers / Page 30 Past President Nate Tillis Director of Environmental Director (2022) Programs Maintenance Supervisor NEW Water (GBMSD) City of Waukesha 2231 N Quincy St.
    [Show full text]
  • DGGE) and PGR Cloning of 16S Rrna Genes
    THE UNIVERSITY OF NEW SOUTH thesis/Dissertation Sheet Surname or Family name:LE Rrst ^ I Other narne/s: Abbreviation for degree as given in the University calendar: MSc | ScliooliBiotechnolo^^^^^^ and Biomolecular ScienoBS Faculty: Science Title:Community analysis and physiological characterisation of bacterial isolates from a nitrifying membrane bioreactor Abstract This thesis focuses on the identification of early colonisers on membrane surfaces used in wastewater treatment, as well as the physiological characterisation of bacterial cultures isolated from different micro- environments of a membrane bioreactor (MBR). The bacterial community composition of early biofilms on membrane surfaces under different hydrodynamic conditions (pressurised and non-pressurised) and of the activated sludge in an MBR were examined by culture-independent, molecular-based methods of PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and PGR cloning of 16S rRNA genes. A bench-scale, nitrifying MBR treating artificial waste was employed. The hollow fibre ultrafiltration membrane was made of polypropylene with an average pore diameter of 0.04 \im. Analysis of DGGE profiles of the sessile communities on membrane surfaces revealed that Tetrasphaera elongata species were important colonisers due to their ability to bind to membrane surfaces irrespective of the hydrodynamic context and exposure time. Interactions between isolates from the bioreactor and membrane surfaces were further investigated by characterising the physiological traits important in biofilm initiation and proliferation on membrane surfaces such as motility, auto-aggregation, co-aggregation, hydrophobicity and quorum sensing. Bacterial strains were isolated from floes and supernatant phases of the activated sludge as well as from pressurised membrane surfaces. Microbacterium sp. were prevalent in all culture collections.
    [Show full text]
  • Methylated Amine-Utilising Bacteria and Microbial Nitrogen Cycling in Movile Cave
    METHYLATED AMINE-UTILISING BACTERIA AND MICROBIAL NITROGEN CYCLING IN MOVILE CAVE DANIELA WISCHER UNIVERSITY OF EAST ANGLIA PHD 2014 METHYLATED AMINE-UTILISING BACTERIA AND MICROBIAL NITROGEN CYCLING IN MOVILE CAVE A thesis submitted to the School of Environmental Sciences in fulfilment of the requirements for the degree of Doctor of Philosophy by DANIELA WISCHER in SEPTEMBER 2014 University of East Anglia, Norwich, UK This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and that use of any information derived there from must be in accordance with current UK Copyright Law. In addition, any quotation or extract must include full attribution. i Table of Contents List of Figures ............................................................................................................... vii List of Tables .................................................................................................................. xi Declaration....................................................................................................................xiii Acknowledgements ...................................................................................................... xiv Abbreviations & Definitions ......................................................................................... xv Abstract........ ................................................................................................................ xix Chapter 1. Introduction
    [Show full text]
  • First Draft Genome Sequence of a Strain Belonging to the Zoogloea Genus and Its Gene Expression in Situ Emilie E
    Muller et al. Standards in Genomic Sciences (2017) 12:64 DOI 10.1186/s40793-017-0274-y EXTENDED GENOME REPORT Open Access First draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ Emilie E. L. Muller1,3†, Shaman Narayanasamy1†, Myriam Zeimes1, Cédric C. Laczny1,4, Laura A. Lebrun1, Malte Herold1, Nathan D. Hicks2, John D. Gillece2, James M. Schupp2, Paul Keim2 and Paul Wilmes1* Abstract The Gram-negative beta-proteobacterium Zoogloea sp. LCSB751 (LMG 29444) was newly isolated from foaming activated sludge of a municipal wastewater treatment plant. Here, we describe its draft genome sequence and annotation together with a general physiological and genomic analysis, as the first sequenced representative of the Zoogloea genus. Moreover, Zoogloea sp. gene expression in its environment is described using metatranscriptomic data obtained from the same treatment plant. The presented genomic and transcriptomic information demonstrate a pronounced capacity of this genus to synthesize poly-β-hydroxyalkanoate within wastewater. Keywords: Genome assembly, Genomic features, Lipid metabolism, Metatranscriptomics, Poly-hydroxyalkanoate, Wastewater treatement plant Introduction Zoogloea species and thus, limited information is avail- Zoogloea spp. are chemoorganotrophic bacteria often able with regards to the genomic potential of the genus. found in organically enriched aquatic environments and Here we report the genome of a newly isolated Zoogloea are known to be able to accumulate intracellular gran- sp. strain as a representative of the genus, with a focus ules of poly-β-hydroxyalkanoate [1]. The combination of on its biotechnological potential in particular for the these two characteristics renders this genus particulary production of biodiesel or bioplastics.
    [Show full text]
  • UC Irvine Electronic Theses and Dissertations
    UC Irvine UC Irvine Electronic Theses and Dissertations Title Understanding of Nitrifying and Denitrifying Bacterial Population Dynamics in an Activated Sludge Process Permalink https://escholarship.org/uc/item/1bd53495 Author Wang, Tongzhou Publication Date 2014 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, IRVINE DISSERTATION Submitted in Partial Satisfaction of the Requirements for the Degree of DOCTOR OF PHILOSOPHY in Engineering by Tongzhou Wang Dissertation Committee Professor Betty H. Olson, Chair Professor Diego Rosso Professor Sunny C. Jiang 2014 © 2014 Tongzhou Wang ii To My Family ii Table of Contents Page LIST OF FIGURES .................................................................................................................. ix LIST OF TABLES .................................................................................................................... xi ACKNOWLEDGEMENTS ..................................................................................................... xii CURRICULUM VITAE ......................................................................................................... xiv ABSTRACT OF THE DISSERTATION ............................................................................... xvii Chapter 1. ................................................................................................................................ Introduction ...................................................................................................................................................
    [Show full text]
  • Universitá Di Bologna MICROBIAL ECOLOGY of BIOTECHNOLOGICAL PROCESSES
    Alma Mater Studiorum – Universitá di Bologna Dottorato di Ricerca in Scienze Biochimiche e Biotecnologiche Ciclo XXVII Settore Concorsuale 03/D1 Settore Scientifico Disciplinare CHIM/11 MICROBIAL ECOLOGY OF BIOTECHNOLOGICAL PROCESSES Presentata da: Dott.ssa Serena Fraraccio Coordinatore Dottorato Relatore Chiar.mo Prof. Chiar.mo Prof. Fabio Fava Santi Mario Spampinato Correlatori Giulio Zanaroli, Ph.D. Assoc. Prof. Ondřej Uhlík, Ph.D. Esame finale anno 2015 Abstract The investigation of phylogenetic diversity and functionality of complex microbial communities in relation to changes in the environmental conditions represents a major challenge of microbial ecology research. Nowadays, particular attention is paid to microbial communities occurring at environmental sites contaminated by recalcitrant and toxic organic compounds. Extended research has evidenced that such communities evolve some metabolic abilities leading to the partial degradation or complete mineralization of the contaminants. Determination of such biodegradation potential can be the starting point for the development of cost effective biotechnological processes for the bioremediation of contaminated matrices. This work showed how metagenomics-based microbial ecology investigations supported the choice or the development of three different bioremediation strategies. First, PCR-DGGE and PCR-cloning approaches served the molecular characterization of microbial communities enriched through sequential development stages of an aerobic cometabolic process for the treatment of groundwater
    [Show full text]
  • Evaluation of FISH for Blood Cultures Under Diagnostic Real-Life Conditions
    Original Research Paper Evaluation of FISH for Blood Cultures under Diagnostic Real-Life Conditions Annalena Reitz1, Sven Poppert2,3, Melanie Rieker4 and Hagen Frickmann5,6* 1University Hospital of the Goethe University, Frankfurt/Main, Germany 2Swiss Tropical and Public Health Institute, Basel, Switzerland 3Faculty of Medicine, University Basel, Basel, Switzerland 4MVZ Humangenetik Ulm, Ulm, Germany 5Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Hamburg, Germany 6Institute for Medical Microbiology, Virology and Hygiene, University Hospital Rostock, Rostock, Germany Received: 04 September 2018; accepted: 18 September 2018 Background: The study assessed a spectrum of previously published in-house fluorescence in-situ hybridization (FISH) probes in a combined approach regarding their diagnostic performance with incubated blood culture materials. Methods: Within a two-year interval, positive blood culture materials were assessed with Gram and FISH staining. Previously described and new FISH probes were combined to panels for Gram-positive cocci in grape-like clusters and in chains, as well as for Gram-negative rod-shaped bacteria. Covered pathogens comprised Staphylococcus spp., such as S. aureus, Micrococcus spp., Enterococcus spp., including E. faecium, E. faecalis, and E. gallinarum, Streptococcus spp., like S. pyogenes, S. agalactiae, and S. pneumoniae, Enterobacteriaceae, such as Escherichia coli, Klebsiella pneumoniae and Salmonella spp., Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Bacteroides spp. Results: A total of 955 blood culture materials were assessed with FISH. In 21 (2.2%) instances, FISH reaction led to non-interpretable results. With few exemptions, the tested FISH probes showed acceptable test characteristics even in the routine setting, with a sensitivity ranging from 28.6% (Bacteroides spp.) to 100% (6 probes) and a spec- ificity of >95% in all instances.
    [Show full text]
  • Stable Isotope Probing of Hypoxic Toluene Degradation at the Sikl ´Os
    FEMS Microbiology Ecology, 94, 2018, fiy088 doi: 10.1093/femsec/fiy088 Advance Access Publication Date: 14 May 2018 Research Article RESEARCH ARTICLE Stable isotope probing of hypoxic toluene degradation at the Siklos´ aquifer reveals prominent role of Rhodocyclaceae Andras´ Tancsics´ 1,*, Anna Roza´ Szalay2, Milan Farkas1, Tibor Benedek1, Sandor´ Szoboszlay3,Istvan´ Szabo´ 3 and Tillmann Lueders2,† 1Regional University Center of Excellence in Environmental Industry, Szent Istvan´ University, Pater´ K. u. 1., 2100 God¨ oll¨ o,˝ Hungary, 2Institute of Groundwater Ecology, Helmholtz Zentrum Munchen,¨ German Research Center for Environmental Health, Ingolstadter¨ Landstr. 1., 85764 Neuherberg, Germany and 3Department of Environmental Safety and Ecotoxicology, Szent Istvan´ University, Pater´ K. u. 1., 2100 God¨ oll¨ o,˝ Hungary ∗Corresponding author: Regional University Center of Excellence in Environmental Industry, Szent Istvan´ University, Pater´ K. u. 1., 2100 God¨ oll¨ o,˝ Hungary. Tel: +36 28 522 000;. E-mail: [email protected] One sentence summary: A combination of 16S rRNA gene amplicon sequencing and T-RFLP fingerprinting of C23O genes from SIP gradient fractions revealed the central role of degraders within the Rhodocyclaceae in hypoxic toluene degradation. Editor: Matthew Stott †Tillmann Lueders, http://orcid.org/0000-0002-9361-5009 ABSTRACT The availability of oxygen is often a limiting factor for the degradation of aromatic hydrocarbons in subsurface environments. However, while both aerobic and anaerobic degraders have been intensively studied, degradation betwixt, under micro- or hypoxic conditions has rarely been addressed. It is speculated that in environments with limited, but sustained oxygen supply, such as in the vicinity of groundwater monitoring wells, hypoxic degradation may take place.
    [Show full text]
  • NGUYEN-DISSERTATION-2017.Pdf (5.044Mb)
    © Copyright by Hang Ngoc Nguyen 2017 All Rights Reserved GRAPHENE AND GRAPHENE OXIDE TOXICITY AND IMPACT TO ENVIRONMENTAL MICROORGANISMS A Dissertation Presented To the Faculty of the Department of Civil and Environmental Engineering University of Houston In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in Environmental Engineering by Hang Ngoc Nguyen August 2017 GRAPHENE AND GRAPHENE OXIDE TOXICITY AND THE IMPACT TO ENVIRONMENTAL MICROORGANISMS _________________________________ Hang Ngoc Nguyen Approved: __________________________________________ Chair of Committee Debora F. Rodrigues, Associate Professor, Civil and Environmental Engineering University of Houston Committee Members: __________________________________________ Yandi Hu, Assistant Professor, Civil and Environmental Engineering University of Houston __________________________________________ Stacey Louie, Assistant Professor, Civil and Environmental Engineering University of Houston __________________________________________ Francisco C. Robles Hernandez, Associate Professor Department of Engineering Technology College of Technology Building University of Houston __________________________________________ Sarah L. Wallace, Aerospace Technologist, Life Science Research National Aeronautics Space Administration NASA Johnson Space Center, Houston __________________________________________ Megan L. Robertson, Assistant Professor Chemical and Biomolecular Engineering University of Houston ___________________________ _________________________________________
    [Show full text]
  • Microbial Morphology and Community Structure in a Suspended Carrier Biofilm Reactor As a Function of Substrate Loading Rates
    African Journal of Microbiology Research Vol. 4(21), pp. 2235- 2242, 4 November, 2010 Available online http://www.academicjournals.org/ajmr ISSN 1996-0808 ©2010 Academic Journals Full Length Research Paper Microbial morphology and community structure in a suspended carrier biofilm reactor as a function of substrate loading rates Fu Bo 1, 2 , Liao Xiaoyi 1, Ding Lili 1, Xu Ke 1 and Ren Hongqiang 1* 1State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, Jiangsu, China. 2Laboratory of Environmental Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, Jiangsu, China. Accepted 13 August, 2010 An aerobic suspended carrier biofilm reactor was efficient in simultaneous organic carbon and nitrogen removal, with COD removal efficiencies of 87.1–99.0% and simultaneous nitrification and denitrification (SND) efficiencies about 96.7-98.8%. The effects of substrate loading on microbial morphology and community structure were investigated by environmental scanning electron microscopy (ESEM), denaturing gel gradient electrophoresis (DGGE) and fluorescence in situ hybridization (FISH). Biofilms formed at different substrate loadings had different morphology and community structures. A higher substrate concentration resulted in denser and thinner biofilms, while a lower substrate concentration resulted in looser and thicker biofilms with significant presence of filamentous bacteria. Both sequence analysis of DGGE bands and FISH analysis indicated the dominance of β-Proteobacteria in the biofilm communities, especially Zoogloea. FISH analysis revealed that the relative abundance of β- proteobacteria ammonia oxidizing bacteria (AOB) was positively correlated with ammonium concentrations, whereas Nitrospira-like nitrite-oxidizing bacteria (NOB) were negatively affected by ammonia and nitrite concentrations.
    [Show full text]