DOCSLIB.ORG

Master Document Template

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Master Document Template Copyright by Alexandra Caya 2014 The Thesis Committee for Alexandra Caya Certifies that this is the approved version of the following thesis: Characterization of the Microbial Community Aerosolized in Residential Showers APPROVED BY SUPERVISING COMMITTEE: Supervisor: Kerry Kinney Maria King Characterization of the Microbial Community Aerosolized in Residential Showers by Alexandra Caya, B.S. Thesis Presented to the Faculty of the Graduate School of The University of Texas at Austin in Partial Fulfillment of the Requirements for the Degree of Master of Science in Engineering The University of Texas at Austin May 2014 Acknowledgements Funding for this research was provided by the National Science Foundation. I would like to thank my advisor, Dr. Kerry Kinney, and our co-collaborator on this project, Dr. Maria King, for their guidance and expertise, without which this research would not have been possible. I would also like to thank Dr. Juan Pedro Maestre and Chloe Wooldridge for helping with sampling, data analysis, and a variety of other things; and Dr. Michal Ziv-El for her guidance and help with sequence processing. iv Abstract Characterization of the Microbial Community Aerosolized in Residential Showers Alexandra Caya, M.S.E. The University of Texas at Austin, 2014 Supervisor: Kerry Kinney A wide range of microorganisms are present in the tap water that reaches residential homes, including potential pathogens. Additionally, biofilms that contain potential pathogens grow in residential premise plumbing, in showerheads, and on shower- associated surfaces. Showers produce respirable droplets, and thus may aerosolize microbes from the water or from shower-associated biofilms. Inhalation of bioaerosols containing potential pathogens is an important human infection route, and previous studies have implicated showers as a source of airborne microbial infections. However, no previous studies have fully characterized the transient changes in the airborne microbial community resulting from residential shower operation. This study is the first to characterize the short-term changes in the airborne bacterial community resulting from shower operation using molecular methods. Shower aerosol samples were collected with a high-throughput bioaerosol sampler, which allowed the collection of short-duration samples to provide a time-series picture of the transient changes in the airborne microbial community during shower operation. Culture- v independent molecular methods were used to quantify the microbial aerosol loads during shower operation, and to identify the genus-level diversity and relative abundances of bacteria present in shower bioaerosols. The results of this research show that residential shower operation does result in an increase in airborne bacterial loads, and impacts the airborne bacterial community diversity. The relative abundances of many specific bacterial genera, some of which contain pathogenic species, were increased during shower operation. Overall, the airborne bacterial community during shower operation is different than the ambient, background airborne community. This research additionally compared different methods to extract DNA from short- duration, environmental bioaerosol samples. The results indicate that different extraction methods can significantly impact resultant microbial quantity and diversity estimates. An extraction method for bioaerosol samples should be chosen carefully based on the specific goals of each research project. vi Table of Contents List of Tables ......................................................................................................... ix List of Figures ..........................................................................................................x Chapter 1: Introduction ............................................................................................1 Objectives .......................................................................................................3 Scope ...............................................................................................................3 Chapter 2: Background and Literature Review .......................................................4 Pathogenic Microbes in Showers ....................................................................4 Bioaerosol Sampling .......................................................................................7 Molecular Methods for Microbial Community Characterization ...................8 DNA Extraction ............................................................................................11 Chapter 3: Characterizing the Bacterial Communities in Residential Shower Aerosols .......................................................................................................................14 3.1 Materials and Methods ............................................................................14 3.2 Results and Discussion ...........................................................................23 3.3 Conclusions .............................................................................................46 Chapter 4: Optimizing DNA Extraction Efficiency for WWC Samples ...............48 4.1 Materials and Methods ............................................................................48 4.2 Results and Discussion ...........................................................................55 4.3 Conclusions .............................................................................................66 Chapter 5: Conclusions ..........................................................................................69 Appendix A: Detailed Protocols for DNA Extraction Methods ............................71 PowerWater (PW) .........................................................................................71 PowerWater + freeze/thaw lysis (PWF) .......................................................71 PowerWater + enzyme cocktail (PWE) ........................................................71 PowerWater with modified elution (PWM) ..................................................72 PowerWater + enzyme cocktail with modified elution (PWEM) .................72 PowerSoil + chemical + enzyme (PS) ..........................................................73 vii PowerSoil + enzyme cocktail (PSE) .............................................................73 Van Burik (VB).............................................................................................74 Van Burik + freeze/thaw lysis (VBF) ...........................................................74 FastDNA SPIN kit (FS) ................................................................................74 Alkaline Lysis (AL) ......................................................................................74 Appendix B: PowerWater DNA Isolation Kit Protocol .........................................76 Appendix C: PowerSoil DNA Isolation Kit Protocol ............................................79 Appendix D: FastDNA Spin Kit Protocol .............................................................81 References ..............................................................................................................83 viii List of Tables Table 1: Drinking water source types for each residential site sampled. ...............15 Table 2: Number of each type of biological sample collected at each residential site. ...........................................................................................................15 Table 3: Equivalent number of E. coli cells per m3 of air during shower operation at each site. ............................................................................................26 Table 4: Genera with the highest relative abundances detected in Site 1 bioaerosols collected during shower operation. Each of these genera increased in relative abundance during shower operation. ...................................36 Table 5: Genera with the highest relative abundances detected in Site 2 bioaerosols collected during shower operation. Each of these genera increased in relative abundance during shower operation. ...................................36 Table 6: Genera with highest relative abundances detected in Site 3 bioaerosols collected during shower operation. The genera highlighted in red decreased in relative abundance during shower operation, while all others increased. ................................................................................37 Table 7: Summary of DNA extraction methods tested. .........................................50 Table 8: Genera with over 20% relative abundance in triplicate samples for each extraction method in the second round of extractions (FS excluded in rarefaction). .......................................................................................64 ix List of Figures Figure 1: Schematic showing sampling locations for residential showers. Sites of biofilm swabbing are marked with a red “X.” ..................................16 Figure 2: Schematic of the wetted wall cyclone bioaerosol sampler used in this study. [Figure from McFarland et al., 2010.] ..............................................18 Figure 3: qPCR standard curve used to convert CT value to equivalent concentration of E. coli cells per mL. ......................................................................19 Figure 4: Number concentration of bacterial 16S rDNA copies in each bioaerosol sample from Site 1. ...........................................................................23
Load more

Recommended publications
  • Developing a Genetic Manipulation System for the Antarctic Archaeon, Halorubrum Lacusprofundi: Investigating Acetamidase Gene Function
    www.nature.com/scientificreports OPEN Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: Received: 27 May 2016 Accepted: 16 September 2016 investigating acetamidase gene Published: 06 October 2016 function Y. Liao1, T. J. Williams1, J. C. Walsh2,3, M. Ji1, A. Poljak4, P. M. G. Curmi2, I. G. Duggin3 & R. Cavicchioli1 No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms.
    [Show full text]
  • Articles, Onomic Units (Otus) of Which Half Were Related to Bacteria Their Numbers Are Highly Variable in Both Time and Space
    Biogeosciences, 4, 115–124, 2007 www.biogeosciences.net/4/115/2007/ Biogeosciences © Author(s) 2007. This work is licensed under a Creative Commons License. Fluorescent pseudomonads isolated from Hebridean cloud and rain water produce biosurfactants but do not cause ice nucleation H. E. Ahern1, K. A. Walsh2, T. C. J. Hill2, and B. F. Moffett2 1University of East London, Romford Road, Stratford, London, UK 2Environment Agency, Wallingford, UK Received: 1 September 2006 – Published in Biogeosciences Discuss.: 4 October 2006 Revised: 11 January 2007 – Accepted: 9 February 2007 – Published: 12 February 2007 Abstract. Microorganisms were discovered in clouds over 1 Introduction 100 years ago but information on bacterial community struc- ture and function is limited. Clouds may not only be a niche There has been a resurgence of interest in microorganisms within which bacteria could thrive but they might also in- in the atmosphere due, in part, to heightened awareness of fluence dynamic processes using ice nucleating and cloud disease epidemiology. Health issues however may be less condensing abilities. Cloud and rain samples were collected important than their role in cloud and rainfall processes and from two mountains in the Outer Hebrides, NW Scotland, link to climate change. Recently it has been reported that UK. Community composition was determined using a com- there are between 1500 and 355 000 bacteria per millilitre of bination of amplified 16S ribosomal DNA restriction analy- cloud water (Sattler et al., 2001, Bauer et al., 2002 and Am- sis and sequencing. 256 clones yielded 100 operational tax- ato et al., 2005). Therefore, as with other aerosol particles, onomic units (OTUs) of which half were related to bacteria their numbers are highly variable in both time and space.
    [Show full text]
  • Doctoral Dissertation Template
    UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE ISOLATION AND CHARACTERIZATION OF NITRATE REDUCING/DENITRIFYING BACTERIA FROM TALLGRASS PRAIRIE SOILS A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By SAMER MUHAMMAD SALIM ABUBAKR Norman, Oklahoma 2012 ISOLATION AND CHARACTERIZATION OF NITRATE REDUCING/DENITRIFYING BACTERIA FROM TALLGRASS PRAIRIE SOILS A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Joseph Suflita, Chair ______________________________ Dr. Kathleen Duncan ______________________________ Dr. Lee Krumholz ______________________________ Dr. Michael McInerney ______________________________ Dr. Mark Nanny © Copyright by SAMER MUHAMMAD SALIM ABUBAKR 2012 All Rights Reserved. Acknowledgements There are several people I would like to thank for making the completion of my degree possible. I would like to thank my graduate advisor, Dr. Kathleen Duncan for her constant guidance and direction to keep my research on track which helped me to develop as a scientist. I am thankful to my other advisory committee members, Dr. Joseph Suflita, Dr. Lee Krumholz, Dr. Michael McInerney, and Dr. Mark Nanny for their constant help and support. Also, I would like to thank Dr. Victoria Parisi and Dr. Housna Mouttaki for teaching me how to use DIONEX and HPLC, Dr. Athenia Oldham for teaching me the basics of Mothur software, and to my friends Dr. Mostafa Elshahed and Dr. Fares Najar for their help and support throughout my Ph.D. program. I would like to thank the department of Microbiology and Plant Biology for giving me the opportunity to teach Introduction to Microbiology Laboratory and Fundamentals of Microbiology Laboratory, a teaching experience that I enjoyed a lot.
    [Show full text]
  • Seleksi Dan Identifikasi Secara Molekuler Bakteri Pendegradasi Insektisida Piretroid Dari Tanah
    SELEKSI DAN IDENTIFIKASI SECARA MOLEKULER BAKTERI PENDEGRADASI INSEKTISIDA PIRETROID DARI TANAH Salindri Prawitasari1, Siti Nur Jannah1*, dan Alina Akhdiya2 1Departemen Biologi, Fakultas Sains dan Matematika, Universitas Diponegoro Jl. Prof. Soedarto, SH, Tembalang, Semarang 2Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumberdaya Genetik Pertanian (BB Biogen) Bogor, Jawa Barat *Penulis korespondensi: [email protected] Abstrak Akumulasi residu insektisida pada lahan pertanian berdampak negatif bagi lingkungan dan organisme di sekitarnya. Salah satu teknologi alternatif untuk merehabilitasi lahan pertanian yang tercemar adalah dengan teknologi bioremediasi. Bioremediasi adalah teknologi untuk memecah atau menguraikan zat pencemar menjadi bahan yang kurang beracun atau tidak beracun (karbondioksida dan air) dengan memanfaatkan organisme atau produk organisme. Penelitian ini bertujuan untuk menyeleksi dan mengidentifikasi secara molekuler bakteri pendegradasi insektisida piretroid sintetik asal sampel tanah Pangalengan. Seleksi terhadap sembilan isolat bakteri tanah asal Pangalengan menggunakan medium NMS cair yang mengandung 100 ppm piretroid menghasilkan dua isolat bakteri yang memiliki kemampuan terbaik dalam mendegradasi piretroid. Isolat S-9 merupakan isolat bakteri yang memiliki kemampuan mendegradasi residu piretroid paling tinggi dibandingkan dengan 8 isolat lainnya, yaitu sebesar 87,38%. Hasil degradasi insektisida tersebut dimanfaatkan oleh bakteri sebagai sumber C, N, dan P untuk mendukung pertumbuhannya. Berdasarkan
    [Show full text]
  • A Report of 42 Unrecorded Bacterial Species Belonging to the Alphaproteobacteria in Korea
    Journal206 of Species Research 5(2):206-219, 2016JOURNAL OF SPECIES RESEARCH Vol. 5, No. 2 A report of 42 unrecorded bacterial species belonging to the Alphaproteobacteria in Korea Hyun Mi Jin1,2, Jung-Hoon Yoon3, Seung-Bum Kim4, Kwang-Yeop Jahng5, Jang-Cheon Cho6, Ki-seong Joh7, Chang-Jun Cha8, Chi-Nam Seong9, Jin-Woo Bae10, Wan-Taek Im11 and Che-Ok Jeon1,* 1Department of Life Science, Chung-Ang University, Seoul 06974, Korea 2Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, Gyeongsangbuk-do 37242, Korea 3Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon 16419, Korea 4Department of Microbiology, Chungnam National University, Daejeon 34134, Korea 5Department of Life Sciences, Chonbuk National University, Jeonju-si 54899, Korea 6Department of Biological Sciences, Inha University, Incheon 22212, Korea 7Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Geonggi 02450, Korea 8Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Korea 9Department of Biology, Sunchon National University, Suncheon 57922, Korea 10Department of Biology, Kyung Hee University, Seoul 02453, Korea 11Department of Biotechnology, Hankyong National University, Anseong 17546, Korea *Correspondent: [email protected] As a subset study to discover indigenous prokaryotic species in Korea, a total of 42 bacterial strains assigned to the class Alphaproteobacteria were isolated from diverse environmental habitats including plant roots, ginseng soil,
    [Show full text]
  • University of Thessaly Isolation and Study of Bacteria Able to Degrade
    University of Thessaly Department of Biochemistry and Biotechnology Isolation and study of bacteria able to degrade pesticides contained in the wastewaters produced by the fruit-packaging industry A thesis submitted by Chiara Perruchon For the degree of Doctor of Philosophy 2014 Institutional Repository - Library & Information Centre - University of Thessaly 09/12/2017 02:48:33 EET - 137.108.70.7 Members of the Examination Committee Assistant Prof. Dimitrios Karpouzas (Environmental Microbiology and Biotechnology), University of Thessaly, Department of Biochemistry and Biotechnology, Supervisor and Member of the Advisory Committee Associate Prof. Konstantinos Ehaliotis (Soil Fertility and Biology), Agricultural University of Athens, Department of Natural Resources Management and Agricultural Engineering, Member of the Advisory Committee Associate Prof. Kalliope Papadopoulou (Plant Biotechnology), University of Thessaly, Department of Biochemistry and Biotechnology, Member of the Advisory Committee Associate Prof. Konstantinos Kormas (Ecology of Aquatic Microorganisms), University of Thessaly, School of Agriculture Prof. Urania Menkissoglou-Spiroudi (Pesticide-Chemical Synthesis and Activity), Aristotle University of Thessaloniki, School of Agriculture Assistant Prof. Dimitrios Mossialos (Microbial Biotechnology), University of Thessaly, Department of Biochemistry and Biotechnology Assistant Prof. Spyridon Ntougias (Environmental Microbiology), Democritus University of Thrace, Department of Environmental Engineering Institutional Repository - Library & Information Centre - University of Thessaly 09/12/2017 02:48:33 EET - 137.108.70.7 Abstract Fruits are particularly vulnerable to fungal infestations or other physiological disorders during storage thus diminishing their market value. Post-harvest fruit treatments with fungicides like thiabendazole (TBZ), imazalil (IMZ), and ortho-phenyl-phenol (OPP), and antioxidants like diphenylamine (DPA) are the most effective means to minimize fruit spoilage in storage.
    [Show full text]
  • Potentially Pathogenic Bacteria in Shower Water and Air of a Stem Cell Transplant Unit Sarah D
    Washington University School of Medicine Digital Commons@Becker Open Access Publications 2009 Potentially pathogenic bacteria in shower water and air of a stem cell transplant unit Sarah D. Perkins Washington University in St Louis Jennie Mayfield Barnes-Jewish Hospital Victoria Fraser Washington University School of Medicine in St. Louis Largus T. Angenent Cornell University Follow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubs Recommended Citation Perkins, Sarah D.; Mayfield, Jennie; Fraser, Victoria; and Angenent, Largus T., ,"Potentially pathogenic bacteria in shower water and air of a stem cell transplant unit." Applied and Environmental Microbiology.75,16. 5363-5372. (2009). https://digitalcommons.wustl.edu/open_access_pubs/1999 This Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in Open Access Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact [email protected]. Potentially Pathogenic Bacteria in Shower Water and Air of a Stem Cell Transplant Unit Sarah D. Perkins, Jennie Mayfield, Victoria Fraser and Largus T. Angenent Downloaded from Appl. Environ. Microbiol. 2009, 75(16):5363. DOI: 10.1128/AEM.00658-09. Published Ahead of Print 6 July 2009. Updated information and services can be found at: http://aem.asm.org/ http://aem.asm.org/content/75/16/5363 These include: REFERENCES This article cites 70 articles, 25 of which can be accessed free at: http://aem.asm.org/content/75/16/5363#ref-list-1 on December 30, 2013 by Washington University in St. Louis CONTENT ALERTS Receive: RSS Feeds, eTOCs, free email alerts (when new articles cite this article), more» Information about commercial reprint orders: http://journals.asm.org/site/misc/reprints.xhtml To subscribe to to another ASM Journal go to: http://journals.asm.org/site/subscriptions/ APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Aug.
    [Show full text]
  • Draft Genome Sequence of Bosea Sp. WAO an Arsenite and Sulfide Oxidizer Isolated from a Pyrite Rock Outcrop in New Jersey Alexandra B
    Walczak et al. Standards in Genomic Sciences (2018) 13:6 https://doi.org/10.1186/s40793-018-0312-4 EXTENDED GENOME REPORT Open Access Draft genome sequence of Bosea sp. WAO an arsenite and sulfide oxidizer isolated from a pyrite rock outcrop in New Jersey Alexandra B. Walczak1*, Nathan Yee2 and Lily Y. Young2 Abstract This genome report describes the draft genome and physiological characteristics of Bosea sp. WAO (=DSM 102914), a novel strain of the genus Bosea in the family Bradyrhizobiaceae. Bosea sp. WAO was isolated from pulverized pyritic shale containing elevated levels of arsenic. This aerobic, gram negative microorganism is capable of facultative chemolithoautotrophic growth under aerobic conditions by oxidizing the electron donors arsenite, elemental sulfur, thiosulfate, polysulfide, and amorphous sulfur. The draft genome is of a single circular chromosome 6,125,776 bp long consisting of 21 scaffolds with a G + C content of 66.84%. A total 5727 genes were predicted of which 5665 or 98.92% are protein-coding genes and 62 RNA genes. We identified the genes aioA and aioB, which encode the large and small subunits of the arsenic oxidase respectively. We also identified the genes for the complete sulfur oxidation pathway sox which is used to oxidize thiosulfate to sulfate. Keywords: Neutrophilic sulfur oxidizer, Sox, Arsenite oxidase gene, Aio,Geomicrobiology,Microbe-mineral interactions, carbon fixation RuBisCO Introduction the Bosea genus is most closely related to the genus Bosea sp. WAO (white arsenic oxidizer) was enriched Salinarimonas which currently consists of two from a pulverized sample of weathered black shale species, Salinarimonas rosea and Salinarmonas ramus obtained from an outcropping near Trenton, NJ that [2].
    [Show full text]
  • Evaluating Efficacy of Plant Growth Promoting Rhizobacteria for Promoting Growth and Preventing Disease in Both Fish and Plants
    Evaluating Efficacy of Plant Growth Promoting Rhizobacteria for Promoting Growth and Preventing Disease in both Fish and Plants by Malachi Astor Williams A dissertation submitted to the Graduate Faculty of Auburn University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Auburn, Alabama May 2, 2020 Keywords: PGPR, disease control, Probiotic, Bacillus spp., Nile Tilapia, Channel Catfish Copyright 2020 by Malachi Astor Williams Approved by Mark R. Liles, Chair, Professor of Biological Sciences Joseph W. Kloepper, Professor of Entomology and Plant Pathology Jeffery S. Terhune, Associate Professor of Fisheries, Aquaculture and Aquatic Sciences Scott R. Santos, Professor of Biological Sciences Abstract Plant growth promoting rhizobacteria (PGPR), are bacteria residing within the rhizosphere of a plant, that elicit health benefits to the plant (Kloepper and Schroth, 1978; Kloepper et al., 2004). To understand the growth promoting and disease-inhibiting activities of PGPR strains, the genomes of 12 different PGPR strains affiliated with the B. subtilis group were sequenced. These B. subtilis strains exhibited high genomic diversity, whereas the genomes of Bacillus amyloliquefaciens strains (a member of the B. subtilis group) and B. velezensis strains (formerly B. amyloliquefaciens subsp. plantarum, now a part of the B. amyloliquefaciens clade (Fan et. al., 2017)) are highly conserved. A total of 2,839 genes were consistently present within the core genome of B. velezensis. Comparative genomic analyses of B. amyloliquefaciens and B. velezensis strains identified conserved genes that have been linked with biological control and colonization of roots or leaves. There were 73 genes uniquely associated with B. velezensis strains with predicted functions related to signaling, transportation, secondary metabolite production, and carbon source utilization.
    [Show full text]
  • Entwicklung Eines Datenbank-Gestützten Computerprogramms Zur Taxonomischen Identifizierung Von Mikrobiellen Populationen Auf Molekularbiologischer Basis
    Entwicklung eines Datenbank-gestützten Computerprogramms zur taxonomischen Identifizierung von mikrobiellen Populationen auf molekularbiologischer Basis Anwendung dieses Programms auf die Charakterisierung der Diversität stickstofffixierender und denitrifzierender Mikroorganismen in Abhängigkeit einer Stickstoffdüngung Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Universität zu Köln vorgelegt von Christopher Rösch aus München Hundt Druck Köln, 2005 Berichterstatter: Prof. Dr. H. Bothe Prof. Dr. D. Schomburg Tag der mündlichen Prüfung: 11. Juli 2005 Meinen Eltern Abstract The present work aimed at developing a novel method which allows to characterize microbial communities from environmental samples in a comprehensive and rapid way. Approaches tried so far either supplied information about the identity of a small fraction of organisms within the total community (e. g. by sequencing of clone libraries), or demonstrated the diversity of organisms without identifying them (e. g. community profiling). In the approach presented here, a method for determining such profiles (by tRFLP analysis) was combined with an automatic analysis by a computer program (TReFID) newly developed for the current study. For the characterization of microorganisms, three different data bases have been constructed: (1) for denitrifying bacteria: a nosZ data base with 607 entries (2) for dinitrogen fixing bacteria: a nifH data base with 1,318 entries (3) for bacteria in general: a 16S rDNA data base with 22,145 entries Thus a comprehensive data set has been developed particularly for the 16S rRNA gene. The use of the TReFID program now allows investigators to characterize bacterial communities from any environmental sample in a rather comprehensive way. Several control analyses showed that the TReFID program is suited for the analysis of environmental samples.
    [Show full text]
  • Oxidation of Thiosulfate by a New Bacterium, Bosea Thiooxidans (Strain BI-42) Gen
    INTERNATIONAL JOURNALOF SYSTEMATIC BACTERIOLOGY,OCt. 1996, p. 981-987 Vol. 46, No. 4 0020-7713/96/$04.00+0 Copyright 0 1996, International Union of Microbiological Societies Oxidation of Thiosulfate by a New Bacterium, Bosea thiooxidans (strain BI-42) gen. nov., sp. nov.: Analysis of Phylogeny Based on Chemotaxonomy and 16s Ribosomal DNA Sequencing SUBIZATA K. DAS,' AJIT K. MISHRA,'" BRIAN J. TINDALL,2 FRED A. RAINEY,2 AND ERKO STACKEBRANDT2 Department of Microbiology, Bose Institute, CIT Scheme VII-M, Calcutta 700 054, India, and DSM-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, 0-38124 Braunschweig, Germany2 A gram-negative bacterium which was capable of oxidizing reduced inorganic sulfur compounds was isolated from agricultural soil and designated BI-42. This new isolate grew on a wide range of organic substrates but was not able to grow autotrophically and lacked ribulose 1,s-bisphosphate carboxylase, a key enzyme of carbon dioxide fixation. These results suggested that strain BI-42 was a chemolithoheterotroph.Ammonia and nitrate were not used as sole nitrogen sources for growth, and strain BI-42 lacked glutamate synthase activity, which resulted in glutamate auxotrophy. The glutamate dehydrogenase activity of this organism was apparently insufficient for ammonia assimilation. On the basis of the results of additional biochemical tests, the G+C content of the DNA, the results of a respiratory ubiquinone analysis, the results of a 16s ribosomal DNA sequence analysis, the fatty acid composition, and the results of a membrane lipid analysis, strain BI-42 was identified as a phylogenetically and physiologically distinct taxon belonging to the alpha subclass of the Proteobucteria.
    [Show full text]
  • Sequedex Documentation Release 1.0-Rc1
    Sequedex Documentation Release 1.0-rc1 Joel Berendzen, Judith Cohn, Nicolas Hengartner, Mira Dimitrijevic, Benjamin McMahon January 06, 2016 Contents 1 Copyright notice 1 2 Introduction to Sequedex 3 2.1 What is Sequedex?............................................3 2.2 What does Sequedex do?.........................................3 2.3 How is Sequedex different from other sequence analysis packages?..................4 2.4 Who uses Sequedex?...........................................4 2.5 How is Sequedex used with other software?...............................5 2.6 How does Sequedex work?........................................5 2.7 Sequedex’s outputs............................................8 3 Installation instructions 15 3.1 System requirements........................................... 16 3.2 Downloading and unpacking for Mac.................................. 16 3.3 Downloading and unpacking for Linux................................. 17 3.4 Downloading and unpacking for Windows 7 or 8............................ 17 3.5 Using Sequedex with Cygwin installed under Windows......................... 19 3.6 Installation and updates without network access............................. 20 3.7 Testing your installation......................................... 20 3.8 Running Sequedex on an example data file............................... 20 3.9 Obtaining a node-locked license file................................... 21 3.10 Installing new data modules and upgrading Sequedex - User-installs.................. 21 3.11 Installing new data modules
    [Show full text]