Food Contamination with Psyhcrophilic Bacteria
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Laboratory Exercises in Microbiology: Discovering the Unseen World Through Hands-On Investigation
City University of New York (CUNY) CUNY Academic Works Open Educational Resources Queensborough Community College 2016 Laboratory Exercises in Microbiology: Discovering the Unseen World Through Hands-On Investigation Joan Petersen CUNY Queensborough Community College Susan McLaughlin CUNY Queensborough Community College How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/qb_oers/16 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] Laboratory Exercises in Microbiology: Discovering the Unseen World through Hands-On Investigation By Dr. Susan McLaughlin & Dr. Joan Petersen Queensborough Community College Laboratory Exercises in Microbiology: Discovering the Unseen World through Hands-On Investigation Table of Contents Preface………………………………………………………………………………………i Acknowledgments…………………………………………………………………………..ii Microbiology Lab Safety Instructions…………………………………………………...... iii Lab 1. Introduction to Microscopy and Diversity of Cell Types……………………......... 1 Lab 2. Introduction to Aseptic Techniques and Growth Media………………………...... 19 Lab 3. Preparation of Bacterial Smears and Introduction to Staining…………………...... 37 Lab 4. Acid fast and Endospore Staining……………………………………………......... 49 Lab 5. Metabolic Activities of Bacteria…………………………………………….…....... 59 Lab 6. Dichotomous Keys……………………………………………………………......... 77 Lab 7. The Effect of Physical Factors on Microbial Growth……………………………... 85 Lab 8. Chemical Control of Microbial Growth—Disinfectants and Antibiotics…………. 99 Lab 9. The Microbiology of Milk and Food………………………………………………. 111 Lab 10. The Eukaryotes………………………………………………………………........ 123 Lab 11. Clinical Microbiology I; Anaerobic pathogens; Vectors of Infectious Disease….. 141 Lab 12. Clinical Microbiology II—Immunology and the Biolog System………………… 153 Lab 13. Putting it all Together: Case Studies in Microbiology…………………………… 163 Appendix I. -
A DNA Ligase from the Psychrophile Pseudoalteromonas Haloplanktis Gives Insights Into the Adaptation of Proteins to Low Temperatures
Eur. J. Biochem. 267, 3502±3512 (2000) q FEBS 2000 A DNA ligase from the psychrophile Pseudoalteromonas haloplanktis gives insights into the adaptation of proteins to low temperatures D. Georlette1,Z.O.JoÂnsson2,3, F. Van Petegem4, J.-P. Chessa1, J. Van Beeumen4,U.HuÈ bscher2 and C. Gerday1 1Laboratory of Biochemistry, Institute of Chemistry, B6a Universite de LieÁge, Sart-Tilman, Belgium; 2Institute of Veterinary Biochemistry, UniversitaÈtZuÈrich-Irchel, ZuÈrich, Switzerland; 3Department of Pathology, Brigham & Women's Hospital, Boston, MA, USA; 4Laboratory for Protein Biochemistry and Protein Engineering, Department of Biochemistry Physiology and Microbiology, Gent, Belgium The cloning, overexpression and characterization of a cold-adapted DNA ligase from the Antarctic sea water bacterium Pseudoalteromonas haloplanktis are described. Protein sequence analysis revealed that the cold- adapted Ph DNA ligase shows a significant level of sequence similarity to other NAD1-dependent DNA ligases and contains several previously described sequence motifs. Also, a decreased level of arginine and proline residues in Ph DNA ligase could be involved in the cold-adaptation strategy. Moreover, 3D modelling of the N-terminal domain of Ph DNA ligase clearly indicates that this domain is destabilized compared with its thermophilic homologue. The recombinant Ph DNA ligase was overexpressed in Escherichia coli and purified to homogeneity. Mass spectroscopy experiments indicated that the purified enzyme is mainly in an adenylated form with a molecular mass of 74 593 Da. Ph DNA ligase shows similar overall catalytic properties to other NAD1-dependent DNA ligases but is a cold-adapted enzyme as its catalytic efficiency (kcat/Km) at low and moderate temperatures is higher than that of its mesophilic counterpart E. -
EXTREMOPHILES – Vol
EXTREMOPHILES – Vol. I - Extremophiles: Basic Concepts - Charles Gerday EXTREMOPHILES: BASIC CONCEPTS Charles Gerday Laboratory of Biochemistry, University of Liège, Belgium Keywords: extremophiles, thermophiles, halophiles, alkaliphiles, acidophiles, metallophiles, barophiles, psychrophiles, piezophiles, extreme conditions Contents 1. Introduction 2. Effects of Extreme Conditions on Cellular Components 2.1. Membrane Structure 2.2. Nucleic Acids 2.2.1. Introduction 2.2.2. Desoxyribonucleic Acids 2.2.3. Ribonucleic Acids 2.3. Proteins 2.3.1. Introduction 2.3.2. Thermophilic Proteins 2.3.3. Psychrophilic Proteins 2.3.4. Halophilic Proteins 2.3.5. Piezophilic Proteins 2.3.6. Alkaliphilic Proteins 2.3.7. Acidophilic Proteins 3. Conclusions Acknowledgments Glossary Bibliography Biographical Sketch Summary Extremophiles are organisms which permanently experience environmental conditions which mayUNESCO be considered as extreme –in comparisonEOLSS to the physico-chemical characteristics of the normal environment of human cells: the latter belonging to the mesophile or temperate world. Some eukaryotic organisms such as fishes, invertebrates, yeasts, fungi, and plants have partially colonized extreme habitats characterized by low temperature and/orSAMPLE of elevated hydrostatic pressure. CHAPTERS In general, however, the organisms capable of thriving at the limits of temperature, pH, salt concentration and hydrostatic pressure, are prokaryotic. In fact, some organisms depend on these extreme conditions for survival and have therefore developed unique adaptations, especially at the level of their membranes and macromolecules, and affecting proteins and nucleic acids in particular. The molecular bases of the various adaptations are beginning to be understood and are briefly described. The study of the extremophile world has contributed greatly to defining, in more precise terms, fundamental concepts such as macromolecule stability and protein folding. -
Microbial Diversity Course 2005 Attempt to Cultivate Mesophile
Microbial Diversity course 2005 Attempt to cultivate mesophile Archaea from marine sediments Lois MAIGNIEN Ghent University Introduction The diversity and ecology of the Archaea domain remains a very intriguing question and a promising field of research. Indeed, it has fisrt been observed that Archaea were thriving in very limited ecological niches, often associated with extreme temperature, salt concentration, or low pH. Methanogens, though very successful in mesophilic anaerobic environments, don’t display the same variety of energy metabolisms as most bacteria. Their growth is restricted to strict anaerobic environments; their substrate range is limited to CO2/H2, acetate and a few methylated compounds. Alternative energy metabolism such as anaerobic respiration (some halophiles and crenarchaeota) using a wide range of terminal electron acceptor such as nitrate (pyrobaculum, pyrococcus), iron III (pyrodictium), sulphate (Archaeoglobus), elemental sulfur (Ignicoccus) or aerobic respiration on sulfur or oxygen are all present in this domain. Some archaea are also able to carry fermentation and even thrive on light energy through the use of bacteriorhodopsin (Halobacterium). Thus, archaea possess in theory high diversity of energy metabolism. So why archaeal cells would display and use this metabolic diversity only in extreme environments? However, several clue from molecular surveys, especially in marine environment, such as 16s clone library and fosmid cloning and sequencing show that Archaea are much more widespread than previously thought, even in mesophilic environments. The main problem that prevent further understanding of their metabolism and environmental contribution have been the inability to cultivate them. An increasing interest for this environmental microbiology mystery, growing number of cultivation attempts, new cultivation methods, and valuable information from metagenomics should progressively reveal the environmental diversity of mesophilic Archaea and provide a better understanding of their contribution to various environments. -
Chapter 02282
Psychrophiles and Psychrotrophs$ Craig L Moyer, Western Washington University, Bellingham, WA, United States R Eric Collins, University of Alaska Fairbanks, Fairbanks, AK, United States Richard Y Morita, Oregon State University, Corvallis, OR, United States r 2017 Elsevier Inc. All rights reserved. Glossary Cryophiles Cold-loving eukaryotes. Barophiles (also known as piezophiles) Pressure-loving Homeophasic adaptation The ability of the cell bacteria and archaea. membrane to maintain a relatively constant viscosity Cryobiosis A temporary state of reduced metabolism in (fluidity) throughout the growth temperature range. which metabolic activity is absent or undetectable due to Membrane fluidity The ability of the cell membrane to freezing. To initiate cryobiosis, the organism freezes all of remain fluid in order to modulate the activity of the the water within its cell(s). This allows the organism to intrinsic proteins which perform functions such as electron endure the freezing temperatures until more transport, ion pumping, and nutrient uptake. hospitable conditions return. Studies have shown that the Psychrophiles Cold-loving bacteria and archaea. longer an organism remains in cryobiosis, the longer it takes Psychrotrophs Cold-tolerant bacteria and archaea. for the organism to come out of cryobiosis. This is because Thermocline In the stratification of warm surface water the organism must use its own energy to come out of over cold deeper water, the transition zone of rapid cryobiosis, and the longer it stays in cryobiosis the less temperature decline between two layers. energy it will retain. Introduction Psychrophiles are cold-loving bacteria or archaea, whereas cryophiles are cold-loving higher biological forms (e.g., polar fish). -
Microbiologically Contaminated and Over-Preserved Cosmetic Products According Rapex 2008–2014
cosmetics Article Microbiologically Contaminated and Over-Preserved Cosmetic Products According Rapex 2008–2014 Edlira Neza * and Marisanna Centini Department of Biotechnologies, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, Siena 53100, Italy; [email protected] * Correspondence: [email protected]; Tel.: +355-685-038-408 Academic Editors: Lidia Sautebin and Immacolata Caputo Received: 25 December 2015; Accepted: 25 January 2016; Published: 30 January 2016 Abstract: We investigated the Rapid Alert System (RAPEX) database from January 2008 until week 26 of 2014 to give information to consumers about microbiologically contaminated cosmetics and over-preserved cosmetic products. Chemical risk was the leading cause of the recalls (87.47%). Sixty-two cosmetic products (11.76%) were recalled because they were contaminated with pathogenic or potentially pathogenic microorganisms. Pseudomonas aeruginosa was the most frequently found microorganism. Other microorganisms found were: Mesophilic aerobic microorganisms, Staphylococcus aureus, Candida albicans, Enterococcus spp., Enterobacter cloacae, Enterococcus faecium, Enterobacter gergoviae, Rhizobium radiobacter, Burkholderia cepacia, Serratia marcescens, Achromabacter xylosoxidans, Klebsiella oxytoca, Bacillus firmus, Pantoea agglomerans, Pseudomonas putida, Klebsiella pneumoniae and Citrobacter freundii. Nine cosmetic products were recalled because they contained methylisothiazolinone (0.025%–0.36%), benzalkonium chloride (1%), triclosan (0.4%) in concentrations higher than the limits allowed by European Regulation 1223/2009. Fifteen products were recalled for the presence of methyldibromo glutaronitrile, a preservative banned for use in cosmetics. Thirty-two hair treatment products were recalled because they contained high concentrations of formaldehyde (0.3%–25%). Keywords: microbiologically contaminated; over-preserved cosmetics; formaldehyde; RAPEX 1. Introduction The European Commission (EC) has an early warning system for safety management called the Rapid Alert System (RAPEX). -
Extremophiles — Link Between Earth and Astrobiology
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Directory of Open Access Journals Zbornik Matice srpske za prirodne nauke / Proc. Nat. Sci, Matica Srpska Novi Sad, ¥ 114, 5—16, 2008 UDC 133.52:57 Dejan B. Stojanoviã1 , Oliver O. Fojkar2 , Aleksandra V. Drobac-Åik1 , Kristina O. Åajko3 , Tamara I. Duliã1 ,ZoricaB.Sviråev1 1 Faculty of Sciences, Department of Biology and Ecology, Trg Dositeja Obradoviãa 2, 21000 Novi Sad, Serbia 2 Institute for nature conservation of Serbia, Radniåka 20A, 21000 Novi Sad, Serbia 3 Faculty of Sciences, Department of Physics, Trg Dositeja Obradoviãa 4, 21000 Novi Sad, Serbia EXTREMOPHILES — LINK BETWEEN EARTH AND ASTROBIOLOGY ABSTRACT: Astrobiology studies the origin, evolution, distribution and future of life in the universe. The most promising worlds in Solar system, beyond Earth, which may har- bor life are Mars and Jovian moon Europa. Extremophiles are organisms that thrive on the edge of temperature, hypersalinity, pH extremes, pressure, dryness and so on. In this paper, some extremophile cyanobacteria have been discussed as possible life forms in a scale of astrobiology. Samples were taken from solenetz and solonchak types of soil from the Voj- vodina region. The main idea in this paper lies in the fact that high percentage of salt found in solonchak and solonetz gives the possibility of comparison these types of soil with “soil" on Mars, which is also rich in salt. KEYWORDS: Astrobiology, extremophiles, cyanobacteria, halophiles 1. INTRODUCTION 1.1. About astrobiology Astrobiology studies the origin, evolution, distribution and future of life in the universe. -
Eubacteria and Archaea Communities in Seven Mesophile Anaerobic
Abendroth et al. Biotechnology for Biofuels (2015) 8:87 DOI 10.1186/s13068-015-0271-6 RESEARCH ARTICLE Open Access Eubacteria and archaea communities in seven mesophile anaerobic digester plants in Germany Christian Abendroth1,2, Cristina Vilanova1, Thomas Günther3, Olaf Luschnig2,4 and Manuel Porcar1,5* Abstract Background: Only a fraction of the microbial species used for anaerobic digestion in biogas production plants are methanogenic archaea. We have analyzed the taxonomic profiles of eubacteria and archaea, a set of chemical key parameters, and biogas production in samples from nine production plants in seven facilities in Thuringia, Germany, including co-digesters, leach-bed, and sewage sludge treatment plants. Reactors were sampled twice, at a 1-week interval, and three biological replicates were taken in each case. Results: A complex taxonomic composition was found for both eubacteria and archaea, both of which strongly correlated with digester type. Plant-degrading Firmicutes as well as Bacteroidetes dominated eubacteria profiles in high biogas-producing co-digesters; whereas Bacteroidetes and Spirochaetes were the major phyla in leach-bed and sewage sludge digesters. Methanoculleus was the dominant archaea genus in co-digesters, whereas Methanosarcina and Methanosaeta were the most abundant methanogens in leachate from leach-bed and sewage sludge digesters, respectively. Conclusions: This is one of the most comprehensive characterizations of the microbial communities of biogas-producing facilities. Bacterial profiles exhibited very low variation within replicates, including those of semi-solid samples; and, in general, low variation in time. However, facility type correlated closely with the bacterial profile: each of the three reactor types exhibited a characteristic eubacteria and archaea profile. -
Clostridium Aldrichii S P . Nov., a Cellulolytic Mesophile Inhabiting A
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1990, p. 268-272 Vol. 40, No. 3 0020-7713/90/030268-05$02.OO/O Copyright 0 1990, International Union of Microbiological Societies Clostridium aldrichii sp. nov., a Cellulolytic Mesophile Inhabiting a Wood-Fermenting Anaerobic Digester? JUNCHANG C. YANG,l* DAVID P. CHYNOWETH,l DONNA S. WILLIAMS,, AND ANMING L12$ Bioprocess Engineering Research Laboratory, Agricultural Engineering Department,' and Microbiology and Cell Science Department,2 University of Florida, Gainesville, Florida 3261 1 An anaerobic, mesophilic, spore-forming, cellulolytic bacterium was repeatedly isolated from a wood- fermenting anaerobic digester. Cells of this organism were gram-positive rods, motile with a bundle of polar flagella, and formed subterminal oblong spores. The colonies in agar had an irregular shape with many platelike structures and were greyish white. Cellulose, xylan, and cellobiose served as substrates for growth. Acetate, propionate, butyrate, isobutyrate, isovalerate, lactate, succinate, H,, and CO, were products of cellobiose fermentation. The optimal temperature and pH for growth were 35°C and 7, respectively. The DNA composition was 40 mol% G+C. The name Clostridium aldn'chii sp. nov. is proposed. The type strain is P-1 (= OGI 112, = ATCC 49358). Woody biomass generally was not considered to be bio- 10 ml; resazurin (0.5 mg/ml), 1 ml; L-cysteine hydrochloride, degradable under anaerobic conditions until Zeikus and 0.5 g; Na,S . 9H20, 0.2 g. The agar concentration was 1.5% Ward (22) showed that a methane fermentation occurs in the (wthol). The pH was adjusted to 7.0 with NaHCO,. The heartwood of live trees and Chynoweth and co-workers (4, medium was prepared and dispensed with continuous flush- 9) showed that the carbohydrates of poplar and other hard- ing of the gas mixture mentioned above. -
Effects of Temperature on CRISPR/Cas System Eddie Beckom Augustana College, Rock Island Illinois
Augustana College Augustana Digital Commons Meiothermus ruber Genome Analysis Project Biology 2019 Effects of Temperature on CRISPR/Cas System Eddie Beckom Augustana College, Rock Island Illinois Dr. Lori Scott Augustana College, Rock Island Illinois Follow this and additional works at: https://digitalcommons.augustana.edu/biolmruber Part of the Bioinformatics Commons, Biology Commons, Genomics Commons, and the Molecular Genetics Commons Augustana Digital Commons Citation Beckom, Eddie and Scott, Dr. Lori. "Effects of Temperature on CRISPR/Cas System" (2019). Meiothermus ruber Genome Analysis Project. https://digitalcommons.augustana.edu/biolmruber/45 This Student Paper is brought to you for free and open access by the Biology at Augustana Digital Commons. It has been accepted for inclusion in Meiothermus ruber Genome Analysis Project by an authorized administrator of Augustana Digital Commons. For more information, please contact [email protected]. Eddie Beckom BIO 375 Dr. Lori R. Scott Biology Department, Augustana College 639 38th Street, Rock Island, IL 61201 Temperature Effect on Complexity of CRISPR/Cas Systems What is Meiothermus ruber? Meiothermus ruber is a Gram-negative thermophilic rod-shaped eubacteria . The genus name derives from the Greek words ‘meion’ and ‘thermos’ meaning ‘lesser’ and ‘hot’ to indicate the thermophilic characteristics of Meiothermus ruber. (Nobre et al., 1996; Euzeby, 1997). It lives in thermal environments with an optimal temperature of 60℃. Meiothermus ruber belongs to the bacterial phylum Deinococcus-Thermus. The order Thermales, which is housed within the Thermus group and consists of 6 genera (Vulcanithermus, Oceanithermus, Thermus, Marinithermus, Meiothermus, Rhabdothermus), all containing genera with proteins that are thermostable. (Albuquerque and Costa, 2014). M. ruber is one of eight currently known species in the genus Meiothermus (Euzeby, 1997). -
Life in Extreme Environments
insight review articles Life in extreme environments Lynn J. Rothschild & Rocco L. Mancinelli NASA Ames Research Center, Moffett Field, California 94035-1000, USA (e-mail: [email protected]; [email protected]) Each recent report of liquid water existing elsewhere in the Solar System has reverberated through the international press and excited the imagination of humankind. Why? Because in the past few decades we have come to realize that where there is liquid water on Earth, virtually no matter what the physical conditions, there is life. What we previously thought of as insurmountable physical and chemical barriers to life, we now see as yet another niche harbouring ‘extremophiles’. This realization, coupled with new data on the survival of microbes in the space environment and modelling of the potential for transfer of life between celestial bodies, suggests that life could be more common than previously thought. Here we examine critically what it means to be an extremophile, and the implications of this for evolution, biotechnology and especially the search for life in the Universe. ormal is passé; extreme is chic. While thriving in biological extremes (for example, nutritional Aristotle cautioned “everything in extremes, and extremes of population density, parasites, moderation”, the Romans, known for their prey, and so on). excesses, coined the word ‘extremus’, the ‘Extremophile’ conjures up images of prokaryotes, yet the superlative of exter (‘being on the outside’). taxonomic range spans all three domains. Although all NBy the fifteenth century ‘extreme’ had arrived, via Middle hyperthermophiles are members of the Archaea and French, to English. At the dawning of the twenty-first Bacteria, eukaryotes are common among the psychrophiles, century we know that the Solar System, and even Earth, acidophiles, alkaliphiles, piezophiles, xerophiles and contain environmental extremes unimaginable to the halophiles (which respectively thrive at low temperatures, low ‘ancients’ of the nineteenth century. -
Flagella As a Test System Isthat Highly Purified P
MOLECULAR BASIS OF BIOLOGICAL STABILITY TO HIGH TEMPERA TURES* BY HENRY KOFFLERt G. E. MALLETTt AND JIMMY ADYE LABORATORIES OF BACTERIOLOGY, DEPARTMENT OF BIOLOGICAL 'SCIENCES, PURDUE UNIVERSITY, WEST LAFAYETTE, INDIANA Communicated by A. K. Balls, April 1, 1957 One of the most plausible explanations for the ability of thermophilic organisms to grow at temperatures that usually are lethal to other organisms is that they possess relatively heat-stable proteins. Substantial support for this hypothesis recently has been furnished by Koffler and his associates,1 2 who showed that cytoplasmic proteins obtained from thermophilic bacteria are strikingly more heat- stable than those from mesophiles. Their experiments extend previous reports3-7 that the activity of certain enzymes from thermophiles is more heat-stable than that of similar preparations from mesophilic cells. Unfortunately, the available data, except Campbell's,5 were obtained with impure enzymes and thus do not enable one to distinguish between inherent thermostability and external stabilization. Camp- bell's experiments, however, were performed with purified enzymes. He showed that crystalline amylase isolated from cultures of Bacillus coagulans grown at 550 C. is markedly more heat-stable than a similar isolate from cultures grown at 350 C. Though one could argue that even crystalline proteins may contain sta- bilizing contaminants in minute yet effective concentrations, the most reasonable ex- planation for this finding is that the observed difference in relative thermostability is due to molecular differences and not to external substances. Campbell's observa- tion confirms our own conclusions regarding the relative thermostability of flagella from thermophiles. These experiments were presented in preliminary accounts before2, 8 and are described more fully in this paper.