Microbiology Lecture Notes PDF

Welcome to Microbiology Dr. Aaron Fay  Introductions Instructor Nitrogenase Complex Aaron W. Fay, Ph.D. -Inorganic Biochemist -Microbiologist -Anatomy FeMo-co FeV-co The Main Themes of Microbiology imscn0523...

Welcome to Microbiology Dr. Aaron Fay  Introductions Instructor Nitrogenase Complex Aaron W. Fay, Ph.D. -Inorganic Biochemist -Microbiologist -Anatomy FeMo-co FeV-co The Main Themes of Microbiology imscn052306_02_03 What are microbes (microorganisms)? cells and infectious agents too small to be seen with the naked eye – < 0.2 mm (= 200 m) examples include: – Bacteria (Escherichia coli, Salmonella species) – Archaea – Fungi yeasts, for example, Saccharomyces species molds, for example, Penicillium species – Protozoa – Algae – Parasitic Worms – Viruses – (are they alive or not alive ???) Human Immunodeficiency Virus (HIV)  Bacterial Size, Shape & Arrangement Size – varies – 1 – 2 m in width, typically – 2 – 10 m in length, typically – Exceptions Nanobacteria – less than 0.2 m A few very large bacteria Thiomargarita Epulopiscium namibiensis fishelsoni 750 m 80 x 600 m  Where are microbes found? Today, we know that microbes are found almost everywhere Before the invention of the microscope, microbes were unknown  Microbes in the Fossil Record Evolutionary Biology Microbes (prokaryotes) first appeared about 3.5 billion years ago They were the only life forms on Earth for over 1.5 billion years until eukaryotes appeared ~ 2 billion years ago  Microbes in the Environment Environmental Microbiology Microbial photosynthesis accounts for most of the atmospheric oxygen on Earth Microbes are essential for decomposition of dead organisms Many biologically important elements (S, N, P) are cycled by microbes  Impact of Microbiology Earth’s life support: agriculture, energy, environment legumes ruminants Harnessing the Power of Microbes Industrial Microbiology and Food Microbiology Microbes can be used to make or preserve food products (e.g., yogurt, salami, cheeses) Microbes can produce important compounds (e.g. antibiotics, MSG, ethanol)  Bioremediation to clean up toxic waste may involve more than one type of microbe may involve naturally- occurring or engineered microbes  Biotechnology Recombinant Biology, Molecular Biology, and Agricultural Microbiology Microbes can be altered or manipulated to produce useful products or modify other organisms. – insulin – proteins – enzymes  Microbial Diseases Some microbes cause infectious diseases Only a few percent of all microbes are associated with disease  Pathogens that shape global history Some cause disease in plants and animals (including humans) and are still a major threat today Example: The Plague (Black Death) killed one-third of Europe’s population (~ 25 million people) from ~1347 – 50 Eventually over the next 80 years, it killed 75% of the European population The Triumph of Death, Pieter Brueghel, the Elder (c. 1562), Museo del Prado, Madrid Plague, Arnold Böcklin, 1898 Kunstmuseum Basel, Switzerland Pathogens that Shape Global History Why do you think the mortality associated with Pneumonia and Influenza has been so greatly reduced in the last century? Modern sanitation and medical treatment (vaccination and antibiotics)  Sub-Disciplines by Organism Microbiologists are sometimes referred to by the type of microbial system that they study – Bacteriology: Study of prokaryotes – Mycology: Study of fungi – Phycology: Study of algae – Protozoology: The study of protozoa – Virology: The study of viruses – Immunology: The study of the immune system  Microbial Classification Taxonomy is the science of classification Carl von Linné began systematically classifying living things Every organism has a two-name (binomial) designation – Genus and species Note italics and capitalization! What constitutes a species?? Microorganisms challenge our ability to create schemes to organize and classify them  Naming Microbes Binomial nomenclature developed by Carolus Linnaeus (Carl von Linné) ~ 1735 each organism is given a genus and species name – example: Staphylococcus aureus genus names are like last names species names are like first names Where do names come from? – description of an organism / habitat / in honor of a researcher / miscellaneous  Taxonomy Copyright © The McG raw-Hill Compan ies, In c. Permission re quired for repro duction or display. Dom ain: Eukarya (All eukaryot ic organisms) Dom ain: Eukarya (All eukaryot ic organisms) Kingdom Kings Kingdom: Anim alia Lemur Kingdom: Protista inc ludes protozoa and algae Phylum/ Sea squirt Sea st ar Play Phylum : Chordata Phylum : Ciliophora only protozoa with cilia Class/Domain Chess Cla ss: Mamma lia Cla ss: Hy menos tom ea Single cells w ith regular rows of cilia; rapid Order On sw im mers Order: P rimat es Order: Hym enostoma tida Elongate oval c ells with cilia in the oral cavity Family Fine Family: Hominoidea Family: Parameciida e Cells rot ate while swimm ing and have ora l grooves. Genus Green Ge nus: Hom o Ge nus: Parame cium Pointe d, cigar-shaped ce lls with Species ma cronuc lei and micronuclei Satin Species: sapiens Species: Caudat um Cells cylindric al, long and (a) pointed a t one end (b)  The Five Kingdom Model Copyright © The McG raw-Hill Compan ies, In c. Permission re quired for repro duction or display. Robert Whittaker (1959) Chorda tes Angios perms Gy mnosperms Art hropods Annelids Echinoderms Ferns Mosses Mollusks Animals PLANTS Yea sts Club fungi Nemat odes (Plantae) FUNGI Molds Plants (Myce teae) ANIMALS (Anim alia) Fla tworm s Sponges Fungi (microbes) Red algae Green Slime molds Ciliates Fla gellates First multicellular organisms appe are d 0.6 billion yea rs ago. algae Brown Amoebas algae Protists (microbes) PROTISTS (Protista) EUKARYOTES Dia tom s Apicomplexans Monera (microbes) Dinoflage llates Early euk ary ote s First eukaryotic PROKARYO TE S cells appeared  2 billion ye ars ago. MONERA Arc hae a Bacteria 5 kingdom s First cells appeared 2 cell ty pes Earlie st cell 3–4 billion ye ars ago.  New Views of Phylogeny Carl Woese (1975) Copyright © The McG raw-Hill Compan ies, In c. Permission re quired for repro duction or display. Used 16S rRNA Domain Bacteria Cyanobacteria Chlam ydias Gram-positive Endospore Gram-negative Spir ochetes bacteria producers bacteria Methane producers Domain Ar chaea Pr okar yotes that live i n Pr okar yotes that live in Domain Eukarya Eukaryotes extrem e salt extrem e heat Three “Domains” 1. Archaea (all microbes) 2. Bacteria (all microbes) Ancestral Cell Line (first living cells) 3. Eukarya (some microbes)  Three Domain System for Classification of Biological Organisms developed by Carl Woese based on 16S rRNA nucleotide sequences The Early Years of Microbiology What Does Life Really Look Like? – Antoni van Leeuwenhoek (Dutch) began making and using simple microscopes often made a new microscope for each specimen examined water and visualized tiny animals, fungi, algae, and single-celled protozoa; “animalcules” – by end of 19th century, these organisms were called microorganisms  First Recorded Observations of Microbes Antony van Leeuwenhoek Early Microscopy ~1670 Discovery of Microorganisms Robert Hooke (1635 - 1703) First person to publish the depiction of a microorganism Described the fruiting structure of molds in 1665 (~20 years before Leeuwenhoek)  Microscope Developed by Robert Hooke Lens Light source Adjustment screws Sample  Image Observed by Hooke’s Microscope The fruiting structure of molds : “Hairy Mould” colony  Hooke vs. Leeuwenhoek First to publish depiction First to accurately describe of a microorganism the microorganisms Discovered molds Discovered bacteria Both should be considered as “founding” modern microbiology  Hooke or Leeuwenhoek ? ASM News, June 2004 The Golden Age of Microbiology Scientists searched for answers to four questions – Is spontaneous generation of microbial life possible? – What causes fermentation? – What causes disease? – How can we prevent infection and disease? Spontaneous Generation (Abiogenesis) vs. Biogenesis Spontaneous Generation – life arises from non-living things (soil, the environment, bad air) – first proposed by Aristotle Biogenesis – life arises only from living organisms, which may be too small to see experiments of Francesco Redi ~ 1668 Francesco Redi’s Experiment Observation: raw meat attracts flies, and later maggots Question: What causes maggots on rotting meat? Hypothesis: maggots form only when flies are present Experiment/ Test: place meat in both uncovered and covered jars Result: only meat in open jars produced maggots Conclusion: hypothesis is supported by results – The Theory of Spontaneous Generation is debunked!  Louis Joblot 1710 Copyright © The McG raw-Hill Compan ies, In c. Permission re quired for repro duction or display. French mathematician Jablot’s Experiment Boiled hay infusions Infusions Open container became cloudy Covered Uncovered Sealed container remained clear Dust Dust Argued that contamination came from outside of the Heavy container (dust) Remains clear; microbial no growth growth Franz Schulze and Theodor Schwann 1836 Copyright © The McG raw-Hill Compan ies, In c. Permission re quired for repro duction or display. Shultze and Schwann’sTest German biologists Air inlet After Priestly (1774) Flame heats air. discovered oxygen Previously sterilized infusion Treated incoming gas with remains sterile. heat or chemicals No growth observed in boiled broth media  Louis Pasteur 1864 Copyright © The McG raw-Hill Compan ies, In c. Permission re quired for repro duction or display. Pasteur’s Experiment French microbiologist Used swan-necked flasks Microbes being Untreated air allowed destroyed in and out of flasks Vigorous heat Broth free of is applied. live cells (sterile) No growth in undisturbed flasks Contacting the broth with the dust results in rapid microbial Neck on second Neck intact; airborne growth sterile flask microbes are is broken; trapped at base, growth occurs. and broth is sterile.  Spontaneous Generation vs. Biogenesis Pasteur’s Experiments – When the “swan-necked flasks” remained upright, no microbial growth appeared – When the flask was tilted, dust from the bend in the neck seeped back into the flask and made the infusion cloudy with microbes within a day  Louis Pasteur: Swan-Necked Flask Experiment Observations: – broth boiled and left in open containers → cloudy – broth boiled and covered → not cloudy Question: – What causes growth of microbes in broth? Hypothesis: – boiling broth in a swan-necked flask (prevents entry of air-born microbes) will prevent microbial growth Experiment: – boiled broth in open or swan-necked flasks – flasks were observed for several days  Louis Pasteur: Swan-Necked Flask Experiment Results: – regular, open flasks – microbes grow – swan-necked flasks – no microbial growth Conclusions: – hypothesis supported – boiling in swan-necked flasks where airborne microbes cannot fall into the broth prevents growth of microbes Microbes do not arise spontaneously in broth led to the idea and use of aseptic techniques The Scientific Method  The Scientific Method Debate over spontaneous generation led in part to development of scientific method – A group of observations leads scientist to ask question about some phenomenon – The scientist generates hypothesis (potential answer to question) – The scientist designs and conducts experiment to test hypothesis – Based on observed results of experiment, scientist either accepts, rejects, or modifies hypothesis  The Scientific Method (framework for scientific research) The Germ Theory of Disease Robert Koch – 1876 – German physician – studied anthrax cattle disease – developed “Germ Theory” Koch’s Postulates  Koch’s Postulates 1. Observation 2. Cultivation  Koch’s Postulates 3. Introduction  Koch’s Postulates 4. Recovery  Koch’s Postulates 1. Observation of disease signs and symptoms 2. Cultivation of organism in pure culture 3. Introduction of pure culture into healthy experimental animal 4. Recovery of same organism from experimental animals Significance of Koch’s Postulates scientific method to prove causation of disease links specific organisms with specific diseases gives a target for treatment of disease – Microbes cause disease!!! can test treatments on cultured organism in the laboratory  Also Developed by Koch – Simple staining techniques – First photomicrograph of bacteria – First photomicrograph of bacteria in diseased tissue – Techniques for estimating colony-forming units per mL (CFU/mL) – Use of steam to sterilize media – Use of Petri dishes – Aseptic techniques – Bacteria exist as distinct species  Pioneers in Disease Prevention How Can We Prevent Infection and Disease? – Semmelweis and handwashing – Lister’s antiseptic technique – Nightingale and nursing – Snow – infection control and epidemiology – Jenner’s vaccine – field of immunology – Ehrlich’s “magic bullets” – field of chemotherapy The Golden Age of Microbiology  Cellular Microorganisms: Prokaryotes and Eukaryotes Two cell types: Microbial members: Prokaryotes 1. Bacteria (pro= before, Karyon= nut or kernel) 2. Archaea Eukaryotes 1. Protozoa (eu= true, Karyon= nut or kernel) 2. Algae 3. Fungi Fun Facts! “Crazy” Archaea! “Crazy” Archaea!  “Crazy” Bacteria! Streptomyces thermoautotrophicus can grow in the covering soil of a burning charcoal pile! Microbes on Mars? How important are Prokaryotes? During the course of life, the # of E. coli in the gut of each human being far exceeds the total # of people that now live and have ever lived. A whole 10% of each human’s dry body weight consists of bacteria, some of which, though not a congenital part of our bodies, we can’t live without. How important are Prokaryotes? Bacteria/Archaea inhabit effectively every space suitable for life. Most do not reside on the Earth’s surface, but are found in oceanic and terrestrial sub-surfaces. Estimated # of prokaryotic cells on earth: 5 x 1030! The total amount of carbon in these cells equals that of all plants on earth. The collective contents of nitrogen and phosphorus in prokaryotic cells is over 10 times more than that of all plant biomass.  Human Microbiome Bacterial to human cells 3:1* to 1.3:1** That’s 100,000,000,000,000 bacterial cells in our bodies! *report put together by the American Academy of Microbiology/ASM called FAQ: Human Microbiome http://academy.asm.org/index.php/faq-series/5122-humanmicrobiome) **Sender et al 2016, http://biorxiv.org/content/biorxiv/early/2016/01/06/036103.full.pdf Importance of the Microbiome? Benefits ✓ Food digestion ✓ Nutrition (vitamins, energy) ✓ Metabolic regulation, co-metabolism ✓ Development: terminal differentiation of mucosa ✓ “Education”, regulation of immune system ✓ Colonization resistance to pathogens Turnbaugh et al, 2007. Nature 449:804-810; Dethlefsen et al, 2007 Nature 449:811-818  Importance of the Microbiome? Affect vaccine potency* Alter drug metabolism** Shifts in the microbiota may be associated with: inflammatory bowel disease, obesity, cardiovascular disease, eczema and other skin diseases, vaginal infections "Disease might arise from a disturbed microbial community (Friedrich, 2008. JAMA 300:777-778) *http://www.cell.com/trends/immunology/abstract/S1471-4906%2814%2900114-8 **http://www.pnas.org/content/106/34/14728.long Importance of the Microbiome?