Lecture1.pdf The main themes of microbiology
- 1. 1 Microbiology: A Systems Approach, 2nd ed. Chapter 1: The Main Themes of Microbiology
- 2. 2 Chapter 1 Topics – The Scope of Microbiology – Impact of Microorganisms – Human use of Microorganisms – Infectious diseases and the human condition – The General Characteristics of Microorganisms – History of Microbiology – Systematics (Taxonomy) and Evolution
- 3. 3 1.1 The Scope of Microbiology • Microbiology: The study of living things too small to be seen without magnification – Microorganisms or microbes - microscopic organisms – Commonly called “germs, bugs, viruses, agents…” but not all terms are accurate. – Not all cause disease (most of them are benign) – Many of them are useful or even essential for human life
- 4. 4 Major Groups of Microorganisms • Bacteria, Archaea, Algae, Protozoa, Helminthes, and Fungi • Viruses- non-cellular, parasitic, protein- coated genetic elements that can infect all living things, including other microorganisms (most microbiologists do not consider viruses “microorganisms” but “pathogens”)
- 5. 5 Branches of Microbiology • Agricultural microbiology • Biotechnology • Food, dairy, and aquatic microbiology • Genetic engineering and recombinant DNA technology • Immunology • Public health microbiology and epidemiology • Many, many more
- 6. 6 Emerging Areas of Microbiology • Emerging Pathogens • Marine microbiology • Geo-microbiology • Astro- (Exo)-microbiology
- 7. 7 Importance of Microbiology • First cellular organisms were bacteria • Primary production and decomposition as part of global biogeochemical cycles • Human use of microorganisms • Importance for human health • Infectious diseases
- 8. 8 1.2 The Impact of Microbes on Earth: Small Organisms with a Giant Effect • Microorganisms have a profound influence on all aspects of the earth and its residents • Bacterial-like organisms in the fossil record as far back as 3.8 billion years ago (prokaryotes- “organisms without a true nucleus”) • ~2 billion years ago, eukaryotes (“organisms with a true nucleus”) emerged
- 9. 9 Bacteria appeared approximately 3.8 billion years ago. Fig. 1.1 Evolutionary timeline
- 10. 10 Ubiquity of Microorganisms • Found nearly everywhere • Occur in large numbers • Live in places many other organisms cannot Figure 1.2
- 11. 11 Microbial Involvement in Energy and Nutrient Flow • Bacteria conducted photosynthesis before plants appeared – Anoxygenic photosynthesis – Oxygenic photosynthesis • account for >50% of the earth’s oxygen • Biological decomposition and nutrient recycling
- 12. 12 1.3 Human Use of Microorganisms • Humans have been using microorganisms for thousands of years – Baker’s and brewer’s yeast – Cheeses & other dairy products – Moldy bread on wounds Figure 1.3: Microbial leaching, fermentation, oil biodegradation
- 13. 13 Biotechnology & Bioremediation • Biotechnology- when humans manipulate (micro)organisms to make products in an industrial setting – Genetic engineering- create new products and “genetically modified organisms” (GMOs) – Recombinant DNA technology- technology used to engineer GMOs capable of synthesizing desirable proteins (i.e. medicines, hormones, and enzymes) • Bioremediation - activity of microbes in the environment helping to restore stability or clean up toxic pollutants – Oil spills – Chemical spills – Water and sewage treatment
- 14. 14 1.4 Infectious Diseases and the Human Condition • Pathogens - disease-causing “agents”
- 15. 15 Figure 1.4 The most common infectious diseases worldwide.
- 16. 16 Worldwide Infectious Diseases • Increasing number of emerging diseases (SARS, AIDS, hepatitis C, viral encephalitis) • Other diseases previously not linked to microorganisms now are: gastric ulcers, certain cancers, schizophrenia, multiple sclerosis, obsessive compulsive disorder, coronary artery disease …. and the list is growing …. • Increasing number of drug-resistant strains of disease-causing bacteria
- 17. 17 1.5 The General Characteristics of Microorganisms • Cellular Organization – “Prokaryotic” vs. “eukaryotic” cells • Prokaryotic (bacterial and archaeal) cells are about 10 times smaller than eukaryotic cells • Prokaryotic cells lack many cell structures such as double membrane-bound organelles • All prokaryotes are microorganisms, but only some eukaryotes are
- 18. 18 There is a difference between the cell structure of a prokaryote and eukaryote. Viruses are neither but are considered particles. Fig. 1.5 Cell structure
- 19. 19 There are six main types of microbes: 1.) Bacterium or Archaeon, 2.) Fungus, 3.) Alga, 4.) Virus, 5.) Protozoon (Protozoan), 6.) Helminth. Fig. 1.6 The six types of microorganisms
- 20. 20 Viruses • Are NOT independently living cellular organisms • Much simpler than cells- basically a small amount of DNA or RNA wrapped in protein and sometimes by a additional lipid membrane • Individuals are called a virus particle or virion • Depend on the infected cell’s machinery to multiply and disperse
- 21. 21 Microorganisms vary in size - 1µm to 200 nm. Fig. 1.7 The size of things
- 22. 22 Lifestyles of Microorganisms • Majority of microorganisms lives a free existence called “free-living” (in soil, water, rocks, for example) or as “saprophytes (saprotrophs)” • Some are parasites (mooching off goodies from living beings, but can live freely), some of these are opportunistic pathogens • Fewer are obligate parasites (exo- or endo-parasitic), some of these are pathogens
- 23. 23 Lifestyles of Microorganisms What are the sources of • Energy, • Reductant and • Carbon? How do cells dispose of the harvested electrons • Fermentation • Respiration
- 24. 24 1.6 The Historical Foundations of Microbiology • Key to the study of microorganisms was the development of the microscope • Earliest record of microbes was from the work of Robert Hooke in the 1660s • The most detailed observations of microbes was possible only after Antonie van Leeuwenhoek created the single- lens microscope, further perfected by Ernst Abbé abd Carl Zeiss (~late 19th century) – Leeuwehoek is known as the father of bacteriology & protozoology
- 25. 25 Microorganisms were first observed by Antonie van Leeuwenhoek, using a primitive microscope. Fig. 1.9 Leeuwenhoek’s microscope
- 26. 26 History of Microbiology • Scientific Method • Spores and sterilization • Spontaneous generation • Aseptic technique • Germ theory
- 27. 27 Establishment of the Scientific Method • Early scientists tended to explain natural phenomena by a mixture of belief, superstition, and argument • During the 1600s, true scientific thinking developed • This led to the development of the scientific method – Formulate a hypothesis – Most use the deductive approach to apply the scientific method – Experimentation, analysis, and testing ==> conclusions – Results either support or refute the hypothesis • Hypotheses can eventually become theories • Theories can eventually become laws or principles
- 28. 28 Figure 1.10
- 29. 29 The Development of Medical Microbiology • The Discovery of Spores and Sterilization – Louis Pasteur- worked with infusions in the mid- 1800s – John Tyndall- showed evidence that some microbes have very high heat resistance and are difficult to destroy – Ferdinand Cohn- spores and sterilization • The Development of Aseptic Techniques – Physicians and scientist began to suspect that microorganisms could cause disease – Joseph Lister- introduced aseptic technique
- 30. 30 Spores and sterilization • Some “microbes” in dust and air were resistant to high heat. • Spores were later identified. • The term “sterile” was introduced, which meant completely eliminating all life forms from objects or materials.
- 31. 31 Spontaneous generation Early belief that some forms of life could arise from vital forces present in nonliving or decomposing matter. (flies from manure, etc)
- 32. 32 Louis Pasteur showed microbes caused fermentation & spoilage, and disproved spontaneous generation. Fig. 1.11 Louis Pasteur
- 33. 33 Aseptic technique Ignaz Semmelweis, a Hungarian “OB/GYN” established link between “infection” and diseases after labor. Joseph Lister an English Army Surgeon first introduced the technique in order to reduce microbes in a medical setting and prevent wound infections.
- 34. 34 Germ theory of disease Many diseases are caused by the growth of microbes in the body and not by sins, bad character, or poverty, etc. • Robert Koch was the first to clearly show the causal relationship between bacteria as causal agents and disease in infected animals (including humans).
- 35. 35 Robert Koch verified the Germ theory (Koch’s postulates). Fig. 1.12 Robert Koch
- 36. 36 1.7 Taxonomy: Naming, Classifying, and Identifying Microorganisms • Microbial nomenclature- naming microorganisms • Taxonomy- classifying living things originated over 250 years ago with the work of Carl von Linné • Identification- discovering, comparing and recording the traits of organisms so they can be named and classified • Levels of Classification
- 37. 37 Nomenclature • Binomial (scientific) nomenclature • Genus – Bacillus, always capitalized • species - subtilis, lowercase • Both italicized or underlined – Bacillus subtilis (B. subtilis)
- 38. 38 Levels of Classification • Domain • Kingdom • Phylum or Division • Class • Order • Family • Genus • species
- 39. 39 Figure 1.12
- 40. 40 Identification • The process of discovering, comparing and recording the phenetic (physical, biochemical) and genetic traits of organisms, thereby, placing them in a taxonomic scheme.
- 41. 41 The five-kingdom system became the standard until molecular biology techniques were used to develop the Domain system. Fig. 1.14 Traditional Margulis-Whittaker system of classification
- 42. 42 Subdivisions or Kingdoms • Protista (protists) • Fungi • Plantae (plants) • Animalia (animals)
- 43. 43 The Origin and Evolution of Microorganisms • Phylogeny- the degree of relatedness by descent between groups of living things • Based on the process of evolution- hereditary information in living things changes gradually through time; these changes result in structural and functional changes through many generations – Two preconceptions: • All new species originate from preexisting species • Closely related organisms have similar features because they evolved from a common ancestor • Phylogeny usually represented by a tree- showing the divergent nature of evolution
- 44. 44 Evolution • Classification schemes allow for a universal tree of life “phylogenetic tree”. • Living things change gradually over millions of years • Changes favoring survival are retained & less beneficial changes are lost.
- 45. 45 Domains • Domain system proposed later than the Five-kingdom system • Bacteria - true bacteria, peptidoglycan • Archaea - odd “bacteria” originally believed to only live in extreme environments (high salt, heat, etc) • Eukarya- have a nucleus, & organelles
- 46. 46 The Domain system was developed by Dr. Carl Woese. The basis of this system is the ssu rRNA sequence information. Fig. 1.15 The Woese system - universal tree of life