CHAPTER 1: The Evolution of Microorganisms and Microbiology - - Because not all “prokaryotes” are the same and therefore should not be grouped together in a single kingdom. Currently argued that the term prokaryote is not meaningful and should be abandoned. Great progress Microorganisms – organisms and acellular biological entities too small to be seen clearly by the unaided eye - 1 millimeter or less in diameter Often colonial, consisting of small aggregations of cells Some are multicellular - If multicellular, they lack of highly differentiated tissues Cells exhibited one of two possible “floor plans” a. Prokaryotic cells - Greek pro, before and karyon, nut or kernel; organisms with a primordial nucleus - Have an open floor plan - Contents are not divided into compartments (“rooms”) by membranes (“walls”) - Lack the membrane-delimited nucleus observed in Eukaryotic cells (1) Learned about the detailed structure of microbial cells from the use of electron microscopy. (2) Microbiologists have determined the biochemical and physiological characteristics of many different microorganism (3) Sequences of nucleic acids and protein from a wide variety of organism have been compared. *Comparison of ribosomal RNA (rRNA), begun by Carl Woese in the 1970s. Two very different groups of organisms with prokaryotic cell architecture a. Bacteria b. Archaea ** Protista is not a cohesive taxonomic unit and should be divided into three or more kingdoms. these studies lead to reject the 5-kingdom system in favor of that divides cellular organisms into three domains, 3 Cellular domains 1. Bacteria (true bacteria or eubacteria) 2. Archaea (archaeobacteria, archaebacteria) 3. Eukarya (all eukaryotic organisms b. Eukaryotic cells - Greek eu, true, and karyon, nut or kernel - Have a nucleus but also many other membrane-bound organelles - Separates some cellular materials and processes from others. Classification scheme that divided organisms into (5) five kingdoms 1. 2. 3. 4. 5. Monera All organisms with prokaryotic cell structure Protista Fungi Animalia Plantae *microorganisms (except for viruses and other acellular infectious agents, which have their own classification system) were placed in the first three kingdoms. ** the 5-kingsom system is no longer accepted by microbiologists Roma Flores - 2B1 Figure 1.2 Universal Phylogenetic Tree. Evolutionary relationships are based on rRNA sequence comparisons. By Dr. Norman Pace CHAPTER 1: The Evolution of Microorganisms and Microbiology Bacteria - - - - Single-celled organisms Most have cell walls that contain the structural molecule peptidoglycan. Most exhibit typical prokaryotic cell structure (lack membrane-bound nucleus) ex. Phylum Planctomycetes Abundant in soil, water, air, extreme temperatures, pH or salinity Major inhabitants of our skin, mouth, and intestines. They contribute to the development of the body’s immune system. Microbes help maintain the health and wellbeing of their human hosts. Some cause disease: - The plague (Black death) an anthropod-borne disease Most play beneficial roles: - Break down dead plant and animal material - Make bread, cheese, antibiotics, vitamins, enzymes and other products Cyanobacteria produce significant amounts of oxygen. Archaea - - Distinctive rRNA sequence Lack peptidoglycan in their cell wall Unique membrane lipids Some have unusual metabolic characteristics, such as the methanogens which generate methane (natural) gas. Found in extreme environments, including those with high temperatures (Thermophiles) and high concentrations of salt (extreme halophiles) Eukarya - Many free-living, principal hunters and grazers of the microbial world - Obtain nutrients by ingesting organic matter - Found in different environments and inhabitants of the intestinal tracts of animals, where they aid in digestion of complex materials such as cellulose. c. Slime molds - Behave like protozoa in one stage of their life cycle but like fungi in another. - Hunt for and engulf food particles, consuming decaying vegetation and other microbes. d. Water molds - Protists that grow on the surface of freshwater and moist soil. - Feed on decaying vegetation such as logs and mulch. - Some produced devasting plant infections Ex: Great Potato Famine 2. Fungi - Range from unicellular forms (yeast) to molds and mushrooms. - Moods and mushrooms are multicellular fungi that form thin, thread-like structure called Hyphae. - They absorb nutrients from their environment, including the organic molecules the use as sources of carbon and energy. - Beneficial roles: - Bread rise, producing antibiotics and decomposing dead organisms - Some fungi associate with plant roots to form mycorrhizae. Acellular infectious agents - Microorganisms classified as protists or fungi Animals and plants are also placed in this domain. 1. Protists - Generally unicellular but larger than most bacteria and archaea. Major Protists a. Algae - Photosynthetic - Together with cyanobacteria, produce about 75% of the plant’s oxygen - foundation of aquatic food chains b. Protozoa - Unicellular - Animal-like protists that are motile Roma Flores - 2B1 3. - Viruses smallest of all microbes requires host cell to replicate Acellular entities that must invade a host cell to multiply. Composed of proteins and a nucleic acid Extremely small Smallpox, rabies, influenza, AIDS, common colds and some cancers. 4. Viroid and satellites - Composed only of ribonucleic acid (RNA) Viroid - Causes numerous plant diseases Satellites CHAPTER 1: The Evolution of Microorganisms and Microbiology - 5. - Cause plant diseases and some important animal diseases such as hepatitis * There must have been a single molecule that could do both cellular work and replicate itself. Prions Infectious agents Composed of only protein Responsible for causing a variety of spongiform encephalopathies *Microbes are the dominant organisms on Earth. Evidence for Origin of Life Definition of life - cells and organization response to environmental changes growth and development biological evolution energy use and metabolism regulation and homeostasis reproduction Attributes of importance to paleobiologist are an: - Orderly structure The ability to obtain and use energy (metabolism) Ability to reproduce, Extant organisms - Organisms present today, to explore the origin of life Some have the represent “relics” of ancient life forms Microbial Fossil * The first discovery of primitive cellular life was the 1977 discovery of microbial fossils in the Swartkoppie chert. Chert is a type of granular sedimentary rock rich in silica Swartkoppie chert fossils as well as those from the Archaean Apex Chart of Australia have been dated about 3.5 billion years old. Thomas Cech, 1981 - *RNA found in ribosomes that is responsible for forming peptide bonds – bonds that hold together amino acids, the building blocks of proteins. Ribozymes – catalytic RNA molecules Original molecule must have fulfilled protein and hereditary function - - - Three different molecules fulfill the roles of: Proteins have two major roles in modern cells: 1. Structural 2. Catalytic Roma Flores - 2B1 Ribozymes - RNA molecules that form peptide bonds - perform cellular work and replication Earliest cells may have been RNA surrounded by liposomes Walter Gilbert, 1986 Earliest Molecules – RNA 1. Catalysts 2. Structural molecules 3. Hereditary molecules Discovered a catalytic RNA molecule in a protist (Tetrahymena sp.) - Coined the term RNA world RNA world - To describe a precellular stage in the evolution of life in genetic information, as well as catalyzing other chemical reactions - A lipid membrane must have formed around RNA Liposomes – vesicle bounded by a lipid bilayer Marin Hanczyc, Shelly Fujikawa and Jack Szostak, 2003 CHAPTER 1: The Evolution of Microorganisms and Microbiology - Experiment showed that clay triggers the formation of liposomes that grow and divide. Endosymbiotic Hypothesis - Earliest Molecules – RNA – 2 - - Cellular pool of RNA in modern day cells exists in and is associated with the ribosome (rRNA, tRNA, mRNA) - RNA catalytic in protein synthesis - RNA may be precursor to double stranded DNA Adenosine 5’ triphosphate (ATP) is the energy currency and is a ribonucleotide RNA can regulate gene expression - - *Proteins, DNA and cellular energy can be traced back to RNA Earliest Metabolism - Early energy sources under harsh conditions - inorganics, e.g., FeS Photosynthesis cyanobacteria evolved 2.5 billion years ago Stromatolites – mineralized layers of microorganisms The Evolution of metabolism the evolution of energy-conserving metabolic processes. Hydrogenosome - - - Evolution of 3 Domains of Life - Dr. Norman Pace Developed a universal phylogenetic tree Universal phylogenetic tree - based on comparisons of small subunit rRNA (SSU rRNA) - aligned rRNA sequences from diverse organisms are compared and differences counted to derive a value of evolutionary distance - relatedness, but not time of divergence, is determined this way. - The root or origin of modern life is on bacterial branch but nature still controversial Archaea and Eukarya evolved independently of Bacteria Archaea and Eukarya diverged from common ancestry Roma Flores - 2B1 endosymbiont was an anaerobic bacterium that produced H2 and CO2 as end products of its metabolism. The host become dependent of the H2 produced by the endosymbiont. The capacity to perform aerobic respiration, it evolved into a mitochondrion. Evolution of Cellular Microbes - Mutation of genetic material led to selected traits New genes and genotypes evolved Bacteria and Archaea increase genetic pool by horizontal gene transfer within the same generation Microbial Species - Last Universal Common Ancestor (LUCA) - anaerobic endosymbiont Hydrogen hypothesis Another metabolic strategy, oxygen-releasing photosynthesis, appears to have evolved as early as 2.5 Billion years ago. Fossils of cyanobacteria - Endosymbiosis is an interaction between two organisms in which one organism lives inside the other. Origin of three eukaryotic organelles: 1. Mitochondria – bacterial endosymbiont of an ancestral cell in the eukaryotic lineage list its ability to live independently 2. Chloroplasts – if the intracellular bacterium used aerobic respiration 3. Hydrogenosomes from endosymbiont Mitochondria and chloroplasts - Contain DNA and ribosomes; both like bacterial DNA and ribosomes - ISSU rRNA genes show bacterial lineage - genome sequences closely related to bacterium Rickettsia prowazekii and cyanobacteria genus Prochloron, respectively - Eukaryotic microbes fit definition of reproducing isolated populations - Bacteria and Archaea do not reproduce sexually and are referred to as strains - a strain consists of descendants of a single, pure microbial culture - may be biovars, serovars, morphovars, pathovars binomial nomenclature - genus and species epithet CHAPTER 1: The Evolution of Microorganisms and Microbiology Microbiology and Its Origins Lazzaro Spallanzani (1729-1799) Roman Philosopher Lucretius (about 98-55 BCE) and Physician Girolamo Fracastoro (1478 – 1553) - suggested that disease was caused by invisible living creatures. - - Microbiology – define not only by the organisms it studies but also by the tools used to study them. - Microbiologists often remove microorganisms from their natural habitats and culture them isolated from other microbes: this is called Pure or Axenic culture. - Earliest microscopic observation organisms Using a microscope supplied by Galileo of Robert Hoek - Credited with publishing the first drawing of microorganisms in the scientific literature Detailed drawing of fungus Mucor in his book Mircigraphia - Prototype of the microscopes built and used by the amateur Antony van Leeuwenhoek Antony van Leeuwenhoek of Delft, the Netherlands - - Simple microscope composed double convex glass lenses held between two silver plates. Magnifies 50 to 300 times At 45-degree angle Sent detailed letters describing his discoveries to the Royal Society of London - Both bacteria and protists Spontaneous generation – that living organisms could develop from non-living matter Who challenged it? Francesco Redi, Italian Physician - Discredited spontaneous generation showed that maggots on decaying meat came from fly eggs John Needham (1713-1781) - - his experiment: - mutton broth in flasks boiled sealed results: broth became cloudy and contained microorganisms he thought organic matter contained a vital force that could confer the properties of life on nonliving matter. Roma Flores - 2B1 Theodore Schwann - - Francesco Stelluti his experiment: - broth in flasks (water and seeds) sealed boiled results: no growth of microorganisms he proposed that air carried germs to the culture medium but also commented that the external air might be required for growth of animals already in the medium. allowed air to enter flask containing a sterile nutrient solution after the air had passed through a red-hot-tube results: flask remained sterile Georg Friedrich Schroder and Theodor von Dusch - - allowed air to enter a flask of heat-sterilized medium after it had passed through sterile cotton wool results: No growth occurred in the medium even though the air had not been heated Pouchet - claimed in 1959, to have carried out experiments conclusively proving that microbial growth could occur without air contaminations Louis Pasteur (1822-1895) - - ‘Swan-neck flask’ experiments - placed nutrient solution in flasks - created flasks with long, curved necks - boiled the solutions - left flasks exposed to air results: no growth of microorganisms also showed how to keep solutions sterile Final Blow to Theory of Spontaneous Generation John Tyndall (1820-1893) - - demonstrated that dust carries microorganisms showed that if dust was absent, nutrient broths remained sterile, even if directly exposed to air also provided evidence for the existence of exceptionally heat-resistant forms of bacteria •Ferdinand Cohn (1828-1898) - heat-resistant endospores bacteria could produce CHAPTER 1: The Evolution of Microorganisms and Microbiology The Role of Microorganisms in Disease - - Was not immediately obvious Infectious disease believed to be due to supernatural forces or imbalances of 4 bodily-fluid ‘humors’ Establishing connection depended on development of techniques for studying microbes Robert Koch (1843-1910) - Greek Physician Galen - Microorganisms cause diseases – the Germ Theory of disease. Agostini Bassi (1773-1856) - showed that a disease of silkworms was caused by a fungus M. J. Berkeley (ca. 1845) established the relationship between Bacillus anthracis and anthrax used criteria developed by his teacher Jacob Henle (1809-1895) these criteria now known as Koch’s postulates still used today to establish the link between a particular microorganism and a particular disease Limitations of Koch’s Postulates - Some organisms cannot be grown in pure culture Using humans in completing the postulates is unethical Molecular and genetic evidence may replace and overcome these limits - demonstrated that the great Potato Blight of Ireland was caused by a water mold The Development of Techniques for Studying Microbial Pathogens Heinrich de Bary (1853) Koch’s work led to discovery or development of: - showed that smut and rust fungi caused cereal crop diseases Louis Pasteur - - demonstrated microorganisms carried out fermentations, helping French wine industry developed pasteurization to avoid wine spoilage by microbes showed that the pébrine disease of silkworms was caused by a protozoan he did not agree and believed that fermentations were carried out by living organisms. Pasteurization - Charles Chamberland (1851-1908) - Indirect evidence for the germ theory of disease came from: Joseph Lister - - - provided indirect evidence that microorganisms were the causal agents of disease developed a system of surgery designed to prevent microorganisms from entering wounds as well as methods for treating instruments and surgical dressings his patients had fewer postoperative infections developed a system of antiseptic surgery designed to prevent microorganisms from entering wounds Agar Petri dishes nutrient broth and nutrient agar methods for isolating microorganisms developed porcelain bacterial filters used by Ivanoski and Beijerinck to study tobacco mosaic disease - determined that extracts from diseased plants had infectious agents present which were smaller than bacteria and passed through the filters - infectious agents were eventually shown to be viruses Pasteur and Roux - discovered that incubation of cultures for long intervals between transfers caused pathogens to lose their ability to cause disease (termed ‘attenuation’) Pasteur and his coworkers - developed vaccines for chicken cholera, anthrax, and rabies Immunological Studies - once established, led to study of host defenses - immunology Edward Jenner (ca. 1798) - Roma Flores - 2B1 used a vaccination procedure to protect individuals from smallpox CHAPTER 1: The Evolution of Microorganisms and Microbiology NOTE: this preceded the work establishing the role of microorganisms in disease! Emil von Behring (1854-1917) and Shibasaburo Kitasato (1852-1931) - developed antitoxins for diphtheria and tetanus evidence for humoral (antibody-based) immunity Major Fields in Microbiology - Elie Metchnikoff (1845-1916) - discovered bacteria-engulfing, phagocytic cells in the blood evidence for cellular immunity The Development of Industrial Microbiology and Microbial Ecology - - Louis Pasteur - - demonstrated that alcohol fermentations and other fermentations were the result of microbial activity developed the process of pasteurization to preserve wine during storage - Developments in Microbial Ecology Sergei Winogradsky (1856-1953) and Martinus Beijerinck (1851-1931) - - studied soil microorganisms and discovered numerous interesting metabolic processes (e.g., nitrogen fixation) pioneered the use of enrichment cultures and selective media - - Microbiology Has Basic and Applied Aspects - - Basic aspects are concerned with individual groups of microbes, microbial physiology, genetics, molecular biology and taxonomy Applied aspects are concerned with practical problems – disease, water, food and industrial microbiology Molecular and Genomic Methods - Led to a second golden age of microbiology (rapid expansion of knowledge) Discoveries - restriction endonucleases (Arber and Smith) first novel recombinant molecule (Jackson, Symons, Berg) DNA sequencing methods (Woese, Sanger) bioinformatics and genomic sequencing and analysis Roma Flores - 2B1 Medical microbiology – diseases of humans and animals Public health microbiology – control and spread of communicable diseases Immunology – how the immune system protects a host from pathogens Microbial ecology is concerned with the relationship of organisms with their environment - –less than 1% of earth’s microbial population has been cultured Agricultural microbiology is concerned with the impact of microorganisms on agriculture - food safety microbiology - animal and plant pathogens Industrial microbiology began in the 1800s - fermentation - antibiotic production - production of cheese, bread, etc. Microbial physiology studies metabolic pathways of microorganisms Molecular biology, microbial genetics, and bioinformatics study the nature of genetic information and how it regulates the development and function of cells and organisms Microbes are a model system of genomics R. Stanier and C.B. van Niel - concept of prokaryote, described prokaryotes in terms of what they lacked in comparison to eukaryotic cells. - Pointed out that prokaryotes lack a membrane-bound nucleus, a cytoskeleton, membrane-bound organelles and internal membranous structures such as endoplasmic reticulum and Golgi apparatus. Microorganisms – organisms and acellular biological entities too small to be seen clearly by the unaided eye - 1 millimeter or less in diameter Often colonial, consisting of small aggregations of cells Some are multicellular - If multicellular, they lack of highly differentiated tissues Cells exhibited one of two possible “floor plans” c. Prokaryotic cells - Greek pro, before and karyon, nut or kernel; organisms with a primordial nucleus - Have an open floor plan - Contents are not divided into compartments (“rooms”) by membranes (“walls”) - Lack the membrane-delimited nucleus observed in Eukaryotic cells CHAPTER 1: The Evolution of Microorganisms and Microbiology Two very different groups of organisms with prokaryotic cell architecture c. Bacteria d. Archaea ** Protista is not a cohesive taxonomic unit and should be divided into three or more kingdoms. these studies lead to reject the 5-kingdom system in favor of that divides cellular organisms into three domains, 3 Cellular domains 4. Bacteria (true bacteria or eubacteria) 5. Archaea (archaeobacteria, archaebacteria) 6. Eukarya (all eukaryotic organisms d. Eukaryotic cells - Greek eu, true, and karyon, nut or kernel - Have a nucleus but also many other membrane-bound organelles - Separates some cellular materials and processes from others. Classification scheme that divided organisms into (5) five kingdoms 6. 7. 8. 9. 10. Monera All organisms with prokaryotic cell structure Protista Fungi Animalia Plantae *microorganisms (except for viruses and other acellular infectious agents, which have their own classification system) were placed in the first three kingdoms. ** the 5-kingsom system is no longer accepted by microbiologists - - Because not all “prokaryotes” are the same and therefore should not be grouped together in a single kingdom. Currently argued that the term prokaryote is not meaningful and should be abandoned. Great progress (4) Learned about the detailed structure of microbial cells from the use of electron microscopy. (5) Microbiologists have determined the biochemical and physiological characteristics of many different microorganism (6) Sequences of nucleic acids and protein from a wide variety of organism have been compared. *Comparison of ribosomal RNA (rRNA), begun by Carl Woese in the 1970s. Roma Flores - 2B1 Figure 1.2 Universal Phylogenetic Tree. Evolutionary relationships are based on rRNA sequence comparisons. By Dr. Norman Pace Bacteria - - - Single-celled organisms Most have cell walls that contain the structural molecule peptidoglycan. Most exhibit typical prokaryotic cell structure (lack membrane-bound nucleus) ex. Phylum Planctomycetes Abundant in soil, water, air, extreme temperatures, pH or salinity Major inhabitants of our skin, mouth, and intestines. They contribute to the development of the body’s immune system. Microbes help maintain the health and wellbeing of their human hosts. Some cause disease: - The plague (Black death) an anthropod-borne disease Most play beneficial roles: CHAPTER 1: The Evolution of Microorganisms and Microbiology - - Break down dead plant and animal material - Make bread, cheese, antibiotics, vitamins, enzymes and other products Cyanobacteria produce significant amounts of oxygen. Archaea - - Distinctive rRNA sequence Lack peptidoglycan in their cell wall Unique membrane lipids Some have unusual metabolic characteristics, such as the methanogens which generate methane (natural) gas. Found in extreme environments, including those with high temperatures (Thermophiles) and high concentrations of salt (extreme halophiles) Eukarya - Microorganisms classified as protists or fungi Animals and plants are also placed in this domain. 6. Protists - Generally unicellular but larger than most bacteria and archaea. Major Protists e. Algae - Photosynthetic - Together with cyanobacteria, produce about 75% of the plant’s oxygen - foundation of aquatic food chains f. Protozoa - Unicellular - Animal-like protists that are motile - Many free-living, principal hunters and grazers of the microbial world - Obtain nutrients by ingesting organic matter - Found in different environments and inhabitants of the intestinal tracts of animals, where they aid in digestion of complex materials such as cellulose. g. Slime molds - Behave like protozoa in one stage of their life cycle but like fungi in another. - Hunt for and engulf food particles, consuming decaying vegetation and other microbes. h. Water molds - Protists that grow on the surface of freshwater and moist soil. Roma Flores - 2B1 - Feed on decaying vegetation such as logs and mulch. Some produced devasting plant infections Ex: Great Potato Famine 7. Fungi - Range from unicellular forms (yeast) to molds and mushrooms. - Moods and mushrooms are multicellular fungi that form thin, thread-like structure called Hyphae. - They absorb nutrients from their environment, including the organic molecules the use as sources of carbon and energy. - Beneficial roles: - Bread rise, producing antibiotics and decomposing dead organisms - Some fungi associate with plant roots to form mycorrhizae. Acellular infectious agents 8. - Viruses smallest of all microbes requires host cell to replicate Acellular entities that must invade a host cell to multiply. Composed of proteins and a nucleic acid Extremely small Smallpox, rabies, influenza, AIDS, common colds and some cancers. 9. Viroid and satellites - Composed only of ribonucleic acid (RNA) Viroid - Causes numerous plant diseases Satellites - Cause plant diseases and some important animal diseases such as hepatitis 10. Prions - Infectious agents - Composed of only protein - Responsible for causing a variety of spongiform encephalopathies *Microbes are the dominant organisms on Earth. Evidence for Origin of Life Definition of life - cells and organization response to environmental changes growth and development biological evolution energy use and metabolism regulation and homeostasis reproduction CHAPTER 1: The Evolution of Microorganisms and Microbiology Attributes of importance to paleobiologist are an: - Orderly structure The ability to obtain and use energy (metabolism) Ability to reproduce, Extant organisms - Organisms present today, to explore the origin of life Some have the represent “relics” of ancient life forms Microbial Fossil * The first discovery of primitive cellular life was the 1977 discovery of microbial fossils in the Swartkoppie chert. Chert is a type of granular sedimentary rock rich in silica Swartkoppie chert fossils as well as those from the Archaean Apex Chart of Australia have been dated about 3.5 billion years old. Thomas Cech, 1981 - Discovered a catalytic RNA molecule in a protist (Tetrahymena sp.) *RNA found in ribosomes that is responsible for forming peptide bonds – bonds that hold together amino acids, the building blocks of proteins. Earliest Molecules – RNA Ribozymes – catalytic RNA molecules Three different molecules fulfill the roles of: Original molecule must have fulfilled protein and hereditary function 4. Catalysts 5. Structural molecules 6. Hereditary molecules - Proteins have two major roles in modern cells: 3. Structural 4. Catalytic * There must have been a single molecule that could do both cellular work and replicate itself. - Ribozymes - RNA molecules that form peptide bonds - perform cellular work and replication Earliest cells may have been RNA surrounded by liposomes Walter Gilbert, 1986 - - Coined the term RNA world RNA world - To describe a precellular stage in the evolution of life in genetic information, as well as catalyzing other chemical reactions - A lipid membrane must have formed around RNA Liposomes – vesicle bounded by a lipid bilayer Marin Hanczyc, Shelly Fujikawa and Jack Szostak, 2003 - Experiment showed that clay triggers the formation of liposomes that grow and divide. Earliest Molecules – RNA – 2 Roma Flores - 2B1 CHAPTER 1: The Evolution of Microorganisms and Microbiology - - Cellular pool of RNA in modern day cells exists in and is associated with the ribosome (rRNA, tRNA, mRNA) - RNA catalytic in protein synthesis - RNA may be precursor to double stranded DNA Adenosine 5’ triphosphate (ATP) is the energy currency and is a ribonucleotide RNA can regulate gene expression - - *Proteins, DNA and cellular energy can be traced back to RNA Earliest Metabolism - Early energy sources under harsh conditions - inorganics, e.g., FeS Photosynthesis cyanobacteria evolved 2.5 billion years ago Stromatolites – mineralized layers of microorganisms The Evolution of metabolism the evolution of energy-conserving metabolic processes. Another metabolic strategy, oxygen-releasing photosynthesis, appears to have evolved as early as 2.5 Billion years ago. Fossils of cyanobacteria Evolution of 3 Domains of Life Dr. Norman Pace - Developed a universal phylogenetic tree Universal phylogenetic tree - based on comparisons of small subunit rRNA (SSU rRNA) - aligned rRNA sequences from diverse organisms are compared and differences counted to derive a value of evolutionary distance - relatedness, but not time of divergence, is determined this way. Last Universal Common Ancestor (LUCA) - - The root or origin of modern life is on bacterial branch but nature still controversial Archaea and Eukarya evolved independently of Bacteria Archaea and Eukarya diverged from common ancestry Endosymbiotic Hypothesis - Endosymbiosis is an interaction between two organisms in which one organism lives inside the other. Roma Flores - 2B1 Origin of three eukaryotic organelles: 4. Mitochondria – bacterial endosymbiont of an ancestral cell in the eukaryotic lineage list its ability to live independently 5. Chloroplasts – if the intracellular bacterium used aerobic respiration 6. Hydrogenosomes from endosymbiont Mitochondria and chloroplasts - Contain DNA and ribosomes; both like bacterial DNA and ribosomes - ISSU rRNA genes show bacterial lineage - genome sequences closely related to bacterium Rickettsia prowazekii and cyanobacteria genus Prochloron, respectively Hydrogenosome - anaerobic endosymbiont Hydrogen hypothesis - - endosymbiont was an anaerobic bacterium that produced H2 and CO2 as end products of its metabolism. The host become dependent of the H2 produced by the endosymbiont. The capacity to perform aerobic respiration, it evolved into a mitochondrion. Evolution of Cellular Microbes - Mutation of genetic material led to selected traits New genes and genotypes evolved Bacteria and Archaea increase genetic pool by horizontal gene transfer within the same generation Microbial Species - - Eukaryotic microbes fit definition of reproducing isolated populations - Bacteria and Archaea do not reproduce sexually and are referred to as strains - a strain consists of descendants of a single, pure microbial culture - may be biovars, serovars, morphovars, pathovars binomial nomenclature - genus and species epithet Microbiology and Its Origins Roman Philosopher Lucretius (about 98-55 BCE) and Physician Girolamo Fracastoro (1478 – 1553) CHAPTER 1: The Evolution of Microorganisms and Microbiology - suggested that disease was caused by invisible living creatures. Microbiology – define not only by the organisms it studies but also by the tools used to study them. - Microbiologists often remove microorganisms from their natural habitats and culture them isolated from other microbes: this is called Pure or Axenic culture. - Theodore Schwann - Francesco Stelluti - Earliest microscopic observation organisms Using a microscope supplied by Galileo of Robert Hoek - Credited with publishing the first drawing of microorganisms in the scientific literature Detailed drawing of fungus Mucor in his book Mircigraphia - Prototype of the microscopes built and used by the amateur Antony van Leeuwenhoek - - Simple microscope composed double convex glass lenses held between two silver plates. Magnifies 50 to 300 times At 45-degree angle Sent detailed letters describing his discoveries to the Royal Society of London - Both bacteria and protists Spontaneous generation – that living organisms could develop from non-living matter Who challenged it? Francesco Redi, Italian Physician - Discredited spontaneous generation showed that maggots on decaying meat came from fly eggs John Needham (1713-1781) - - his experiment: - mutton broth in flasks boiled sealed results: broth became cloudy and contained microorganisms he thought organic matter contained a vital force that could confer the properties of life on nonliving matter. allowed air to enter flask containing a sterile nutrient solution after the air had passed through a red-hot-tube results: flask remained sterile Georg Friedrich Schroder and Theodor von Dusch - - allowed air to enter a flask of heat-sterilized medium after it had passed through sterile cotton wool results: No growth occurred in the medium even though the air had not been heated Pouchet - Antony van Leeuwenhoek of Delft, the Netherlands - broth in flasks (water and seeds) sealed boiled results: no growth of microorganisms he proposed that air carried germs to the culture medium but also commented that the external air might be required for growth of animals already in the medium. - claimed in 1959, to have carried out experiments conclusively proving that microbial growth could occur without air contaminations Louis Pasteur (1822-1895) - - ‘Swan-neck flask’ experiments - placed nutrient solution in flasks - created flasks with long, curved necks - boiled the solutions - left flasks exposed to air results: no growth of microorganisms also showed how to keep solutions sterile Final Blow to Theory of Spontaneous Generation John Tyndall (1820-1893) - - demonstrated that dust carries microorganisms showed that if dust was absent, nutrient broths remained sterile, even if directly exposed to air also provided evidence for the existence of exceptionally heat-resistant forms of bacteria •Ferdinand Cohn (1828-1898) - heat-resistant endospores bacteria could Lazzaro Spallanzani (1729-1799) - his experiment: Roma Flores - 2B1 The Role of Microorganisms in Disease produce CHAPTER 1: The Evolution of Microorganisms and Microbiology - - Was not immediately obvious Infectious disease believed to be due to supernatural forces or imbalances of 4 bodily-fluid ‘humors’ Establishing connection depended on development of techniques for studying microbes - Greek Physician Galen - Microorganisms cause diseases – the Germ Theory of disease. Agostini Bassi (1773-1856) - showed that a disease of silkworms was caused by a fungus M. J. Berkeley (ca. 1845) established the relationship between Bacillus anthracis and anthrax used criteria developed by his teacher Jacob Henle (1809-1895) these criteria now known as Koch’s postulates still used today to establish the link between a particular microorganism and a particular disease Limitations of Koch’s Postulates - Some organisms cannot be grown in pure culture Using humans in completing the postulates is unethical Molecular and genetic evidence may replace and overcome these limits - demonstrated that the great Potato Blight of Ireland was caused by a water mold The Development of Techniques for Studying Microbial Pathogens Heinrich de Bary (1853) Koch’s work led to discovery or development of: - showed that smut and rust fungi caused cereal crop diseases Louis Pasteur - - demonstrated microorganisms carried out fermentations, helping French wine industry developed pasteurization to avoid wine spoilage by microbes showed that the pébrine disease of silkworms was caused by a protozoan he did not agree and believed that fermentations were carried out by living organisms. Pasteurization - Charles Chamberland (1851-1908) - Indirect evidence for the germ theory of disease came from: Joseph Lister - - - provided indirect evidence that microorganisms were the causal agents of disease developed a system of surgery designed to prevent microorganisms from entering wounds as well as methods for treating instruments and surgical dressings his patients had fewer postoperative infections developed a system of antiseptic surgery designed to prevent microorganisms from entering wounds Agar Petri dishes nutrient broth and nutrient agar methods for isolating microorganisms developed porcelain bacterial filters used by Ivanoski and Beijerinck to study tobacco mosaic disease - determined that extracts from diseased plants had infectious agents present which were smaller than bacteria and passed through the filters - infectious agents were eventually shown to be viruses Pasteur and Roux - discovered that incubation of cultures for long intervals between transfers caused pathogens to lose their ability to cause disease (termed ‘attenuation’) Pasteur and his coworkers - developed vaccines for chicken cholera, anthrax, and rabies Immunological Studies - once established, led to study of host defenses - immunology Edward Jenner (ca. 1798) Robert Koch (1843-1910) Roma Flores - 2B1 used a vaccination procedure to protect individuals from smallpox CHAPTER 1: The Evolution of Microorganisms and Microbiology NOTE: this preceded the work establishing the role of microorganisms in disease! Emil von Behring (1854-1917) and Shibasaburo Kitasato (1852-1931) - developed antitoxins for diphtheria and tetanus evidence for humoral (antibody-based) immunity Major Fields in Microbiology - Elie Metchnikoff (1845-1916) - discovered bacteria-engulfing, phagocytic cells in the blood evidence for cellular immunity The Development of Industrial Microbiology and Microbial Ecology - - Louis Pasteur - - demonstrated that alcohol fermentations and other fermentations were the result of microbial activity developed the process of pasteurization to preserve wine during storage - Developments in Microbial Ecology Sergei Winogradsky (1856-1953) and Martinus Beijerinck (1851-1931) - - studied soil microorganisms and discovered numerous interesting metabolic processes (e.g., nitrogen fixation) pioneered the use of enrichment cultures and selective media Microbiology Has Basic and Applied Aspects - - Basic aspects are concerned with individual groups of microbes, microbial physiology, genetics, molecular biology and taxonomy Applied aspects are concerned with practical problems – disease, water, food and industrial microbiology Molecular and Genomic Methods - Led to a second golden age of microbiology (rapid expansion of knowledge) Discoveries - restriction endonucleases (Arber and Smith) first novel recombinant molecule (Jackson, Symons, Berg) DNA sequencing methods (Woese, Sanger) bioinformatics and genomic sequencing and analysis Roma Flores - 2B1 - - Medical microbiology – diseases of humans and animals Public health microbiology – control and spread of communicable diseases Immunology – how the immune system protects a host from pathogens Microbial ecology is concerned with the relationship of organisms with their environment - –less than 1% of earth’s microbial population has been cultured Agricultural microbiology is concerned with the impact of microorganisms on agriculture - food safety microbiology - animal and plant pathogens Industrial microbiology began in the 1800s - fermentation - antibiotic production - production of cheese, bread, etc. Microbial physiology studies metabolic pathways of microorganisms Molecular biology, microbial genetics, and bioinformatics study the nature of genetic information and how it regulates the development and function of cells and organisms Microbes are a model system of genomics R. Stanier and C.B. van Niel - concept of prokaryote, described prokaryotes in terms of what they lacked in comparison to eukaryotic cells. - Pointed out that prokaryotes lack a membrane-bound nucleus, a cytoskeleton, membrane-bound organelles and internal membranous structures such as endoplasmic reticulum and Golgi apparatus.
