Microbiology: Scope and History PDF

The Scope and History of Microbiology Chapters 1, 2, 13, 18  It is a microbial world! microbes impact our lives in many different ways  Tree of life: the 3 domains most of the diversity of life on our planet is microbial!  Tree of life: the 3 domains we can make a singl...

The Scope and History of Microbiology Chapters 1, 2, 13, 18  It is a microbial world! microbes impact our lives in many different ways  Tree of life: the 3 domains most of the diversity of life on our planet is microbial!  Tree of life: the 3 domains we can make a single phylogenetic tree for all cellular organisms on the planet because all cells have some universally conserved genes, such as the genes for ribosomal RNA this does not work for viruses: there is not a single universal viruses are the most abundant conserved gene in and most diverse form of life viruses on our planet  Tree of life: the 3 domains we can make a single phylogenetic tree for all cellular organisms on the planet because all cells have some universally conserved genes, such as the genes for ribosomal RNA all cells have a shared common ancestor (Last Universal Common Ancestor)  Tree of life: the 3 domains we can make a single phylogenetic tree for all cellular organisms on the planet because all cells have some universally conserved genes, such as the genes for ribosomal RNA ? controversy and debate about how it went from LUCA to current 3 domains and some people even argue that LUCA was a virus! origins of eukaryotes is a very active area of research and debate (e.g., discovery of the “Asgard” Archaea)  Tree of life: the 3 domains tree of life in 1969: tree of life after development of molecular biology, DNA sequencing, and use of ribosomal RNA genes for evaluating relationships amongst cellular organisms: © 2018 Pearson Education, Inc. © 2018 Pearson Education, Inc.  Microbial diversity application of molecular biology techniques to study microbes in natural environments has completely revolutionized our understanding of the diversity of organisms present on our planet diversity of bacterial phyla  It is a microbial world! microbes were the first life forms microbes were the only life forms for most of the history of Earth all life on Earth (including human) depends on microbes microbes are the most abundant organisms and make up most of the living mass on Earth 018 Pearson Education, Inc.  It is a microbial world! 8 Pearson Education, Inc. © 2018 Pearson Education, Inc.  It is a microbial world! >.01.1 1 1 10 50 Chlorophyll a concentration (mg/m 3) most of Earth’s surface is covered by water the water is full of microbes can see the microbes from space 1/2 of every breath of O2 comes from microbes in the oceans It is a microbial world! SeaWiFS Biosphere Data NASA/Goddard Space Flight Center Scientific Visualization Studio Norman Kuring (NASA/GSFC)  It is a microbial world! there are an estimated 2.5 x 1030 microbial cells on the planet! although they are tiny individually, when you add them all up they © 2018 Pearson Education, Inc. account for a major portion of the planet’s biomass  It is a microbial world! microbes are everywhere they live in complex communities lake water sewage scraped off a human tongue  It is a microbial world! microbes are everywhere Fig 1.10 they live in complex communities human digestive system  Microbes are everywhere! Extremophiles: organisms that live in what seem like impossible conditions to us can be Bacteria or Archaea (also a few eukaryotic extremophiles) extremes of: salt temperature pressure pH (and combinations)  It is a microbial world! our planet is based on a foundation of microbiology every aspect of the biological functioning of our planet is driven by microbes even some non-biological functions, such as climate, are affected by microbes © 2018 Pearson Education, Inc. The start of life on Earth one plausible hypothesis for the origin of life on earth is that it happened at the bottom of the oceans small compartments in rocks contained biological materials and allowed those materials replicated in there lipid bilayers then replaced the rock compartments to form cells with membranes  The start of life on Earth this is one view: others believe first cells were RNA-based and that DNA was invented after first cells existed – and possibly that viruses invented DNA  The start of life on Earth fossil Bacteria from 3.45 bya stromatolites: current and fossil formations in rocks caused by microbes - the most persistent evidence of life in Earth history most recent evidence for oldest microbial life is 3.7 billion years ago in stromatolite structures agrees with genetic molecular clock studies that suggest life’s origin was at least 4 billion years ago  Microbes have global impacts production of O2 by oxygenic phototrophs (ancestors of the current cyanobacteria) created the banded iron formations found in rocks by oxidation of Fe2+ to Fe3+ after all the Fe2+ was used up, O2 accumulated and changed Earth’s atmosphere from anaerobic to aerobic: the Great Oxidation Event  Microbes have global impacts Earth’s atmosphere was anaerobic (i.e., no O2) when the planet formed production of O2 by cyanobacteria changed Earth’s atmosphere from anaerobic to aerobic this resulted in the formation of the ozone layer, which blocked some of the UV light and allowed colonization of the land also allowed the evolution of aerobic organisms anaerobes that could not tolerate O2 became restricted to specific environments © 2018 Pearson Education, Inc.  Microbes have global impacts large-scale growths of microbes in the oceans such as algal blooms can have dramatic impacts on the local environment - can change the O2 and nutrient availability, and also cause additional changes when the blooms end and the cells die  What are microorganisms? micro = small microorganisms: 1. single-celled microscopic organisms some can be multi-cellular at certain times some are colonial 3 different types of cellular microorganisms: bacteria archaea eukaryotes 2. viruses microscopic but not cellular not physiologically active a huge variety of shapes, sizes and lifestyles  What are microorganisms? micro = small a single colony of bacteria on a petri plate contains >107 cells  The typical prokaryotic cell what makes a prokaryote a prokaryote? no internal membrane-bound organelles no nucleus usually small cells have distinct organization includes Bacteria and Archaea and structures The typical prokaryotic cell what makes a prokaryote a prokaryote? there are exceptions….. Gemmata: a nucleated bacterium no internal membrane-bound organelles no nucleus usually small cells includes Bacteria and Archaea  The typical prokaryotic cell what makes a prokaryote a prokaryote? there are exceptions….. specialized membrane systems in phototrophic bacteria no internal membrane-bound organelles no nucleus usually small cells includes Bacteria and Archaea  The typical prokaryotic cell what makes a prokaryote a prokaryote? there are exceptions….. Epulopiscium fishelsoni Thiomargarita namibiensis ~0.6 mm long (smaller cells are ~0.5 mm diameter eukaryotes) no internal membrane-bound organelles no nucleus usually small cells includes Bacteria and Archaea  June 2022 this one is quite exceptional!  this organism challenges our traditional concepts of bacterial cells quite unusual in terms of overall metabolism and biology: >5x105 copies of the genome in each cell, compartmentalization with ribosomes inside organelles where translation takes place  Typical eukaryotic cells what makes a eukaryote a eukaryote? internal membrane-bound organelles have a nucleus usually large cells: 10-100 μm diameter include algae, protozoa, fungi (animals and plants) Origin of eukaryotes Eukaryotic cells arose by mergers of different prokaryotic cells nucleus probably originated within an archaeal cell mitochondrion evolved by endosymbiosis of a bacterium chloroplasts evolved from a cyanobacterium other proposed variations on this scheme exist In 2017: scientists discovered a new group of Archaea in the environment (only detected by sequencing DNA from the environment) that are the closest known relatives to eukaryotes. They make a lot of proteins formerly considered specific to eukaryotes, so this helps close one of the gaps between the different groups.  2020: scientists grew one of the Asgard archaea in culture in the lab - it took them 12 years to grow it! Will only grow with another organism present (syntrophy) cells sometimes have long protrusions  Most eukaryotes are microbes Most of the space on the eukaryote tree is taken up by microorganisms – most are protists but there is also an extremely high diversity of species within the fungi, many of which are also microbes  Most eukaryotes are microbes there is a very complex evolutionary history within the eukaryotic domain, with several cases of secondary endosymbioses (where a eukaryote was taken into another eukaryote as an endosymbiont)  Viruses viruses are the most abundant and most diverse form of life on the planet infect eukaryotes, Bacteria and Archaea (and other viruses?) lack many attributes of cells: no inherent metabolism cannot reproduce without a host cell obligate intracellular parasites (symbionts) Bacteriophages viruses that infect Bacteria are called “bacteriophage” or “phage” means “bacterium eater” phages are the most abundant type of virus, and therefore the most abundant form of life on the planet: >106 phages in every 1 ml of the oceans = >1030 in the oceans alone! 10X more abundant than cells in ~every environment examined Visualizing microbes with microscopes need specialized equipment (microscopes) to observe microbes, especially most prokaryotes, because of their small size microscopes from the 1600s microscopes have been around for a long time!  Microscopy microscope technology is now very advanced many different types of microscopes and techniques light microscope bright-field phase contrast dark-field manipulation of the light to improve contrast and visibility of cells  Microscopy some cells are large and pigmented and this makes them easier to see with bright- field microscopy purple bacterial cells (~5 µm) algal cells (~15 µm) Microscopy - Stains use of stains helps make it easier to see small cells on a light microscope Microscopy - Stains The Gram stain: a very important differential stain that distinguishes two types of bacteria due to differences in their cell wall structures (section 2)  Microscopy fluorescence microscopy: visualizing cells through molecules that emit light cyanobacteria in a light microscope and in a fluorescence microscope bacterial cells stained with a chemical that binds to DNA and fluoresces  Microscopy fluorescence microscopy: visualizing cells through molecules that emit light development of new and brighter DNA stains in the 1990s allowed people to count viruses this way  Microscopy - other techniques differential interference contrast microscopy atomic force microscopy confocal scanning laser microscopy electron microscopy (EM) transmission (TEM) scanning (SEM) “The role of the infinitely small in nature is infinitely large” -Louis Pasteur (1822-1895) The Impact of Microorganisms microbes have huge impacts on humans as agents of disease very different situation today compared with 100 years ago only a very small proportion of microbes is harmful to humans The Impact of Microorganisms microbes are extremely important in agriculture The Impact of Microorganisms extremely important in food production many of our foods are “generated” by microbes, called ”fermented foods” The Impact of Microorganisms many industries, including the ever-increasing biofuels industry, are dependent on microbes, or affected by them (e.g., microbial pipeline fouling) The first microbiologists Robert Hooke (1635-1703) Hooke made the first published description of a microorganism in 1665 (fungi) The first microbiologists Antoni van Leeuwenhoek (1632-1723) c = red blood cells seen through his microscope he made the first observation of Bacteria in 1676 (published in 1684)  The rise of microbiology It was ~150 years later that these first observations of microbes were followed by major breakthroughs and microbiology became a scientific discipline Several key scientists were responsible for these breakthroughs Louis Pasteur: vaccines, fermentation, disproved spontaneous generation Robert Koch: pure cultures, microbial causes of disease Martinus Beijerinck: enrichment cultures, first discovery of a virus Sergei Winogradsky: chemolithotrophy (= eating rocks)  The rise of microbiology At the time of Pasteur and Koch, these were 4 of the most important questions relating to microbiology: is spontaneous generation of life possible? what causes fermentation? what causes disease? can infection and disease be prevented? Louis Pasteur and spontaneous generation the theory of SPONTANEOUS GENERATION: organisms can arise spontaneously from non-living material if you leave some food sitting around, it will eventually rot when examined in a microscope, it is full of microorganisms they weren’t there before - so where did they come from? Pasteur showed that microorganisms that looked like the ones in rotting material could be found in the environment and the air - so he believed these organisms were coming from the air and then growing on the material Louis Pasteur and spontaneous generation the theory of SPONTANEOUS GENERATION: organisms can arise spontaneously from non-living material It had been shown that if you heated liquid broth in a flask to kill all the microbes, and then sealed the flask, nothing would grow so, in that case there was no “spontaneous generation” But skeptics claimed this was caused by the heating of the air, and that it was only a lack of fresh air that prevented the spontaneous generation Pasteur’s defeat of spontaneous generation - 1864 invented swan-necked flasks (now called “Pasteur flasks”) to allow him to perform an experiment and disprove the theory liquid still had contact with “fresh air” but nothing grows growth only happened when liquid contacted material that settled out of the air this allowed improvements to food preservation: e.g., milk “pasteurization”  Pasteur’s other accomplishments 1. Pasteur used an experimental approach to show it was microorganisms that caused fermentation, and which ones: fungi ferment sugars to ethanol bacteria ferment sugars to acids The Pasteur Institute in Paris 2. Did experiments with yeast and bread-making to improve quality and reproducibility in bread production 3. Developed vaccines against: anthrax, fowl cholera, rabies 4. Contributed to the concept of the “germ theory of disease” Robert Koch (1843-1910): What causes disease? -essentially proved the germ theory of disease -studied the cause of Anthrax -examined colonies of microorganisms and pioneered work on growing bacteria and using pure cultures -formulated his famous postulates -his work allowed development of treatments and preventative measures to limit spread of infectious diseases  Koch’s postulates used a combination of theory and experimental work to establish the protocol for proving that a specific organism causes a disease was done using Bacillus anthracis (causes anthrax) as a model satisfying these criteria is not possible for every infectious disease - need a suitable animal model, etc.  Koch’s postulates used a combination of theory and experimental work to establish the protocol for proving that a specific organism causes a disease was done using Bacillus anthracis (causes anthrax) as a model note that the organism needs to be grown on its own (= in pure culture) for this to work Koch was instrumental in developing the idea of pure culture and the use of solid growth surfaces for getting colonies (he started by growing colonies on slices of potatoes)  Koch and tuberculosis proved that tuberculosis was caused by a bacterium (Mycobacterium tuberculosis) observed the bacterium in in sputum from lung tissues infected patients 1/7 deaths at that time were from TB cultured the bacterium in coagulated serum  Koch and tuberculosis Fig. 1.31 proved that tuberculosis was caused by a bacterium (Mycobacterium tuberculosis) developed a special staining technique to see the bacterial cells, which was needed because of the cell wall structure of this bacterium used guinea pigs to do the experiments to satisfy his postulates awarded the Nobel Prize in 1905 also discovered cause of cholera