Topic 1 Microbial World Students 2024 PDF

Topic 1 Microbial World  What is microbiology? the study of microbes examines how microbes interact with humans, with food, and how they can be used by humans Disciplinary basis for molecular biology and biotechnology Definitions (microbe, microorganism)  Classifying Microbes Prokaryotic...

Topic 1 Microbial World  What is microbiology? the study of microbes examines how microbes interact with humans, with food, and how they can be used by humans Disciplinary basis for molecular biology and biotechnology Definitions (microbe, microorganism)  Classifying Microbes Prokaryotic cell Eukaryotic cell Figure 1.7 Microorganisms versus macroorganisms  Historical Roots of Microbiology Robert Hooke (1635-1703) – early microscopes allowed first description of microbes: fruiting structures of “molds” (i.e., fungi)  Historical Roots of Microbiology Antonie van Leeuwenhoek (1632-1723) – improvements in lens construction allowed first description of bacteria  I then most always saw, with great wonder, that in the said matter there were many very little living animalcules, very prettily a-moving. -antonie van Leeuwenhoek Why study microbiology? Microorganisms were the first life on Earth Microorganisms established biosphere conditions that allowed multicellular organisms to evolve – O2! Multicellular organisms evolved from microorganisms >50% of the biomass on Earth is comprised of microorganisms Microorganisms will be on Earth forever Why study microbiology? Our understanding of life (e.g., evolution, metabolism, biochemistry, and genetics) has arisen largely from studies of microorganisms We still know very little about the microorganisms that are present on Earth Figure 1.10 Why study microbiology? fast, cheap, and easy to grow produce enzymes and other molecules for industrial/medical uses most have small numbers of genes, making them simpler to study genetic manipulation of single- celled bacteria is usually much easier than multicellular eukarya Figure 1.10 Studying the genetics of microbes can help us use them to benefit humans e.g., mass-production of molecules Figure 1.25 Biogeochemistry Biotechnology Thanks Handelsman J. 2007. Encyclopedia of Life Sciences Environment Health Agriculture Food Jo Handelsman Core features of life metabolism growth reproduction and at least on Earth, these are achieved by… genetic variation/evolution response/adaptation homeostasis* *maintaining internal organization and order, usually by expending energy to do so  How do microbes get energy? heterotroph: ingests preformed organic molecules autotroph: produces organic molecules Figure 1.17 How do microbes get energy? One example: Organic molecules are broken down by microbes to harness chemical energy (ATP) fermentation aerobic respiration Figure 1.18 Microbes can also help in biogeochemical cycling as they interact with the environment – cycling inorganic molecules to organic molecules and back microbes live in diverse groups in nature many different members (populations) form a microbial community and ecosystem Macromolecules  The Phylogenetic Tree divided into three domains based on ribosomal RNA sequences Eukarya Archaea Bacteria Figure 1.8 Thanks to [Carl] Woese, the tree of life gained a third great trunk, more solid branches, and new twigs. Woese died in 2012, and Nobels cannot be awarded posthumously, but it's absurd that someone who unveiled the full extent of life should be denied by something as trivial as death” – Ed Yong Homework (pgs 9-10 in 3rd ed, 10-11 in 2nd) Question #1 will be a midterm question each of the three domains have important commonalities and defining characteristics Figure 1.9 C Viruses Technically, viruses aren’t considered “alive” don’t replicate outside of a host cell little to no biochemical activity outside of a host cell inert and nonreactive outside of a host cell  The Phylogenetic Tree divided into three domains based on ribosomal RNA sequences Eukarya Archaea Bacteria Figure 1.8  Origin of Life Early Earth conditions were harsh little oxygen in the atmosphere high temperatures high CO2 planet surface was a chemical soup, with a reducing atmosphere initial synthesis of first macromolecules Figure 1.12  First life molecules In the 1950s, a grad student named Stanley Miller worked with his mentor, Harold Urey, to simulate the “spark” that might have started forming organic molecules from the primordial soup Figure B1.3  Requirements of early life genetic information storage the ability to catalyze biochemical reactions a way of separating the cell interior from the external environment  Ribozymes RNA behaving like enzymes reaction catalyst genetic information storage self-replicating Figure B5.4  Micelles may have been an early form of plasma membrane Figure 1.14 RNA world Prior to the last universal common ancestor (LUCA) Conceived by Carl Woese Figure 1.15 Double-Stranded DNA provides a “backup copy” of the genetic information more stable than RNA Figure 1.19 Figure 1.12 Features Membrane bound ATP as chemical energy DNA to RNA to protein Eats CO2 Fixes N2 Anaerobe Thermophile https://en.wikipedia.org/wiki/Hydrothermal_vent  Origin of Life How to circumvent the scarcity of readily oxidized electron donors away from hydrothermal vents? Ancestors of the cyanobacteria are first to solve the problem and produce O2 as a toxic byproduct Figure 1.12 multicellular fossils dating to about 0.5 billion ybp have been found—meaning microbes dominated the planet for approximately 3.5 billion years! microbial fossil records exist, largely in fossilized “stromatolites” (carbonate pedestals with photosynthetic microbial mat on top) Figure 1.13 Modern stromatolites Steep Rock Lake Belt, NW Ontario 2.7-billion-year-old “The ones in the Ottawa river are Ordivician… they’re around 250-260 million years old.” “But they’re actually just an example of the most primitive life form that started way back around 8 billion years ago…” “They're still growing today. So [a] first life form [and] they're still with us and they'll Allan Donaldson, a retired probably be here after we professor in the earth destroy ourselves” sciences department at Carleton University.  Modern RNA DNA is transcribed into messenger RNA (mRNA) mRNA is translated into proteins Figure 1.20 other forms of RNA (transfer RNA - tRNA, ribosomal RNA - rRNA) show RNA versatility for critical life processes Knowing the way basic systems work allows us to examine microbial genomes from two different perspectives: 1. Examining effects of single mutations in DNA individually (microbial genetics) Figure 1.22 2. Studying and comparing pieces of genomes to each other across domains (phylogeny) Figure 1.23  Origin of Eukaryotes Endosymbiotic theory Primitive prokaryotic microbes ingested other microbes, starting a symbiotic relationship, forming the first basic eukaryotes. Figure 1.16  Microbes and Disease microbes weren’t always associated with disease historically, disease believed to be caused by wordinfo “bad air” or “angry gods” when microbes were discovered, it was thought they could spontaneously form from nonliving matter Wikipedia Microbes and Disease Louis Pasteur (1822-1895) discovered that living organisms discriminate between optical isomers explained biological nature of alcoholic fermentation developed vaccines for anthrax, fowl cholera, and rabies developed pasteurization introduced sanitization in hospitals disproved spontaneous generation and developed methods for controlling growth  Louis Pasteur disproved spontaneous generation theory in the late 1800s Figure 1.26 Robert Koch (1843-1910) Figure 1.27B determined Bacillus anthracis was the cause of anthrax and Mycobacterium was the cause of tuberculosis  Robert Koch (1843-1910) established basic rules for determining which microbes caused which diseases – Koch’s postulates Figure 1.27A Koch’s postulates can be used to show a specific microbe causes a specific disease The cause and effect are proven if: the suspected microbe is identified in every person with the disease, but not those without the illness a pure culture of the suspected microbe is obtained experimental inoculation of the suspected microbe into a healthy test host causes the same illness the suspected microbe is recovered from the experimentally inoculated host organism Koch’s postulates in action: gastric ulcers ulcers are sores on the lining of the stomach, thought to be caused by excess acid in the 1980s, researchers isolated the microbe Helicobacter pylori from ulcerated tissue by applying classic Koch’s postulate rules, this microbe was found to be the causative agent of stomach ulcers Some microbial diseases have had a profound impact on humanity, such as bubonic plague Figure 1.28 Black Death Figure 1.29 Diseases have long ravaged human populations Bubonic plague (“Black Death”) in the 1300s Exploration of the Americas in the 1500‒1600s bringing European diseases to indigenous humans Spanish flu in the early 1900s (H1N1) Figure 18.1 In the twentieth century, we have seen a dramatic drop in deaths from infectious diseases. Figure 1.30 Causes of Death: North America, 1900 Causes of Death: North America, 2000 Prevention of Infection antiseptics sanitation improvements food/water safety personal hygiene vaccination antibiotics  Despite advances in vaccinations, antibiotics, sanitation, and medical care, infectious diseases still take a heavy toll on human life. Figure 18.2