Allies and Enemies: How the World Depends on Bacteria Read Online Free PDF Page A

falls and cyanobacteria slow their metabolism, other bacteria devour the oxygen. Purple bacteria prefer
    anoxic conditions, so they live deep in the mat until the oxygen has been depleted. In the night, the purple bacteria swim upward and feast on organic wastes from the cyanobacteria. The sunlight returns, and
     
    the purple bacteria descend to escape the photosynthesis about to replenish the upper mat with oxygen. As they digest their meal, these
    bacteria expel sulfide compounds that diffuse to the top layer. There,
    sulfur-requiring photosynthetic bacteria join the cyanobacteria (and some algae) in a new cycle. An undisturbed mat literally breathes: absorbing oxygen and emitting it, expelling carbon dioxide and inhaling it one breath every 24 hours. Microbial mats’ diurnal cycle makes them a distinctive microbial community.
    Communities are mixtures of species within an ecosystem. Ecosystems contain living communities that interact with the nonliving things around them: air, water, soil, and so on. Bacteria participate in every phase of ecosystem life, but to learn about bacteria microbiologists must remove them from the environment and study one species at a time in a laboratory. A collection of bacterial cells all of the same species is called a population, or in lab talk a pure culture.
    Microbiologists learn early in their training the tricky job of keeping all other life out of a pure culture by using aseptic technique.
    Aseptic—loosely translated as “without contamination”—technique
    requires that a microbiologist manipulate cultures without letting in
     
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    allies and enemies
    any unwanted bacteria. They accomplish this by briefly heating the
    mouth of test tubes over a Bunsen burner flame, similarly flaming metal inoculating loops, and learning to keep sterilized equipment from touching unsterilized surfaces. Surgeons follow the same principles after they scrub up for surgery.
    Under the microscope
    For the two centuries following van Leeuwenhoek’s studies, microscopes improved, but microbiologists still needed a way to distinguish cells from inanimate matter in a specimen. They tested a variety of chemical dyes on bacteria with usually unsatisfactory results. In 1884, Danish physician Hans Christian Gram formulated through trial and error a stain for making bacteria visible in the tissue of patients with respiratory infection. On a glass slide, Gram’s recipe turned some of the bacteria dark purple and others pink. The new method served Gram’s purposes for diagnosing disease, but he had no notion of the
    impact the Gram stain would have on bacteriology.
     
    The Gram stain divides all bacteria into two groups: gram-positive and gram-negative. This easy procedure serves as the basis
    for all identifications of bacteria from the sick, from food and water, and from the environment. Every student in beginning microbiology
    commences her education by learning the Gram stain.
    Bacteria with thick cell walls of peptidoglycan retain a crystal violet-iodine complex inside the wall. These cells turn purple and are
    termed gram-positive. Other species cannot retain the stain-iodine complex when rinsed with alcohol. These gram-negative cells
    remained colorless, so Gram added a final step by soaking the bacteria in a second stain, safranin, that turned all the colorless cells pink.
    All bacteriologists now use the Gram stain as the first step in identification, monitoring food and water for contamination, and diagnosing infectious disease.
    In the more than 100 years since Gram invented the technique,
    microbiologists have yet to figure out all the details that make some
    cells gram-positive and others gram-negative. The thick peptidoglycan layer in gram-positive cell walls has an intricate mesh of cross-links. This structure acts as a net to retain the large crystal chapter 1 · why the world needs bacteria
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    violet-iodine aggregate and might keep the alcohol from reaching the
    stain and washing it out.