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Microbiology (Bruslind)

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    What is microbiology? If we break the word down it translates to “the study of small life,” where the small life refers to microorganisms or microbes. But who are the microbes? And how small are they? Generally microbes can be divided into two categories: the cellular microbes (or organisms) and the acellular microbes (or agents). In the cellular camp we have the bacteria, the archaea, the fungi, and the protists (a bit of a grab bag composed of algae, protozoa, slime molds, and water molds). Cellular microbes can be either unicellular, where one cell is the entire organism, or multicellular, where hundreds, thousands or even billions of cells can make up the entire organism. In the acellular camp we have the viruses and other infectious agents, such as prions and viroids. In this textbook the focus will be on the bacteria and archaea (traditionally known as the “prokaryotes,”) and the viruses and other acellular agents.

    • 1: Introduction to Microbiology
      Generally microbes can be divided into two categories: the cellular microbes (or organisms) and the acellular microbes (or agents). Cellular microbes include bacteria, the archaea, the fungi, and the protists ( algae, protozoa, slime molds, and water molds). Cellular microbes can be either unicellular or multicellular. Acellular microbes include viruses and other infectious agents, such as prions and viroids.
    • 2: Microscopes
      With the advent of molecular biology there’s a lot of microbiology nowadays that happens without a microscope. But if you want to actually visualize microbes, you’ll need the ability to magnify – you’ll need a microscope of some type. And, since “seeing is believing,” it was the visualization of microbes that got people interested in them in the first place.
    • 3: Cell Structure I
      Cellular organisms are divided into two broad categories, based on their cell type: prokaryotic or eukaryotic. Generally, prokaryotes are smaller, simpler, with a lot less stuff, and eukaryotes are larger, more complex. The crux of their key difference can be deduced from their names: “karyose” is a Greek word meaning “nut” or “center,” a reference to the nucleus. “Pro” means “before,” while “Eu” means “true,” indicating that prokaryotes lack a nucleus while eukaryotes have a true nucleus.
    • 4: Bacteria - Cell Walls
      It is important to note that not all bacteria have a cell wall. Having said that though, it is also important to note that most bacteria (about 90%) have a cell wall and they typically have one of two types: a gram positive cell wall or a gram negative cell wall.
    • 5: Bacteria - Internal Components
      We have already covered the main internal components found in all bacteria, namely, cytoplasm, the nucleoid, and ribosomes. Remember that bacteria are generally thought to lack organelles, those bilipid membrane-bound compartments so prevalent in eukaryotic cells (although some scientists argue that bacteria possess structures that could be thought of as simple organelles). But bacteria can be more complex, with a variety of additional internal components to be found.
    • 6: Bacteria - Surface Structures
      What have we learned so far, in terms of cell layers? All cells have a cell membrane. Most bacteria have a cell wall. But there are a couple of additional layers that bacteria may, or may not, have. These would be found outside of both the cell membrane and the cell wall, if present.
    • 7: Archaea
      The Archaea are a group of organisms that were originally thought to be bacteria (which explains the initial name of “archaeabacteria”), due to their physical similarities. More reliable genetic analysis revealed that the Archaea are distinct from both Bacteria and Eukaryotes, earning them their own domain in the Three Domain Classification originally proposed by Woese in 1977, alongside the Eukarya and the Bacteria.
    • 8: Introduction to Viruses
      Viruses are typically described as obligate intracellular parasites, acellular infectious agents that require the presence of a host cell in order to multiply. Viruses that have been found to infect all types of cells – humans, animals, plants, bacteria, yeast, archaea, protozoa…some scientists even claim they have found a virus that infects other viruses! But that is not going to happen without some cellular help.
    • 9: Microbial Growth
      Provided with the right conditions (food, correct temperature, etc) microbes can grow very quickly. It’s important to have knowledge of their growth, so we can predict or control their growth under particular conditions. While growth for muticelluar organisms is typically measured in terms of the increase in size of a single organism, microbial growth is measured by the increase in population, either by measuring the increase in cell number or the increase in overall mass.
    • 10: Environmental Factors
      What environmental conditions can affect microbial growth? Temperature, oxygen, pH, water activity, pressure, radiation, lack of nutrients…these are the primary ones. We will cover more about metabolism (i.e. what type of food can they eat?) later, so let us focus now on the physical characteristics of the environment and the adaptations of microbes.
    • 11: Microbial Nutrition
      All microbes have a need for three things: carbon, energy, and electrons. There are specific terms associated with the source of each of these items, to help define organisms.
    • 12: Energetics & Redox Reactions
      Metabolism refers to the sum of chemical reactions that occur within a cell. Catabolism is the breakdown of organic and inorganic molecules, used to release energy and derive molecules that could be used for other reactions. Anabolism is the synthesis of more complex molecules from simpler organic and inorganic molecules, which requires energy.
    • 13: Chemoorganotrophy
      Chemoorganotrophy is a term used to denote the oxidation of organic chemicals to yield energy. In other words, an organic chemical serves as the initial electron donor. The process can be performed in the presence or absence of oxygen, depending upon what is available to a cell and whether or not they have the enzymes to deal with toxic oxygen by-products.
    • 14: Chemolithotrophy & Nitrogen Metabolism
      Chemolithotrophy is the oxidation of inorganic chemicals for the generation of energy. The process can use oxidative phosphorylation, just like aerobic and anaerobic respiration, but now the substance being oxidized (the electron donor) is an inorganic compound. The nitrogen cycle depicts the different ways in which nitrogen, an essential element for life, is used and converted by organisms for various purposes.
    • 15: Phototrophy
      Phototrophy (or “light eating”) refers to the process by which energy from the sun is captured and converted into chemical energy, in the form of ATP. The term photosynthesis is more precisely used to describe organisms that both convert sunlight into ATP (the “light reaction”) but then also proceed to use the ATP to fix carbon dioxide into organic compounds (the Calvin cycle). These organisms are the photoautotrophs. In the microbial world, there are also photoheterotrophs.
    • 16: Taxonomy & Evolution
      It is believed that the Earth is 4.6 billion year old, with the first cells appearing approximately 3.8 billion years ago. Those cells were undoubtedly microbes, eventually giving rise to all the life forms that we envision today, as well as the life forms that went extinct before we got here. How did this progression occur?
    • 17: Microbial Genetics
      Bacteria do not have sex, which presents a real problem for bacteria (and archaea, too); how do they get the genetic variability that they need? They might need a new gene to break down an unusual nutrient source or degrade an antibiotic threatening to destroy them – acquiring the gene could mean the difference between life and death. We are going to explore the processes that bacteria use to acquire new genes, the mechanisms known as Horizontal Gene Transfer (HGT).
    • 18: Genetic Engineering
      Genetic engineering is the deliberate manipulation of DNA, using techniques in the laboratory to alter genes in organisms. Even if the organisms being altered are not microbes, the substances and techniques used are often taken from microbes and adapted for use in more complex organisms.
    • 19: Genomics
      Genomics is a field that studies the entire collection of an organism’s DNA or genome. It involves sequencing, analyzing, and comparing the information contained within genomes. Since sequencing has become much less expensive and more efficient, vast amounts of genomic information is now available about a wide variety of organisms, but particularly microbes, with their smaller genome size. In fact, the biggest bottleneck currently is not the lack of information but the lack of computing power.
    • 20: Microbial Symbioses
      Symbiosis, strictly defined, refers to an intimate relationship between two organisms. The relationship could be good, bad, or neutral for either partner. A mutualistic relationship is one in which both partners benefit, while a commensalistic relationship benefits one partner but not the other. In a pathogenic relationship, one partner benefits at the expense of the other. This chapter looks at a few examples of symbiosis, where microbes are one of the partners.
    • 21: Bacterial Pathogenicity
      A microbe that is capable of causing disease is referred to as a pathogen, while the organism being infected is called a host. The ability to cause disease is referred to as pathogenicity, with pathogens varying in their ability. An opportunistic pathogen is a microbe that typically infects a host that is compromised in some way, either by a weakened immune system or breach to the body’s natural defenses, such as a wound. The measurement of pathogenicity is called virulence.
    • 22: The Viruses
      Since viruses lack ribosomes (and thus rRNA), they cannot be classified within the Three Domain Classification scheme with cellular organisms. Alternatively, Dr. David Baltimore derived a viral classification scheme, one that focuses on the relationship between a viral genome to how it produces its mRNA. The Baltimore Scheme recognizes seven classes of viruses.

    This page titled Microbiology (Bruslind) is shared under a CC BY-NC-SA license and was authored, remixed, and/or curated by Linda Bruslind (Open Oregon State) .

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