Microbiology For Dummies
Overview
Microbiology For Dummies (9781119544425) was previously published as Microbiology For Dummies (9781118871188). While this version features a new Dummies cover and design, the content is the same as the prior release and should not be considered a new or updated product.
Microbiology is the study of life itself, down to the smallest particle
Microbiology is a fascinating field that explores life down to the tiniest level. Did you know that your body contains more bacteria cells than human cells? It's true. Microbes are essential to our everyday lives, from the food we eat to the very internal systems that keep us alive. These microbes include bacteria, algae, fungi, viruses, and nematodes. Without microbes, life on Earth would not survive. It's amazing to think that all life is so dependent on these microscopic creatures, but their impact on our future is even more astonishing. Microbes are the tools that allow us to engineer hardier crops, create better medicines, and fuel our technology in sustainable ways. Microbes may just help us save the world.
Microbiology For Dummies is your guide to understanding the fundamentals of this enormously-encompassing field. Whether your career plans include microbiology or another science or health specialty, you need to understand life at the cellular level before you can understand anything on the macro scale.
- Explore the difference between prokaryotic and eukaryotic cells
- Understand the basics of cell function and metabolism
- Discover the differences between pathogenic and symbiotic relationships
- Study the mechanisms that keep different organisms active and alive
You need to know how cells work, how they get nutrients, and how they die. You need to know the effects different microbes have on different systems, and how certain microbes are integral to ecosystem health. Microbes are literally the foundation of all life, and they are everywhere. Microbiology For Dummies will help you understand them, appreciate them, and use them.
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About The Author
Jennifer C. Stearns, PhD, is an Assistant Professor in the Department of Medicine at McMaster University. She studies how we get our gut microbiome in early life and how it can keep us healthy over time. Michael G. Surette, PhD, is a Professor in the Department of Medicine at McMaster University, where he pushes the boundaries of microbial research. Julienne C. Kaiser, PhD, is a doctoral career educator.
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microbiology for dummies
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When you're studying microbiology, you need to know the key differences between the three domains of life, how scientists name and classify organisms, and how scientists identify microorganisms.Differences among bacteria, archaea, and eukaryotic microorganismsThere are three domains of life: bacteria (also known as eubacteria), archaea, and eukarya.
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Because you usually can’t see the microorganisms all around you every day, it’s easy to overlook them. But following are ten ways that microbes affect your life in important ways.
Making delicious foods
The yeast Saccharomyces cerevisiae has been used for millennia because it ferments sugars and makes carbon dioxide, which causes bread to rise.
There are many professions where knowing about microbes, either pathogenic or benign, is handy. There are also plenty of situations where applying a microbiology approach to a problem will get you out of a jam. Some are industries that employ microbiologists, and others are situations where a knowledge of microbiology is essential to getting the job done.
Since the beginning of their widespread use in 1943, antibiotics have saved countless lives and changed the way medicine is practiced. Before their discovery, people suffered or died from infectious diseases that today are a mere annoyance, like sexually transmitted diseases and post-operative infections. Today antibiotics are essential in treating life-threatening bacterial infections, like pneumonia and sepsis, and are used preventively in a number of medical procedures (like surgery) and treatments (like cystic fibrosis).
Not only are microorganisms extremely widespread, but within the microbial world there is also an impressive number of different metabolic pathways. You know this because of the compounds that they consume and produce, as well as from the study of microbial genes found in nature.
Recently, scientists have been able to sequence the full genomes of many microorganisms, giving them access to the sequences of all the genes present.
There is no shortage of microbes that cause disease; some are notable for the number of people they infect, and others for the nastiness of the infections they cause. Following is a list of 8 known diseases caused by microbes.
Ebola
Ebola is one of the most lethal viruses to infect humans, with a mortality rate reaching 90 percent in some outbreaks.
Amino acids have an amino group bonded to a carbon skeleton. Each amino acid has one or more special side groups or chains (R) that give it a specific structure or function. Making amino acids from scratch is very expensive in terms of energy, so microbes try their best to get them from their environment.
When they can’t get them from outside, however, they use a kind of template method to reduce the amount of energy spent on different biosynthesis pathways.
Catabolism (the breakdown of compounds for energy conservation) can happen in different ways for different types of microorganisms. In chemoorganotrophs (organisms that derive their energy from organic compounds), there are two forms of catabolic metabolism: fermentation and respiration.
Fermentation is a form of anaerobic catabolism (in the absence of O2) where the organic substrate acts as both the electron donor and the electron acceptor.
Biology
Unlike animal growth, which is measured both in the size and number of individuals, microbial growth is all about the population size. Only the number of cells matters when calculating the size of the population. Because cells are usually grown in solution the level of growth is referred to as culture density or concentration of microbial cells.
Cell division is a process that is necessary for microbial growth. It starts with a single cell that stretches in size until it separates into two separate cells, in a process called binary fission. Each new cell is equipped with the right amount of proteins, nutrients, and importantly, the chromosome, to function as an independent cell.
Bacterial cells make a wide variety of lipids from subunits of fatty acids that have some important functions in the cell. Lipids are the main part of membranes and can be used as stores for longer-term storage of energy. Fatty acids are built by adding two carbons at a time to a growing fatty acid chain.
The enzyme acyl carrier protein (ACP) is essential to this process because it holds onto the growing chain until all the carbons have been added.
Cells can use sugars for all sorts of other things. For example, the backbone of peptidoglycan, a major component of the bacterial cell wall, is made of sugars. Hexoses are six-carbon sugars like glucose, and pentoses are five-carbon sugars like ribose.
When hexoses need to be made, they’re synthesized with gluconeogenesis using intermediates from glycolysis and the citric acid cycle.
Unlike the physical requirements where a specific range or concentration is necessary for optimum growth, the chemical requirements just need to be present in the environment and a microbe will use what it needs. Microbes use compounds containing the following elements and vitamins to make everything in the cell including membranes, proteins, and nucleic acids:
Carbon: Carbon is necessary for all life.
If you imagine the microbial cell as a small factory, then the enzymes are the robots doing all the work. Enzymes are special proteins that are very good at converting things from one form to another. They do this by kicking off the chemical reactions needed for the conversion. The kinds of enzymes a microbe makes determine what type of metabolism the microbe will use to harness energy and grow.
If you’re interested in studying a particular microbe in a laboratory, you’ll need to create an environment that will accommodate its growth well. Culture media contains all the things that a microbe needs for growth. Culture conditions are conditions that are within the microbe’s growth optima (external environmental conditions that allow for the optimal growth of the organism).
Regulation that occurs at the transcriptional level involves proteins that bind to DNA and either enhance or repress transcription. This form of regulation controls the amount of a protein that’s made.
DNA-binding proteins, as their name suggests, are proteins that interact with DNA. There are two kinds of DNA-binding proteins: those that are sequence specific and those that are nonspecific.
Before genes can be passed from parent cells to their progeny, a copy of the genome has to be made in a process called replication. For circular chromosomes, like those in bacteria and archaea, replication begins at the origin of replication and proceeds in two directions away from that point, simultaneously.
The steps involved in DNA replication must happen in a precise order:
Supercoiled double-stranded DNA is relaxed by an enzyme called topoisomerase (or gyrase) and then unwound by an enzyme called helicase, which opens up the two strands in one area at a time.
The concept of spontaneous generation was finally put to rest by the French chemist Louis Pasteur in an inspired set of experiments involving a goose-necked flask. When he boiled broth in a flask with a straight neck and left it exposed to air, organisms grew. When he did this with his goose-necked flask, nothing grew.
Microbiology involves studying microorganisms from many different angles. Each perspective uses a different set of tools, from an ever-improving and changing toolbox. These include the following:
Morphology: The study of the shape of cells. It is analyzed using stains and microscopy.
Metabolism: How an organism gets energy from its environment and the waste it produces as a result.
Glucose is a simple sugar that is used as an energy source by many living cells. Glycolysis (the breakdown of glucose into pyruvate) is the same under fermentation and respiration, but the fate of pyruvate, the product of glycolysis, is different. Whether glucose is respired or fermented depends on whether there is oxygen (O2) present.
Substances have different tendencies to donate or accept electrons. When a really good donor meets a great acceptor, the chemical reaction releases a lot of energy. Oxygen (O2) is the best electron acceptor and is used in many aerobic reactions (reactions with oxygen). Hydrogen gas (H2) is a good electron donor.
Energy can be stored in the chemical bonds within molecules in the cell, but not all chemical bonds are equally energetic. When broken, some bonds will release more energy than others. A phosphate is a phosphorus atom bonded to three oxygen atoms (PO3). When it’s bonded to another molecule, the bond between them is called a phosphate bond.
Biology
A fecal transplant, also known as fecal biotherapy (FBT) or fecal microbiota transplant (FMT), is the administration of fecal matter from a healthy donor to a recipient. The donor may or may not be related to the recipient. In some cases, fecal matter can be transferred via a naso-gastric tube, but fewer side effects are observed when fecal transplants are administered via an enema.
Biology
The purpose of photosynthesis is to harness light energy and use it to move electrons through an electron transport chain. Electron carriers are arranged, in order of increasing electropositivity within a membrane. Through this process, a proton motive force is created that is used to produce ATP.
Electronegative compounds are better at donating electrons than electropositive ones are.
The habitat is an important concept in biology and microbiology in particular because microorganisms are greatly affected by where they live. Microbial habitats — including soils, rivers, lakes, oceans, on the surface of living and dead things, inside other organisms, on man-made structures, and everything in between — provide nutrients and protect cells from harsh conditions.
Biology
Phototrophs are able to capture the energy in light thanks to photosynthetic pigments, like chlorophyll and bacteriochlorophyll, which absorb light energy kicking off a process that eventually results in the production of ATP.
There are two main types of photosynthesis: those that generate oxygen (called oxygenic photosynthesis) and those that don’t (called anoxygenic photosynthesis).
Biology
Making a living from light energy is a double-edged sword — it means being constantly exposed to a source energy that can be harmful. Bright light causes the formation of singlet oxygen (1O2) through photo-oxidation reactions. Singlet oxygen, and free radicals in general, are toxic because they can randomly energize other molecules.
Microorganisms can't be seen with the naked eye, so they're identified in several indirect ways:
Microscopy to identify cell shape or appearance of spores. Cells are often stained to enhance cellular features, and the properties of the cell wall are used in the classification of microorganisms.
Appearance of colonies on laboratory media is a widely used method of distinguishing between different microbes, mainly bacteria.
Microbial experiments often require that we know just how many bacteria, for instance, are present. Knowing the number of microbial cells helps to indicate whether cells are growing or dying and it helps experiments to be consistent from day to day.
Methods for deciphering the number of cells present easily and accurately are used in microbiology labs every day.
Scientists have been peering at microorganisms through microscopes for centuries. For some, the shape of their cells can offer clues to their identity, but it’s often necessary to use stains that tell you a bit more about their cellular structure.
Simple stains contain a single dye that can bind to microbial cells and show off their basic structure.
Many cellular structures are important for cellular function, and these differ between eukaryotic and prokaryotic cells. Here is a list of structures important to prokaryotic cells.
Nucleoid: The nucleoid is the region in the cell where the tangled mass of genetic material, called the chromosome, is found. Unlike the nucleus of eukaryotic cells, the nucleoid does not have a membrane.
Energy can’t be created or destroyed, so it has to be passed around. Within the cell, energy is reused and recycled very efficiently. The same is true outside the cell, where energy is stored in everything, including leaves and rocks on the ground. The trick is getting energy out from where it’s stored.
Another way of thinking about energy is to think about electrons, which are the negatively charged part of atoms.
The terminology used to describe methods for reducing or removing microbes from a surface can sometimes be confusing. There are different reasons for wanting to get rid of microbes, but not all of them require sterilization (the complete eradication of all living things), which is needed for surgical equipment.
Biology
The flu is characterized by a fever, aches, sore throat, and nausea. Seasonal flu epidemics are caused by the influenza viruses A and B. There are several subtypes of influenza A that also circulate every year. The natural source of influenza A is wild birds, but they can infect a host of other animals, including pigs and humans.
Some microbial cells are stationary, but most of them have a means of getting around, called locomotion. Flagella are important for movement. They propel the cell forward or backward. Both prokaryotes and eukaryotes have them, but they’re more complex in eukaryotes.
In prokaryotic cells, flagella spin around and propel the cells very quickly; in eukaryotic cells, they move in a wave motion and propel the cells more slowly.
Changes to an organism’s DNA can also happen on a larger scale than with point mutations, where regions of DNA from two different sources get combined. The process of incorporating sequences from different sources into the same chromosome is called recombination; it occurs in different contexts in eukaryotes and bacteria.
RNA is made through transcription, where an enzyme called RNA polymerase transcribes the DNA sequence into a complementary version with the use of free RNA nucleotides. Three of the bases (adenine, guanine, and cytosine) are the same as in DNA, but the fourth (thymine) is replaced by uracil in RNA. Also, the backbone is slightly different, containing a ribose instead of a deoxyribose sugar.
To keep the many organisms on earth straight, in the 18th century the Swedish botanist Carl Linnaeus developed a simple nomenclature system to classify and name all organisms including bacteria. This system ranks all organisms using the following headings, shown with the example of the bacterium E. coli.
Domain: Bacteria
Phylum: Proteobacteria
Class: Gammaproteobacteria
Order: Enterobacteriales (Order names always end in –iales.
When you're studying microbiology, you need to know the key differences between the three domains of life, how scientists name and classify organisms, and how scientists identify microorganisms.Differences among bacteria, archaea, and eukaryotic microorganismsThere are three domains of life: bacteria (also known as eubacteria), archaea, and eukarya.
Vaccines have been essential in eradicating or preventing life-altering diseases, but lately, they've come under fire. Here are some common myths about vaccines:
Myth 1: Vaccines aren't actually necessary. The truth is that vaccines have been essential to reducing rates of childhood illnesses. Before vaccines, 25 percent of children died before the age of 5 from pneumonia, diarrhea, measles, pertussis, or rubella, among other diseases.
For each microorganism, there is a set of conditions (both physical and chemical) under which it can survive. Microbes have a variety of physical requirements for growth, including temperature, pH, and water stress.
Temperature
Microbes can be separated into groups based on the range of temperatures at which they can survive.
Genetic information not contained in the chromosome of bacteria or archaea is kept as circular double-stranded DNA molecules called plasmids (although some linear plasmids do exist). Plasmids contain only nonessential genes and replicate independent of the chromosome.
Some plasmids exist in many copies inside one cell and are called high-copy-number plasmids, whereas others are less numerous and are called low-copy-number plasmids.
The breakdown of compounds by respiration releases much more energy than does the breakdown of the same compounds by fermentation. This is because the complete reduction of the products of fermentation isn’t possible without oxygen or oxygen substitutes to act as terminal electron acceptors.
The star of this phenomenon is the electron transport chain, which involves several electron acceptors positioned within a membrane in order of reducing power so that the weakest electron acceptors are at one end of the chain and the strongest electron acceptors are at the other end.
Sometimes errors occur during DNA replication that alter the sequence by one or a small number of bases by adding too many nucleotides, too few nucleotides, or a wrong nucleotide. The result is called a point mutation.
Point mutations can have a negative effect, a positive effect, or no effect on the protein. Most of the time, base substitutions have no effect on the final protein, so they’re called silent mutations.
The message contained within an mRNA is converted to protein through translation, where the genetic code is deciphered into amino acids. The bases in mRNA are decoded in threes into codons, each of which encodes an amino acid; there are 20 amino acids. Several different codons encode the same amino acid.
Making a protein involves stringing together many amino acids into a long chain, which then folds into the shape it needs to be in to perform its function.
Biology
There are three domains of life: Bacteria (also known as Eubacteria), Archaea, and Eukarya. The Bacteria and Archaea are made up entirely of microorganisms; the Eukarya contains plants, animals, and microorganisms such as fungi and protists. The Bacteria and Archaea have been grouped together and called Prokaryotes because of their lack of a nucleus, but the Archaea are more closely related to the Eukaryotes than to the Bacteria.
Since the 19th century, there has been an explosion of great microbiological research, leading to many different branches of microbiology, all of which are both basic and applied in nature. Here’s a list of the different fields of microbiology that have developed since the discovery of microorganisms:
Aquatic, soil, and agricultural microbiology study the microorganisms associated with aquatic (including wastewater treatment systems), soil, and agricultural environments, respectively.
Today is perhaps the best time in history to be a microbiologist! The development of new experimental techniques and ability to sequence organisms without actually culturing them in the laboratory first has revealed diversity and complexity in the microbial world not previously known.
Most microorganisms can’t be grown in the lab, so they were previously unknown before the development of DNA sequencing techniques.
Microorganisms that live on and inside other organisms have often adapted to interact with their host organism. There are different kinds of relationships between the host organism and microorganisms that live on or in the host:
Benign: Organisms that live in or on people and are neither harmful nor recognized by their bodies.
The plasma membrane borders the cell and acts as a barrier between the inside of the cell and the outside environment. The membrane serves many important functions in prokaryotic cells, including the following:
Providing sites for respiration and/or photosynthesis
Transporting nutrients
Maintaining energy gradients (the difference in the amount of energy between the inside of the cell and the outside of the cell)
Keeping large molecules out
The plasma membrane is made of a phospholipid bilayer.
Cells build up stores of molecules required for growth inside the cell in higher amounts than are found outside the cell. Water naturally wants to flow into the cell to balance the number of molecules inside and outside, but if the cell were to allow this, it would burst like an overfilled balloon. The cell wall allows the cell to withstand this osmotic pressure.
The proton motive force occurs when the cell membrane becomes energized due to electron transport reactions by the electron carriers embedded in it. Basically, this causes the cell to act like a tiny battery. Its energy can either be used right away to do work, like power flagella, or be stored for later in ATP.
Prokaryotic cells come in many different shapes and sizes that you can see under a microscope. A description of the shape of a cell is called the cell morphology. The most common cell morphologies are cocci (spherical) and bacilli (rods).Coccibacillus are a mix of both, while vibrio are shaped like a comma, spirilla are shaped like a helix (a spiral, sort of like a stretched-out Slinky), and spirochetes are twisted like a screw.
The way that DNA encodes the instructions for proteins is through a set of four molecules called bases, each of which represents a letter of the genetic code (A = adenine, C = cytosine, G = guanine, and T = thymine). The bases are made of carbon and nitrogen rings and are bound to a sugar and a phosphate to form a nucleotideThe nucleotides are connected together to form a long chain with the bases pointing out.
Perhaps one of the most frightening and nastiest of the microbes may be the ones people don’t know about and can’t prepare for. Organizations like the World Health Organization and the U.S. Centers for Disease Control are constantly on the alert for new emerging pathogens, yet these pathogens can still appear without warning.
Cells are able to take up nutrients from the environment thanks to membrane-spanning transporter proteins. Different types of transporters are required to transport the wide range of nutrients that cells need, but this often comes at an energy cost because the cell must build up internal stores at higher concentrations than those found in the environment.
Biology
When it comes to infectious agents, like bacteria, viruses, and fungi, cleaning is an important way to reduce their spread. What people are really trying to do when they wash their hands or wipe a surface is reduce the number of pathogenic microbes present. In reality, all surfaces, including the surfaces of the human body, are teeming with microbes, most of which are just minding their own business.
So, what are microorganisms exactly? Microorganisms are actually a diverse group of organisms. The fact that they’re micro isn’t even true of all microorganisms — some of them form multicellular structures that are easily seen with the naked eye.
There are three main kinds of microorganisms, based on evolutionary lines:
Bacteria are a large group of unicellular organisms that scientists loosely group as Gram-negative and Gram-positive, but in reality there are many different kinds.
The cell needs many compounds for life, including enzymes to perform its many functions, structural molecules to give it shape, as well as nucleic acids to store its genetic material. If it can, the cell will obtain some of these things from its environment, but when it has to make them itself, it uses anabolism.
Biology
At birth, an infant's immune system is extremely tolerant of everything, which is why infants are more vulnerable to infection. Slowly over the first couple years of life, the immune system matures. This process is complex, and it involves learning about which microorganisms are acceptable and can be ignored and which are harmful and should be killed.
The question of why to study microbiology is a good one — the impacts of microorganisms on your life may not be immediately obvious. But the truth is, microorganisms not only have a huge impact but are literally everywhere, covering all the surfaces of your body and in every natural and urban habitat.
In nature, microorganisms contribute to biogeochemical cycling, as well as turnover of material in soil and aquatic habitats.
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