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1.2: Microbes and the World - Biology

1.2: Microbes and the World - Biology


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1.2: Microbes and the World

This Is Biology: The Science of the Living World Revised ed. Edition

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Routes of transmission

Different pathogens have different modes of transmission. For example respiratory pathogens are usually airborne and intestinal pathogens are usually spread by water or food.

The main routes of transmission are listed below.

Person-to-person

Touch

A cold can be caught by shaking the hand of a person who has a cold and who has just used their hand to wipe their dripping nose. The mucus from the nose will be teeming with cold virus particles such as the rhinovirus, which causes one third of colds in adults. Once the cold virus particles are on the hands of the second person they are contaminated and the virus can be transferred into their nose by their fingers.

© idrisesen / iStock

Transmission by person to person contact. Measles, mumps and tuberculosis can be spread by coughing or sneezing. A cough or a sneeze can release millions of microbes into the air in droplets of mucus or saliva which can then infect somebody else if they breathe in the infected particles.

Contaminated blood or other bodily fluids

Hepatitis B and HIV can be spread through sexual intercourse or sharing used syringe needles contaminated with infected blood.

Saliva

A cold or the flu can be caught from the saliva of an infected person when you kiss them.

Air

Measles, mumps and tuberculosis can be spread by coughing or sneezing. A cough or a sneeze can release millions of microbes into the air in droplets of mucus or saliva which can then infect somebody else if they breathe in the infected particles.

Food

Microbes need nutrients for growth and they like to consume the same foods as humans. They can get into our food at any point along the food chain from &lsquoplough to plate&rsquo. Therefore great care must be taken at every stage of food production to ensure that harmful microbes are not allowed to survive and multiply. If they do they can cause the unpleasant symptoms of food poisoning such as sickness and diarrhoea when the contaminated food is eaten.

© panida wijitpanya / iStock Insects can also transmit pathogens to food. House flies are very good at spreading Salmonella and E.coli O157. They feed on faecal waste and transfer microbes from their feet and other body parts to food.

Microbes can be spread from one food to another during the preparation process, for example by unclean hands, or dirty kitchen utensils, and cause illness when those foods are eaten. This is known as cross-contamination.

Water

Some diseases are caused by drinking water that is contaminated by human or animal faeces, which may contain disease-causing microbes. Clean water, hygiene and good sewerage systems prevent the spread of water-borne diseases such as typhoid and cholera.

Insects

Insects are responsible for spreading many diseases. Malaria is spread from person to person by certain species of female mosquito carrying the protozoan Plasmodium falciparum. The parasite enters the human host when an infected mosquito takes a blood meal. Bubonic plague (Black Death) is a bacterial disease of rodents caused by Yersinia pestis. It can be spread to humans and other animals by infected rat fleas. People usually get plague from being bitten by a rodent flea that is carrying the plague bacterium.

Insects can also transmit pathogens to food house flies are very good at spreading Salmonella and E. coli O157. They feed on faecal waste and transfer microbes from their feet and other body parts to food. The microbe does not invade or multiply inside the fly.

Fomites

This is a non-living object such as bedding, towels, toys and barbed wire that can carry disease-causing organisms. The fungus Trichophyton that causes athlete&rsquos foot can be spread indirectly through towels and changing room floors.

The fungus thrives in the damp warm environment found between the toes. The skin between the fourth and fifth toe is usually affected first. A flaky itchy red rash develops. The skin becomes cracked and sore and small blisters may appear. If the infection is left untreated it can spread to other parts of the body.

© AGEphotography / iStock

Transmission by fomites (non-living objects) such as barbed wire.

A puncture wound on the finger caused by a prick from rusted barbed wire may result in tetanus due to infection by spores of the bacterium Clostridium tetani. The spores live mainly in soil and manure, but are also found on dirty or rusting metal objects. If untreated, tetanus (lockjaw) may be fatal.

Microbes and disease

Microbes that cause disease are called pathogens. Find out which microbe is responsible for malaria!

Immune system

An infection can be seen as a battle between the invading pathogens and host. How does the immune system work?

Vaccination

Just a shot in the arm – what do vaccines do?

Antibiotics

Antibiotics are powerful medicines that only fight bacterial infections.

Microbes and food

Food for thought – bread, chocolate, yoghurt, blue cheese and tofu are all made using microbes.

Microbes and the outdoors

The function of microbes as tiny chemical processors is to keep the life cycles of the planet turning.


Customers who bought this item also bought

Review

&ldquoA breakthrough book. . . . well worth owning and reading. No comprehensive horticultural library should be without it.&rdquo &mdash American Gardener

&ldquoDigs into soil in a most enlightening and entertaining way.&rdquo &mdash Dallas Morning News

&ldquoRequired reading for all serious gardeners.&rdquo &mdash Miami Herald

&ldquoThe authors have given gardeners an inside scoop on the scientific research supporting organic gardening.&rdquo &mdash Pacific Horticulture

&ldquoThis intense little book may well change the way you garden.&rdquo &mdash St. Louis Post-Dispatch

&ldquoExceptional. . . . A brief, clear overview of scientific information with which every gardener should be familiar.&rdquo &mdash Monterey Herald

&ldquoSure, it&rsquos a gardening book, but it has all the drama and suspense of an extraterrestrial thriller. A cast of characters without eyeballs or backbones. Battle scenes with bizarre creatures devouring one another. Only this book is about as terrestrial as it gets.&rdquo &mdash Anchorage Daily News

&ldquoAll good gardeners know healthy plants start with healthy soil. But why? And how? In Teaming with Microbes Lowenfels and Lewis reveal the new research in the most practical and accessible way.&rdquo &mdash The Oregonian

&ldquoRead this book and you&rsquoll never think of soil the same way.&rdquo &mdash Seattle Post-Intelligencer

&ldquoSure, it&rsquos a gardening book, but it has all the drama and suspense of an extraterrestrial thriller. . . . Read this book and you&rsquoll never look at soil the same way.&rdquo &mdash B&B Magazine

&ldquoA must read for any gardener looking to create a sustainable, healthy garden without chemicals.&rdquo &mdash Virginian-Pilot

&ldquoIt takes readers underground to meet the critters that live if you let them under the garden.&rdquo &mdash Rockland Courier-Gazette

&ldquo[ Teaming with Microbes ] was one of those &lsquoaha&rsquo moments for me, where I realized I had been growing wrong this whole time.&rdquo  &mdash Matthew Frigon (Founder of Lazy Bee Farms) in Dope Magazine

From the Back Cover

Winner of the Garden Writers Association Gold Award for Best Book Writing

Smart gardeners know that soil is anything but an inert substance. Healthy soil is teeming with life&mdashnot just earthworms and insects, but a staggering multitude of bacteria, fungi, and other microorganisms. When we use chemical fertilizers, we injure the microbial life that sustains healthy plants, and thus become increasingly dependent on an arsenal of artificial substances, many of them toxic to humans as well as other forms of life. But there is an alternative to this vicious circle: to garden in a way that strengthens, rather than destroys, the soil food web&mdashthe complex world of soil-dwelling organisms whose interactions create a nurturing environment for plants. By eschewing jargon and overly technical language, the authors make the benefits of cultivating the soil food web available to a wide audience, from devotees of organic gardening techniques to weekend gardeners who simply want to grow healthy, vigorous plants without resorting to chemicals.

This revised edition updates the original text and includes two completely new chapters&mdashon mycorrhizae (beneficial associations fungi form with green-leaved plants) and archaea (singled-celled organisms once thought to be allied to bacteria).

About the Author

Jeff Lowenfels is the author of a trilogy of award winning books on plants and soil, and he is the longest running garden columnist in North America. Lowenfels is a national lecturer as well as a fellow, hall of fame member, and former president of the Garden Writers of America.

Excerpt. © Reprinted by permission. All rights reserved.

The images in this book have forewarned you: you may find things in your soil that, upon closer examination, will scare the daylights out of you. (In general we advise against putting anything under an electron microscope. At that level, all life has teeth!) The point is, when you get a good look at some of the microarthropods present in soil, you may never want to put your hands in the soil again. Sometimes ignorance really is bliss however, in this instance a little knowledge is not going to hurt you and will actually help you be a better gardener. Just remember, you put your hands in the soil before you knew what was there and never got hurt.

You will want to repeat the following procedures with soils from each of your gardens and lawn areas, and even around specific trees and shrubs. We have done this dozens of times in our own yards, and what we find never fails to astonish us.

Start by digging a hole in the soil at issue, about 12 inches (30 centimeters) square. Use a spade or trowel — it doesn't matter, and measurements don't have to be exact. Put all the soil you dig up onto a tarp or in a box so you can then sift through it, looking for the bigger animals you might find in the soil: worms, beetles, insect larvae — any living organism you can see with the naked eye and pick up without having to resort to tweezers. Keep track of what you are finding.

None of us are trained at identifying all the organisms in our soils, and frankly the variety of them is so great as to be beyond the scope of this book. Do your best in making identifications. Seek help from others. In time you will become sufficiently proficient for the purpose. This is new stuff, and just being exposed to it will make the learning experience easier. It didn't take us very long, and it won't take you long to become familiar with soil food web organisms.


Microbiome metabolism and function

As the first study to include both marker gene and metagenomic data across body habitats from a large human population, we additionally assessed the ecology of microbial metabolic and functional pathways in these communities. We reconstructed the relative abundances of pathways in community metagenomes 22 , which were much more constant and evenly diverse than were organismal abundances (Fig. 2b, see also Fig. 1), confirming this as an ecological property of the entire human microbiome 2 . We were likewise able to determine for the first time that taxonomic and functional alpha diversity across microbial communities significantly correlate (Spearman of inverse Simpson’s r = 0.60, P = 3.6 × 10 −67 , n = 661), the latter within a more proscribed range of community configurations (Supplementary Fig. 5).

Unlike microbial taxa, several pathways were ubiquitous among individuals and body habitats. The most abundant of these ‘core’ pathways include the ribosome and translational machinery, nucleotide charging and ATP synthesis, and glycolysis, and reflect the basics of host-associated microbial life. Also in contrast to taxa, few pathways were highly variable among subjects within any body habitat exceptions included the Sec (orally, pathway relative abundance s.d. = 0.0052 total mean of oral standard deviations = 0.0011 with s.d. = 0.0016) and Tat (globally, pathway s.d. = 0.0055 mean of global standard deviations = 0.0023 with s.d. = 0.0033) secretion systems, indicating a high degree of host–microbe and microbe–microbe interactions in the healthy human microbiota. This high variability was particularly present in the oral cavity for phosphate, mono- and di-saccharide, and amino acid transport in the mucosa and also for lipopolysaccharide biosynthesis and spermidine/putrescine synthesis and transport on the plaque and tongue (http://hmpdacc.org/HMMRC). The stability and high metagenomic abundance of this housekeeping ‘core’ contrasts with the greater variability and lower abundance of niche-specific functionality in rare but consistently present pathways for example, spermidine biosynthesis, methionine degradation and hydrogen sulphide production, all examples highly prevalent in gastrointestinal body sites (non-zero in >92% of samples) but at very low abundance (median relative abundance < 0.0052). This ‘long tail’ of low-abundance genes and pathways also probably encodes much of the uncharacterized biomolecular function and metabolism of these metagenomes, the expression levels of which remain to be explored in future metatranscriptomic studies.

Protein families showed diversity and prevalence trends similar to those of full pathways, ranging from maxima of only ∼ 16,000 unique families per community in the vagina to almost 400,000 in the oral cavity (Fig. 1a, b http://hmpdacc.org/HMGI). A remarkable fraction of these families were indeed functionally uncharacterized, including those detected by read mapping, with a minimum in the oral cavity (mean 58% s.d. 6.8%) and maximum in the nares (mean 77% s.d. 11%). Likewise, many genes annotated from assemblies could not be assigned a metabolic function, with a minimum in the vagina (mean 78% s.d. 3.4%) and maximum in the gut (mean 86% s.d. 0.9%). The latter range did not differ substantially by body habitat and is in close agreement with previous comprehensive gene catalogues of the gut metagenome 3 . Taken together with the microbial variation observed above throughout the human microbiome, functional variation among individuals might indicate pathways of particular importance in maintaining community structure in the face of personalized immune, environmental or dietary exposures among these subjects. Determining the functions of uncharacterized core and variable protein families will be especially essential in understanding role of the microbiota in health and disease.


Plants

In the majority of extreme terrestrial environments, cryptogams (lichens, bryophytes and algae) are the dominant plant species. Cryptogams survive well with high and low water availability and at high and low temperatures ( Cornelissen et al. 2007 ), and occur in communities from the arctic and Antarctica, to geothermal hot springs, and the world’s most extreme deserts. Species-specific physiological responses have been found to explain bryophyte and lichen species’ ability to survive in the most extreme environments (e.g., Llaneza García et al. 2016 Raggio et al. 2016) , and species-specific physiological effects must be included in modeling of the effects of climate change on extreme environments. These extreme systems are rarely nutrient-limited ( Robinson et al. 2003 ), however, global climate change is likely to alter these conditions making nutrient limitation and competition with vascular plants more prevalent, and in some extreme environments, such as the polar systems, cryptogam populations are beginning to decline (e.g., Elmendorf et al. 2012 Bokhorst et al. 2016 ).

Vascular plants are not absent from extreme environments and recent research suggests that interactions with microbes are critical to these plants’ ability to survive in the most extreme environments such as geothermal hot springs, serpentine soils, and mine waste sites. Marquez et al. (2007) found that a three-way interaction among a grass ( Dichanthelium lanuginosum that grows around Yellowstone hot springs), a fungal endophyte ( Curvularia protuberate ), and a virus allows thermal tolerance. Fungal endophytes have been found to confer heat and salt tolerance to native grass species ( Rodriguez et al. 2008 ) and heavy metals tolerance to native forb species ( Sun et al. 2010 ). Vascular plants’ interactions with mycorrhizal fungi also allow survival in environments with extreme temperatures ( Bunn et al. 2009 Zhou et al. 2015 ), high salt ( Reuss-Schmidt et al. 2015 ), and severely low water and nutrients (for review Smith et al. 2010 ). Endophytic bacteria and rhizobacteria have been found to greatly enhance plants’ ability to survive in environments with heavy metals, such as mine sites (e.g., Dell'Amico et al. 2008 Chen et al. 2014 ).


How Do I Prepare for a Career in Microbiology?

In high school, take these classes: In college, take these classes:
4 years of math Biology or Life Science
Biology Calculus
Chemistry Chemistry
Physics General Microbiology
Other science or math electives, such as AP Biology or Microbiology Organic Chemistry
Biochemistry
Physics
Statistics
Other science or math electives, such as Computer Science or Immunology

Additional activities that can help you prepare for a career in microbiology include participating in school science fairs and extracurricular science clubs, joining local and national scientific societies (like ASM), pursuing internships and student research experiences and participating in activities that develop technical, communication and leadership skills.

Immune system

An infection can be seen as a battle between the invading pathogens and the host. Our bodies are equipped to fight off invading microbes that may cause disease. These are called our natural defences.

First line of defence

The first line of defence is non-specific and aims to stop microbes from entering the body. The skin and mucous membranes act as a physical barrier preventing penetration by microbes.

If the skin is cut then the blood produces a clot which seals the wound and prevents microbes from entering.

© CNRI / Science Photo Library A blod clot

The surfaces of the body &ndash the skin, digestive system, and the lining of the nose &ndash are covered by a community of microbes called the normal body flora. They help protect the host from becoming infected with more harmful micro-organisms by acting as a physical barrier. The normal body flora colonises these linings which reduces the area available for pathogens to attach to and become established. It also means that the harmful microbes have to compete with the normal body flora for nutrients. The average human gut contains around one kilo of these good bacteria which is equivalent to one bag of sugar.

The respiratory system &ndash the nose and passageways leading to the lungs &ndash is lined with cells that produce sticky fluid called mucus that traps invading microbes and dust. Tiny hairs called cilia move in a wave-like motion and waft the microbes and dust particles up to the throat, where they are either coughed or sneezed out or swallowed and then passed out of the body in faeces.

The body produces several antimicrobial substances that kill or stop microbes from growing. For example the enzymes in tears and saliva break down bacteria. The stomach produces acid which destroys many of the microbes that enter the body in food and drink. Urine as it flows through the urinary system flushes microbes out of the bladder and urethra.

Second line of defence

If microbes do manage to get inside the body then the second line of defence is activated. This is also non-specific as it stops any type of microbe. Phagocytes are a type of white blood cell that move by amoeboid action. They send out pseudopodia which allows them to surround invading microbes and engulf them. Phagocytes release digestive enzymes which break down the trapped microbes before they can do any harm. This process is called phagocytosis.

© Dr_Microbe / iStock Macrophage engulfing tuberculosis bacteria Mycobacterium tuberculosis. This process is called phagocytosis.

Third line of defence

The third and final line of defence is the immune response. The invading microbe or pathogen is called an antigen. It is regarded as a threat by the immune system and is capable of stimulating an immune response.

Antigens are proteins that are found on the surface of the pathogen. Antigens are unique to that pathogen. The whooping cough bacterium, for example, will have different antigens on its surface from the TB bacterium.

When an antigen enters the body, the immune system produces antibodies against it. Antibodies are always Y-shaped. It is like a battle with the army (antibody) fighting off the invader (antigen). A type of white blood cell called a lymphocyte recognises the antigen as being foreign and produces antibodies that are specific to that antigen. Each antibody has a unique binding site shape which locks onto the specific shape of the antigen. The antibodies destroy the antigen (pathogen) which is then engulfed and digested by macrophages.

White blood cells can also produce chemicals called antitoxins which destroy the toxins (poisons) some bacteria produce when they have invaded the body. Tetanus, diphtheria and scarlet fever are all diseases where the bacteria secrete toxins.

Once the invading microbes have been destroyed the immune response winds down.

Once a person has had a disease they don&rsquot normally catch it again because the body produces memory cells that are specific to that antigen. The memory cells remember the microbe which caused the disease and rapidly make the correct antibody if the body is exposed to infection again. The pathogen is quickly destroyed preventing symptoms of the disease occurring.

Microbes and disease

Microbes that cause disease are called pathogens. Find out which microbe is responsible for malaria!

Routes of transmission

Find out how you can pick up germs and pass them on to others.

Vaccination

Just a shot in the arm – what do vaccines do?

Antibiotics

Antibiotics are powerful medicines that only fight bacterial infections.

Microbes and food

Food for thought – bread, chocolate, yoghurt, blue cheese and tofu are all made using microbes.

Microbes and the outdoors

The function of microbes as tiny chemical processors is to keep the life cycles of the planet turning.


Growing Yeast: Sugar Fermentation

Yeast is most commonly used in the kitchen to make dough rise. Have you ever watched pizza crust or a loaf of bread swell in the oven? Yeast makes the dough expand. But what is yeast exactly and how does it work? Yeast strains are actually made up of living eukaryotic microbes, meaning that they contain cells with nuclei. Being classified as fungi (the same kingdom as mushrooms), yeast is more closely related to you than plants! In this experiment we will be watching yeast come to life as it breaks down sugar, also known as sucrose, through a process called fermentation. Let&rsquos explore how this happens and why!

Problem

What is sugar&rsquos effect on yeast?

Materials

  • 3 Clear glass cups
  • 2 Teaspoons sugar
  • Water (warm and cold)
  • 3 Small dishes
  • Permanent marker

Procedure

  1. Fill all three dishes with about 2 inches of cold water
  2. Place your clear glasses in each dish and label them 1, 2, and 3.
  3. In glass 1, mix one teaspoon of yeast, ¼ cup of warm water, and 2 teaspoons of sugar.
  4. In glass 2, mix one teaspoon of yeast with ¼ cup of warm water.
  5. In glass 3, place one teaspoon of yeast in the glass.
  6. Observe each cups reaction. Why do you think the reactions in each glass differed from one another? Try using more of your senses to evaluate your three glasses sight, touch, hearing and smell especially!

Results

The warm water and sugar in glass 1 caused foaming due to fermentation.

Fermentation is a chemical process of breaking down a particular substance by bacteria, microorganisms, or in this case, yeast. The yeast in glass 1 was activated by adding warm water and sugar. The foaming results from the yeast eating the sucrose. Did glass 1 smell different? Typically, the sugar fermentation process gives off heat and/or gas as a waste product. In this experiment glass 1 gave off carbon dioxide as its waste.

Yeast microbes react different in varying environments. Had you tried to mix yeast with sugar and cold water, you would not have had the same results. The environment matters, and if the water were too hot, it would kill the yeast microorganisms. The yeast alone does not react until sugar and warm water are added and mixed to create the fermentation process. To further investigate how carbon dioxide works in this process, you can mix yeast, warm water and sugar in a bottle while attaching a balloon to the open mouth. The balloon will expand as the gas from the yeast fermentation rises.

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Microbes and disease

A few harmful microbes, for example less than 1% of bacteria, can invade our body (the host) and make us ill. Microbes cause infectious diseases such as flu and measles.

There is also strong evidence that microbes may contribute to many non&ndashinfectious chronic diseases such as some forms of cancer and coronary heart disease. Different diseases are caused by different types of micro-organisms. Microbes that cause disease are called pathogens.

Infectious disease Microbe that causes the disease Type of microbe
Cold Rhinovirus Virus
Chickenpox Varicella zoster Virus
German measles Rubella Virus
Whooping cough Bordatella pertussis Bacterium
Bubonic plague Yersinia pestis Bacterium
TB (Tuberculosis) Mycobacterium tuberculosis Bacterium
Malaria Plasmodium falciparum Protozoan
Ringworm Trichophyton rubrum Fungus
Athletes&rsquo foot Trichophyton mentagrophytes Fungus

It is important to remember that:

  • A pathogen is a micro-organism that has the potential to cause disease.
  • An infection is the invasion and multiplication of pathogenic microbes in an individual or population.
  • Disease is when the infection causes damage to the individual&rsquos vital functions or systems.
  • An infection does not always result in disease!

To cause an infection, microbes must enter our bodies. The site at which they enter is known as the portal of entry.

Microbes can enter the body through the four sites listed below:

  • Respiratory tract (mouth and nose) e.g. influenza virus which causes the flu.
  • Gastrointestinal tract (mouth oral cavity) e.g. Vibrio cholerae which causes cholera.
  • Urogenital tract e.g. Escherichia coli which causes cystitis.
  • Breaks in the skin surface e.g. Clostridium tetani which causes tetanus.

To make us ill microbes have to:

  • reach their target site in the body
  • attach to the target site they are trying to infect so that they are not dislodged
  • multiply rapidly
  • obtain their nutrients from the host
  • avoid and survive attack by the host&rsquos immune system.

Immune system

An infection can be seen as a battle between the invading pathogens and host. How does the immune system work?

Routes of transmission

Find out how you can pick up germs and pass them on to others.

Vaccination

Just a shot in the arm – what do vaccines do?

Antibiotics

Antibiotics are powerful medicines that only fight bacterial infections.

Microbes and food

Food for thought – bread, chocolate, yoghurt, blue cheese and tofu are all made using microbes.

Microbes and the outdoors

The function of microbes as tiny chemical processors is to keep the life cycles of the planet turning.


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