The Microbial World

The Microbial World

Objectives: In this lab you will learn:

• the diversity found within the microbial world.

• the importance of microbes in different ecosystems.

• the importance of microbes to human health.

INTRODUCTION

Most of the living world is small. So small that humans usually ignore the vast majority of living things on the planet. Even biologists, whose job it is to document the biological systems in which we live, often overlooked the smallest but in many ways the most influential of life forms. When scientists began looking in earnest at the microbial world, the discoveries they made revolutionized the study of biology and our understanding of the earth.

In this lab we introduce you to the world of microbes. You will learn what microbes tell us about evolution; how microbes govern the chemical processes that sustain life; how microbes affect our health; and how microbes are being used to shape our future.

Watch the two introductory video clips.

1. What groups of organisms are commonly called microbes? ______

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2. Why do you think that there are so many more tiny organisms than big organisms?

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* MICROBIAL DIVERSITY AND EVOLUTION

Microbes were the first living things on the planet and all the life that has existed since (including you and me) are descendants of these first microbes. Today, all life contains traces of its early microbial ancestors within its genetic material.

Scientists classify life into three major categories. Most of this life is invisible to the naked eye. This week, we introduce you to some of this invisible diversity. We also demonstrate how the evolution of microbes is intricately related to the evolution of all life.

A. People were a bit shocked when they found life flourishing in places like boiling hot springs. These organisms are so distinct that they have been classified into their own major grouping of life called the Archea (See Figure 4-1). Watch the video of Karl Stetter searching for these closest living relatives of the first life.

1. Why does Karl Stetter think that the closest ancestors of the earliest life live today in such remarkably hot habitats? ______

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2. What do many of the microbes that live in these hot habitats require for their metabolism? ______

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B. The ability to sequence strings of genetic code within organisms has allowed scientists to create phylogenies for organisms that left no fossil record. Watch the video describing how this ability changed our view of the tree of life.

1. What characteristics of organisms did Carl Woese use to complete his new phylogeny of life? ______

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2. What conclusion did Carl Woese come to when he completed his tree? ______

C. Watch the video describing the major groupings of life.

1. What are the three major groupings of life? ______

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2. Why can’t we classify viruses in the phylogeny of life? ______

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D. Watch the video describing horizontal gene transfer.

1. What sorts of traits are commonly transferred horizontally from microbe to microbe? ______

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2. Why does horizontal gene transfer make constructing a phylogeny of microbes difficult? ______

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* MICROBIAL METABOLISM AND ECOLOGICAL PROCESSES

Morphologically, microbes are not exceptionally interesting. The almost overwhelming diversity of genetically distinct microbes come in a comparatively small number of morphological types. This morphological blandness is in sharp contrast to the amazing metabolic innovations that have arisen in microbes. Nearly all the chemical processes that are essential for life were developed and continue to be mediated by microbes. In this section we examine some of these important processes.

A. Watch the video describing the importance of microbes to the functioning of a salt marsh.

1. What two major functions do microbes perform in the salt marsh ecosystem?

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2. What kinds of salt marsh organisms rely on microbes? ______

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B. Almost two decades after we landed on the moon, we finally managed to reach the deepest parts of the ocean. Scientists found utterly strange ecosystems that perhaps not surprisingly were governed by microbes. Watch the video on deep sea vents.

1. Why are deep-sea vent systems unique from almost all other ecosystems? ______

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2. Where does almost all the energy used in vent ecosystems come from? ______

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C. No vertebrate organism can directly digest cellulose. Watch the video describing how cows manage to get so fat.

1. What happens in the rumen? What do microbes do? ______

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2. Watch the video on termites. In what way is termite metabolism similar to that of cows?

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* MICROBES AND HUMAN HEALTH

Humans and microbes have interacted with each other for millions of years. In many cases these interactions are either benign or produce mutual benefits. In some cases, however, microbes cause diseases, and these diseases are responsible for most of the pain and suffering experienced by humans. In this section we investigate the profound influence that microbes have on our daily health.

A. When antibiotics were discovered and used on a large scale they revolutionized healthcare. Today, however, many common microbe pathogens have developed resistance to antibiotics. Watch the video on antibiotic resistance.

1. How and why have some microbes developed resistance to antibiotics? ______

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B. People in the United States are afflicted with the diseases of the wealthy: heart disease, diabetes, cancer. Most of the world, however, is burdened by microbe caused diseases that are readily prevented and treated here. Watch the video on disease in the developing world.

1. How many people in the world die each day from infectious diseases? ______

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2. Why is infectious disease such a problem in the developing world? ______

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C. Humans have evolved a complex defense system against potentially harmful microbes. Just as with antibiotics, many microbes have evolved ways to counteract this defense system. Read the article on the common human pathogen salmonella.

1. What defense mechanisms must a salmonella bacteria surmount to infect a human? ______

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2. Why might salmonella have evolved to infect but not kill its human host? ______

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D. Viruses that cause disease are difficult to kill because in some respects they aren’t really alive. Viruses consist of a protein sheath that surrounds a DNA or RNA core. Watch the video on viruses.

1. Why do viruses need to infect other cells in order to proliferate? ______

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2. Why does virus replication sometimes cause disease? ______

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E. HIV infects the cells of the human immune system and is almost always fatal if left untreated. While expensive and complex treatments that can prolong life have been developed in western countries, much of the world is suffering from a global AIDS epidemic. Watch the video about AIDS.

1. What is the possible origin of the AIDS virus? ______

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2. What factors have contributed to the spread of AIDS? ______

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3. What are some possible solutions to the AIDS epidemic? ______

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* USING MICROBES TO SOLVE PROBLEMS

Even in a century that saw the development of the transistor, the microchip, and the atomic bomb it can reasonably be argued that the most profound technical advances of the last century were biological. Humans can now manipulate the functioning of large ecosystems as well as the genetic composition of individual cells. Such abilities offer immense promises, but come with equally large and troubling questions.

Microbes have been at the center of this biological revolution. In this section we examine some of the ways that microbes are being used to solve an array of problems, and we examine some difficult questions these uses sometimes pose.

A. The increase in antibiotic resistant pathogens has spurred a search to find new antibiotics. Many microbes make antibiotics for use in defense or in competition for resources. Most microbes cannot be cultured in the laboratory, however, which makes finding these potentially useful antibiotics difficult. New molecular biology techniques are helping solve this problem. Watch the video describing one of these techniques.

1. How does TerraGen produce useful amounts of substances from microbes that cannot be grown in the lab? ______

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2. How does TerraGen know when it has found a new potential antibiotic? ______

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B. Many bacteria are capable of deriving energy from reduced chemical compounds such as ammonia (NH3), hydrogen sulfide (H2S), and methane (CH4). The bacteria found in deep sea hydrothermal vents are an example. People have started to use these bacteria to break down other energy rich compounds that happen to be toxic to us and most other living organisms. Watch the video describing one such bioremediation project at the Savanna River nuclear weapons factory.

1. How do scientists speed up the natural degradation process? ______

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C. The microbiology revolution has been based on the ability to harness the gene transfer facility of microbes. We now can almost effortlessly transfer genetic traits from one organism to another. While offering endless useful possibilities, this ability also poses troubling questions. Read about some potential problems with genetically engineered corn.

1. How might monarch butterflies come in contact with the Bt toxin? ______

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2. What are the potential benefits of using Bt corn instead of more traditional pest control methods? ______

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D. The starchy tubers of the cassava plant are a staple food of over 500 million people around the world. In Africa, cassava is attacked by the cassava mosaic virus, which severely reduces the health of infected plants. Scientists are using bacteria and the virus itself to combat this serious pest. Watch the video describing work to develop virus resistant cassava plants

1. What are the agrobacteria used for in this procedure? ______

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2. Once you make a virus resistant plant using this procedure how do you think you make more cassava resistant plants? Can you allow the resistant plant to mate with non-resistant plants or do you have to take asexual cuttings? ______

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