Lessons in Environmental Microbiology

Roger Tim Haug

• Editorial: CRC Press
• Año: 2019
• ISBN:
  9780429810473
• Edición: 1
• Categoría: Ciencias físicas
• Categoría: Química

Lessons in Environmental Microbiology provides an understanding of the microbial processes used in the environmental engineering and science fields. It examines both basic theory as well as the latest advancements in practical applications, including nutrient removal and recovery, methanogenesis, suspended growth bioreactors, and more. The information is presented in a very user-friendly manner; it is not assumed that readers are already experts in the field. It also offers a brief history of how microbiology relates to sanitary practice, and examines the lessons learned from the great epidemics of the past. Numerous worked example problems are presented in every chapter.

1

Introduction to Environmental Microbiology

The importance of microorganisms can’t be overemphasized…it is estimated that microbes contain 50% of the biological carbon and 90% of the biological nitrogen on Earth…they greatly exceed every other group of organisms on the planet.

Willey et al. (2008)

Microbiologists like to say, ‘Microbes rule the Earth, and we just live on it.’

Gregory Fournier (2014)

What Is Microbiology?

Microbiology is generally defined as the study of living organisms too small to be seen with the naked eye, the world of microorganisms or microbes. Our eyes can detect an object down to about 0.2 mm, or 200 μ. Below that, individual specks are not visible to us. Having been raised in our modern world, this may seem a somewhat strange division. Why would it make any difference whether we can see an organism with our eyes or not? We grow up immersed in the knowledge of an enormous universe, ranging from the very small as seen through microscopes to the very large as seen through telescopes. We can see down to the molecular level with electron microscopes and peer to the edge of time with the Hubble Space Telescope. We grow up with the wonderful knowledge that instruments can extend the range of our eyes and that the world includes far more than we can see without them.

So why would we make a distinction between biology of the small (microbiology) and biology of everything else (macrobiology)? The answer lies mainly in the history of the science. When we study any science we cannot divorce ourselves from the history of that science. Macrobiology, the study of living systems that we can see with our eyes, is as old as mankind itself. The earliest humans had to learn about nature, both plants and animals, to survive. Macrobiology was self-evident from the earliest time that man could contemplate his own being. Man’s attempts to organize and categorize the living world date to ancient times.

But the world of microbes remained beyond the human senses, too small to be seen. Despite this limitation, mankind learned to benefit from some of the reactions that microbes offer. The fermentation of fruits to wine and the leavening of bread were known to the ancients. But things began to change around the year 1600. Galileo pointed his crude telescope to the sky, forever changing mankind’s view of his place in the universe. If lenses could make distant objects seem closer, could lenses make small things appear bigger? Ironically, it was almost a century after Galileo, about the year 1700, when a Dutch businessman, Anton van Leeuwenhoek (1632–1723), became an expert in grinding lenses and building microscopes. Anton built the best microscopes of the day and discovered the previously unknown world of microorganisms. His best scopes were believed to magnify almost 400 times, quite an accomplishment when you consider that today’s best light microscopes magnify to about 1,000 times. He called the small beings “animalcules” and wrote many letters on his findings to the Royal Society of London, the premiere scientific organization of the time.

But the study of microbes remained largely a curiosity. No one associated such small “animalcules” with disease. It would take another 150 years for man to prove the association of microbes with disease. While van Leeuwenhoek is considered by most as the father of microbiology, the science of microbiology was born in the second half of the 19th century. Because it developed so recently and because some of the microbes were identified as causative agents of the great infectious diseases of that era, microbiology was viewed as its own science. New tools and techniques had to be developed to study the microbes. People began to refer to themselves as microbiologists to distinguish their trade from those that studied the macro world: the biologists, zoologists, plant physiologists, paleontologists, and numerous others. The techniques of this new science also distinguished its practitioners from others. Sterilization and the use of culture media became the tools of their trade.

Today, we know that all life is a continuum and shares the same basic biochemistry. Size doesn’t matter in that regard. In fact, common biochemistry has become one of the grand unifying principles of all biology, whether micro or macro. Nevertheless, the study of microbes deserves special attention for environmental engineers and scientists.

Why Should I Study Microbiology?

Microbes are largely responsible for the global cycles of carbon, nitrogen, and sulfur on planet Earth. They decompose the organic materials produced by photosynthesis and, thereby, save us from being buried in organic debris. They make some of our most cherished products, such as wine, beer, cheese, yogurt, and sauerkraut. Microbes are already important players in the growing biofuel industry. They manufacture fuel ethanol and may someday be major sources of renewable biodiesel. Most recently, man has learned to insert genes into these little biochemical factories to produce valuable molecules such as human insulin and human growth hormone.

Microbes are the heart and soul of modern wastewater treatment, saving us from our own effluents. In the 1970s, there was an effort to develop physical/chemical processes with the idea of replacing biological processes. Having landed man on the moon in 1969, many saw “space age” processes as the way forward. Several sewage treatment plants were built based on physical and chemical processes. None survived the test of time. They were complicated, expensive to operate, and could not match the effluent quality and reliability of their biological counterparts. Since that time, the wastewater industry has learned to adapt nature’s microbes in more and clever ways. Without doubt, biological treatment is the “flagship” process for today’s wastewater treatment and water reclamation industries.

Ever wonder how many cells make up your body? If you’re like me, you’re naturally thinking of your own human cells. It turns out that this number is not that easy to determine, but estimates range from about 5 to 50 trillion (1 trillion = 10¹²). It takes a lot of cells to make you who you are. But there is general agreement that the vast number of human cells is at least equaled by the number of bacterial cells in and on your body. Estimates on the low end suggest that we harbor at least as many bacterial cells as our own human cells. Estimates on the high end suggest that we may harbor 10x the number of bacterial cells. For example, the human intestine contains trillions of bacteria made up of perhaps thousands of different species. The total weight of bacteria in the intestine is estimated at around two pounds. Of course, the very large number of bacterial cells is due to their very small size compared to human cells. You might be a bit disturbed finding out that your human cells may be the minority, but the fact is that our health depends on these microbes. Microbes in your gut communicate with your immune system, break down complex foods, produce vitamins, keep out unfriendly bacteria, and help in other ways we are just beginning to understand. Your gut flora is called a microbiome, and the type and number of different bacterial species is unique to you. There is no normal. Your unique microbiome begins to develop just after birth and stays with you throughout life.

Unfortunately, less friendly bacteria can disturb the normal intestinal flora and be discharged in the infected person’s fecal matter. The fecal-to-oral route of transmission is responsible for many of the infectious diseases that have haunted mankind for all history. You may be surprised to know that infectious disease is the number one killer of people on the planet. Only the developed world has reduced infectious disease to the number three killer behind heart disease and cancer. The World Health Organization (WHO) estimates that 2 to 2.5 billion people on the planet lack proper sanitation. Because of this, about two million people die each year from waterborne, diarrheal diseases. Most of the deaths occur in children under the age of five. Also on the negative side, microbes can spoil some of our other cherished foods. Everyone has suffered food “poisoning,” a reaction to toxins excreted by some microbes as they grow on our food. Public health officials work hard to assure the safety of our food supply and the cleanliness of our restaurants.

The antibiotic penicillin was introduced in the 1940s and ushered in the “golden age” of antibiotics. Unfortunately, many diseases historically “controlled” by antibiotics are staging a comeback. Tuberculosis is a case in point because strains of the causative agent, a bacterium called Mycobacterium tuberculosis, have developed resistance to many of the available antibiotics. Microbes remain the focus of efforts to control infectious disease and improve overall public health.

The Roster of Microbes

OK. You’re now convinced that the study of microbes might be important to you. It might even be interesting. But who are the players on this roster of microbes? Here is a brief roll call of the major players, each a superstar in its own way.

Bacteria. These are the smallest and oldest living organisms on planet Earth. In their most common form, they live as a single individual cell. Accumulations of similar cells can also occur. All bacteria lack a true nucleus and are called prokaryotic as a result. Only the bacteria are prokaryotic, as all other living cells have a distinct nucleus and are called eukaryotic. Cell shape ranges from spherical, rod-shaped, or spiral forms. The cells are very small, typically 1 to 3 μ (microns or 10⁻⁶ meters), which strains the limit of even today’s best light microscopes. Bacteria are capable of the greatest range of metabolic reactions of any living organisms. They can live on organic “food,” but can also “eat” inorganic compounds. Bacteria are the workhorses of modern wastewater treatment. Today, bacteria are divided into two Domains, the eubacteria and the archaeabacteria (more on this later).

Protists or Protoctista. The protists are usually single-celled and many are motile. They are very large compared to the bacteria, generally 10 to 300 μ, and include organic consumers called protozoa as well as the photosynthetic algae. Today’s protists are descendants of the first eukaryotic cells, those that developed a nuclear envelope and multiple chromosomes. One of the most unique features of protozoa is their ability to ingest particulate solids by a process called phagocytosis. It appears they developed this capability early in their evolutionary history. It opened a new source of food supply, including the ability to feed on bacteria. Photosynthetic, single-celled algae are usually classified as protists. Together, the photosynthetic and non-photosynthetic forms are essential in the aquatic food chain.

Fungi. The fungi include the unicellular yeasts and the filamentous, multi-celled molds. These are the green, black, or red “moldy things” that grow on your old cheese and bread at the back of the refrigerator. The yeasts include those wonderful microbes that ferment sugar to ethanol, making both wine and alternative fuels. While a fungal colony is visible to your eye, each individual strand (called a hyphae) usually is not and the fungi are considered part of the microbial world. In an interesting twist of evolution, the fungi gave up mobility and phagocytosis. One might question the wisdom of being non-motile and relying on enzymes excreted outside the cell to break down substrates to small molecules that can then be imported into the cell. Nevertheless, one cannot argue with their success. Fungi are ubiquitous in our environment and are responsible for recycling much of the organic carbon produced by plants. They form symbiotic associations with the roots of about 90% of known plant species, increasing the plant’s access to nutrients and moisture in return for sugars produced by the plant.

Viruses. Viruses are the smallest biological structures containing all information for reproduction. However, they are parasites that require the machinery of a host cell to support their reproduction. They cannot grow or metabolize on their own. All viruses consist of a small piece of genetic material, either DNA or RNA, and are wrapped in a protein shell called a capsid. Some may have a lipid envelope outside the capsid. It’s hard to find something nice to say about viruses because their main business is infecting healthy cells, destroying them, and causing disease. Despite having a bad reputation, viruses are everywhere and in great numbers. They have been called a piece of bad news wrapped in protein. Viruses continue to spark lively debate on what it means to be alive and living. My sense of it is that most folks believe you must have a functioning cell to be called alive. They put viruses in the interesting but non-living category. Others disagree and call them “molecular organisms” to distinguish them from everything else that are “cellular organisms.” What do you think?

Others that are really macro. Some organisms live on the edge of being visible to the human eye. Rotifers and helminths (small worms) fall in this size range and are usually considered part of the macro world. We will include them in our studies because rotifers are important to the aquatic food chain and helminths cause several parasitic diseases that continue to haunt mankind.

The Branches of Microbiology

Microbes are everywhere and affect almost everything from the cold you suffered through last winter to the global cycling of carbon and nutrients. As you might expect, there are many specialty areas or branches within modern microbiology. Here is a sampling. General microbiology is what most students study in high school and college classes on microbiology. Most professional microbiologists specialize from this point. Medical microbiology focuses on the diseases caused by microbes and their control. Pre-med and nursing students all take courses focusing on the medical aspects of microbiology. Clinical microbiology focuses on the identification and control of pathogens and the detection of immune dysfunction. A major goal is to isolate and identify pathogenic microbes from clinical specimens and to do so rapidly. If you get sick and the doctor sends a sample to the lab, you owe much of your eventual cure to the clinical microbiologist who made the detection or developed the technique to do so.

Industrial microbiology is the application of microbes in industrial processes to produce marketable quantities of desirable products. This is a large field and includes many areas of work including: alcohol fermentations to make beer, wine, and distilled spirits; production of fermented dairy products, particularly cheeses, yogurt, and sour cream; production of fermented plant products including preserved olives, sauerkraut, soy sauce, tofu, vinegar, and fermented coffee beans; production of health care products including the indispensable antibiotics; commercial enzymes, most of which are now obtained from microbial sources (Look at the ingredients in your box of detergent. Those enzymes were manufactured by microbes.); production of industrial chemicals such as acetic acid, citric acid, ...