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The 5th edition of Through the Microscope is now finished and available as a website subscription, as an ebook and as a hard copy from lulu.com. For subscribers to the 4th edition who are still using it, the book will stay available until May 15th, 2014. At that point, it will be retired. Thank you for all your support. For more information about the 5th edition, check out the latest news
This is the third edition of Through the Microscope. A new edition has just been published. Please go to the Table of contents for the fourth edition
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Contrary to what you would believe from news and advertising, the vast majority of bacteria are harmless to humans and a large number are actually helpful. Understandably, early work in microbiology focused on pathogenic microbes and treatment of the diseases they caused. Martinus Beijerinck and Sergei Winogradsky began the transition from this early work into the present era where we study the molecular biology of a wide variety of microorganisms. Both were interested in microbes present in the soil and water and their work founded the discipline of environmental microbiology. Much of what we understand about bacteria in the environment and their impact can be traced back to the efforts of these two scientists.
Martinus Beijerinck, depicted in Figure 1-10, was originally trained as a botanist and began his work studying the microorganisms that were present in and around plants. He soon began experiments with microbes in the soil. His greatest contribution was the development of enrichment media. Previously, microbes were cultivated on medium consisting of potatoes or extracts of leftover animal renderings. Such media would support the growth of many different bacteria, with chance and population density dictating what became dominant in the culture. In many cases this was exactly what was desired, but in other cases it was of interest to find bacteria capable of performing certain chemical conversions.
Figure 1.10 Martinus Beijerinck. The Dutch microbiologist Martinus Beijerinck. Drawing by Tammi Henke.
Beijerinck discovered that by adding or removing certain compounds from the medium or incubating under different conditions, it was possible to favor the growth of certain microbes and prevent the growth of others. An example is Beijerinck's work with nitrogen-fixing bacteria, which are important in agriculture and the global cycling of nitrogen. They are capable of taking nitrogen gas (N2) from the air and reducing it to ammonia (NH3). This is an important property since most organisms, including agriculturally important plants, can only use reduced nitrogen compounds such as ammonia. Beijerinck wanted to isolate an organism capable of fixing nitrogen in the presence of air, because all previous isolates fixed nitrogen only under anaerobic conditions. By making medium that did not contain a source of fixed nitrogen and then incubating in the presence of air (containing N2), he demanded that any microbe growing in the medium had to be able to derive its nitrogen by performing aerobic nitrogen fixation. Using this method he succeeded in isolating a new microbe (Azotobacter chroococum) with these capabilities. Similar selective culture techniques (as he liked to call them) enabled his laboratory to isolate sulfur-reducing and sulfur-oxidizing bacteria, Lactobacillus species, green algae and many other microbes. Selective culture techniques have since been applied to many different groups of microorganisms, allowing them to easily be brought into pure culture.
Sergei Winogradsky, pictured in Figure 1-11 was also interested in soil bacteria, especially those involved in the cycling of nitrogen and sulfur compounds. He was one of the first to isolate microorganisms responsible for the conversion of these elements in the soil, obtaining pure cultures of bacteria capable of oxidizing ammonia to nitrate. Winogradsky also studied the consumption of hydrogen sulfide gas by sulfur-oxidizing bacteria directly in their natural habitat.
Figure 1.11 Sergei Winogradsky. The Russian microbiologist Sergei Winogradsky. Drawing by Tammi Henke.
When working with Beggiatoa (one of these sulfur-oxidizing bacteria) he discovered it was obtaining its cell carbon from carbon dioxide. He used the term autotrophy to describe this property, a radical idea at the time, and one not readily accepted by other microbiologists. This led Winogradsky to propose the concept of chemolithotrophy; bacteria capable of growth using purely inorganic sources of carbon and energy. He realized that these microbes were essential for the cycling of nutrients in the environment, and the living world was dependent upon their action, long before others accepted the idea.
As a result of the work of Winogradsky and Beijerinck there was great enthusiasm for identifying and classifying the bacteria inhabiting our natural world. For the first part of the 20th century many scientists isolated microbes and made proposals for their organization into genera and species. In 1909 Sigurd Orla-Jensen suggested a classification scheme based on the functions and abilities of the bacteria, such as growth on certain compounds or the production of specific by-products. The Society of American Bacteriologists, later to become the American Society of Microbiology, applied this technique to prepare a report on the classification of bacteria. This eventually evolved into Bergey's Manual of Determinative Bacteriology in 1923 and subsequent editions have become authoritative reference works.
There was great optimism that as more bacteria were brought into pure culture a clear organization, based on the evolutionary history of microbes, would emerge from studies of their physiology. However, by the 1940's it became clear that bacteria were unwilling to go along with this idea because classification based on one set of properties was often inconsistent with classification using a different set of properties. Scientists threw up their hands and gave up the idea of finding a system of classification based on growth and morphological characteristics.
Figure 1.12 Carl Woese. The American microbiologist Carl Woese, who applied the concept of molecular phylogeny to 16S rRNA and pioneered modern microbial taxonomy. (Source: University of Illinois-Champaign-Urbana)
Several decades passed during which bacteria became tools for understanding life, but their place in evolution was of little interest. Then in 1961 Brian McCarthy and E. T. Bolton developed methods for the comparison of genetic material between species and Linus Pauling and Emile Zuckerkandl formalized the idea of using the makeup of biological molecules, their sequence, as a way to determine phylogenetic relationships. Later, Carl Woese, pictured in Figure 1-12, began to use this insight, choosing the sequence of ribosomal RNA as the basis for evolutionary comparisons. His initial efforts used the smaller RNA, termed 16S, of bacterial ribosomes, which he showed to be a marvelous "evolutionary clock." This analysis was a watershed event for the evolutionary classification of bacteria and in 1977 Woese used this technique to assert that known bacteria should be divided into two separate domains that we now call Bacteria and Archaea, radically changing our view of the microbial world. Because all organisms have ribosomal RNA, this method of analysis has since been applied to the identification and classification of large classes of organisms such as plants and birds, fundamentally reshaping our views of the biological world. As you will read in Figure 1-24 describes significant events in environmental microbiology.
|1887||Sergei Winogradsky studies Beggiatoa and establishes the concept of autotrophy.|
|1888||Martinus Beijerinck develops the technique of enrichment culture.|
|1891||Winogradsky discovers the organisms responsible for nitrification is soil, which is of great importance in agriculture because nitrogen is a limiting nutrient in the soil.|
|1904||Martinus Beijerinck obtains the first pure culture of sulfur-oxidizing bacterium, Thiobacillus denitrificans.|
|1904||Cornelius Johan Koning suggests that fungi are critical for the decomposition of organic matter.|
|1909||Sigurd Orla-Jensen proposes the use of physiological characteristics for the classification of bacteria. He later publishes a monograph on lactic acid bacteria that establishes the criteria for assignment.|
|1920||The Society of American Bacteriologists presents a report on the characterization and classification of bacterial types that becomes the basis for Bergey's manual in 1923.|
|1961||Brian McCarthy and E. T. Bolton describe a method to compare genetic material from different species using hybridization. Using this technique it is possible to quantitatively compare the relatedness of the two species.|
|1965||Emile Zuckerkandl and Linus Pauling publish "Molecules as documents of evolutionary history", making a compelling case for the use of molecular sequences of biological molecules to determine evolutionary relationships.|
|1969||Don Brenner and colleagues establish a more reliable basis for the classification of clinical isolates among members of the Enterobacteriaceae. They use nucleic acid reassociation, where DNA of one organism is allowed to hybridize with another organism. This technique is used to help define a species.|
|1977||Carl Woese uses ribosomal RNA analysis to identify a third form of life, the Archaea, whose genetic makeup is distinct from but related to both Bacteria and Eucarya.|
|1977||Holger Jannasch discovers abundant life at the bottom of the ocean near deep sea hydrothermal vents. The entire system is dependent upon sulfur oxidizing microorganisms. Light and photosynthesis do not drive the process.|
|1982||Karl Stetter isolates hydrothermophilic microbes (Archaea) that can grow at 105°C. The discovery redefines the upper temperature at which life can exist.|
|1994||Gary Olsen, Carl Woese and Ross Overbeek summarize the state of phylogeny in prokaryotes. This causes scientists to rethink the classification of life and emphasizes the importance of microbes.|
Figure 1.24 Significant Events in Environmental Microbiology..