Basic Microbiology and the Tree of Life
When scientists first began to classify living things there were simply "Plants" or "Animals." However, with the invention of the microscope and further study of cells the Five Kingdom system of Animals, Plants, Fungi, Protista and Bacteria was developed. This all changed in the early 1990's after discovery, through DNA technology, of Archaea, organisms that were once thought to be part of the Bacteria "Kingdom." Hence a three branched system called The Tree of Life was developed.
In "Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya," Carl Woese explains the reason for changing how living things are classified:
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Molecular structures and sequences are generally more revealing of
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evolutionary relationships than are classical phenotypes (particularly so
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among microorganisms). Consequently, the basis for the definition of taxa
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has progressively shifted from the organismal to the cellular to the
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molecular level. Molecular comparisons show that life on this planet
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divides into three primary groupings, commonly known as the eubacteria,
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the archaebacteria, and the eukaryotes. The three are very dissimilar, the
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differences that separate them being of a more profound nature than the
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differences that separate typical kingdoms, such as animals and plants.
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Unfortunately, neither of the conventionally accepted views of the natural
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relationships among living systems--i.e., the five-kingdom taxonomy or
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the eukaryote-prokaryote dichotomy--reflects this primary tripartite
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division of the living world. To remedy this situation we propose that a
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formal system of organisms be established in which above the level of
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kingdom there exists a new taxon called a "domain." Life on this planet
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would then be seen as comprising three domains, the Bacteria, the Archaea,
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and the Eucarya, each containing two or more kingdoms. (The Eucarya,
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for example, contain Animalia, Plantae, Fungi, and a number of others yet
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to be defined). Although taxonomic structure within the Bacteria and
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Eucarya is not treated herein, Archaea is formally subdivided into the
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two kingdoms Euryarchaeota (encompassing the methanogens and their
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phenotypically diverse relatives) and Crenarchaeota (comprising the relatively
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tight clustering of extremely thermophilic archaebacteria, whose general
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phenotype appears to resemble most the ancestral phenotype of the Archaea.
The "Domains" of Bacteria and Archaea, being that they are microorganisms, will be studied in this Unit.
Bacteria
Bacteria are single celled prokaryotic organisms. Their cells contain five main structures a nucleoid, which is different from a eukaryotic cell nucleus, because the nucleoid consists of DNA only and does not have a nuclear membrane; ribosomes, cell membrane, cell wall and surface structures which may or may not be part of the cell wall (Todar 2010).
The first known observation of bacteria occurred in 1676 when Antonie van Leeuwenhoek experimented with lenses and designed a microscope. He observed what he called, "animalcules" or "little animals." He wrote about his observations in several letters to the Royal Society. Other scientists were able to confirm his results, but it took about two hundred years until microscopes were developed enough for the science of microbiology to begin development (Madigan and Martinko, 9-10).
Development of the microscope has been essential to the study of bacteria being that they are usually only a few micrometers long. Their shapes vary. They can be rods, spirals, spheres, or even squares (Madigan and Martinko, 3), (Dennis 2010).
Nearly every habitat on Earth, including those with very extreme conditions, contains bacteria. They are found in soil, acidic hot springs, water, organic matter, living bodies of other organisms, oil slicks, deep in the Earth's crust and even in radioactive waste. Bacteria are also extremely prolific in these various habitats. One gram of soil typically contains about forty million bacterial cells. Fresh water usually contains about one million bacterial cells per milliliter. It is estimated that the Earth contains five nonillion, which is 5 x 10
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bacterial cells. Therefore it is not surprising that most species of bacteria have not been studied and only about half have been reproduced in laboratory work (Madigan and Martinko, 6).
Archaea
Since the early 1990's archaea have been recognized as one of the three basic domains in the Tree of Life. Archaea, are also single-celled prokaryotes, and include microorganisms that can live in oceanic hydrothermal vents or in concentrated brines, or in animal guts, or even inside of their host organism's cells. Although the most extreme environments are usually dominated by archaea, they are also the dominant organisms in vast expanses of the ordinary ocean water column and can be found in most any stagnant freshwater ditch or swamp. It is believed that in the very history of life they evolved from bacteria. They perform many diverse and surprising functions including complex chemical reactions. They also have varied physical appearances. Some take on basic geometric shapes like triangles and squares. Others look like amorphous blobs or like sophisticated networks of interconnected structures (Howland, 1).
Scientists group archaea into several categories including: Thermophiles, Methanogens, Halophiles, and others. Thermopilic archaea live in high temperature environments such as hot springs and near volcanic vents. Methanogenic archaea, as their name suggests, produce methane gas and live in anaerobic mud or animal guts where no oxygen is present. Halophilic archaea live in hypersaline environments such as the Dead Sea where most other organisms could not survive (Howland, 2-4).