An Overview of Biological Basics

Microbial Diversity

Life is very tenacious and can exist in extreme environments. Living cells can be found almost anywhere that water is in the liquid state. The right temperature, pH, and moisture levels vary from one organism to another.

Some cells can grow at -20°C (in a brine to prevent freezing), while others can grow at 120°C (where water is under high enough pressure to prevent boiling). Cells that grow best at low temperatures (below 20°C) are usually called psychrophiles, while those with temperature optima in the range of 20°C to 50°C are mesophiles. Organisms that grow best at temperatures greater than 50°C are thermophiles.

Many organisms have pH optima far from neutrality; some prefer pH values down to 1 or 2 ,while others may grow well at pH9. Some organisms can grow at low pH values and high temperatures.

Although most organisms can grow only where water activity is high, others can grow on barely moist solid surfaces or in solutions with high salt concentrations.

Some cells require oxygen for growth and metabolism. Such organisms can be termed aerobic. Others organisms are inhibited by the presence of oxygen and grow only anaerobically. Some organisms can switch the metabolic pathways to allow them to grow under either circumstance. Such organisms are facultative.

Often organisms can grow in environments with almost no obvious source of nutrients. Some cyanobacteria (formely called blue-green algae) can grow in an environment with only a little moisture and a few dissolved minerals. These bacteria are photosynthetic and can convert CO₂ from the atmosphere into the organic compounds necessary for life. They can also convert N₂ into NH₃ for use in making the essential building blocks of life. Such organisms are important in colonizing nutrient- deficient environments.

Organisms from these extreme environments (extremephiles) often provide the human race with important tools for processes to make useful chemicals and medicinals. They are also key to the maintenance of natural cycles and can be used in the recovery of metals from low-grade ores or in the desulfurization of coal or other fuels. The fact that organisms can develop the capacity to exist and multiply in almost any environment on earth is extremely useful.

Not only do organisms occupy a wide variety of habitats, but they also come in a wide range of sized and shapes. Spherical, cylindrical, ellipsoidal, spiral and pleomorphic cells exists. Special names are used to describe the shape of bacteria. A cell with a spherical or elliptical shape is often called a coccus (plural ,cocci);a cylindrical cell is a rod or bacillus (plural, bacilli); a spiral-shaped cell is a spirillum (plural, spirilla). Some cells may change shape in response to changes in their local environment.

Thus, organisms can be found in the most extreme environments and have evolved a wondrous array of shapes, sizes, and metabolic capabilities. This great diversity provides the engineer with an immerse variety of potential tools. We have barely begun to learn how to exploit these tools.

The situation is complicated by the bewildering variety of organisms present. A systematic approach to classifying these organisms is an essential aid to their intelligent use, Taxonomy is the development of approaches to organize and summarize our knowledge about the variety organism that exist. Although a knowledge of taxonomy may seem remote from the need of the engineer, it is necessary for efficient communication among engineers and scientists working with living cells. Taxonomy can allso play a critical role in patent litigation involving bioprocesses.

While taxonomy is concerned with approaches to classification, nomenclature refers to the actual naming of organisms. For microorganisms we us a dual name (binary nomenclature). The names are given in Latin or are Latinized. A genus is a group of related species, while a species includes organisms that are substantially alike. A common gut organism that has been well studied is Esherichia Coli. Escherichia is the genus and coli the species. When writing a report or paper, it is common practice to give the full name when the organism is first mentioned, but in subsequent discussion to abbreviate the genus to the first letter. In this case we would use E.coli .Although organisms that belong to the same species all share the same major characteristics, there are substle and often technologically important variations within species. An E.coli used in one laboratory may differ from that used in another. Thus, various strains and substrains a re disignated bu the addition of letters and numbers. For example, E.coli B/rA will differ in growth and physiological properties from E.coli K12.

Now that we know how to name organisms, we could consider broader classification up to the next level of kingdoms. There is no universal agreement on how to classify microorganisms at this level. Such classification is rather arbitrary and need not concern us. However, we must be aware that there are two primary cell types: eukaryotes and procaryotes around the cell's genetic information.

Procaryotes have a simple structure with a single chromosome. Procaryotic cells have no nuclear membrane and no organelles, such as the mitochondria and endoplasmic reticulum. Eucaryoteshave a more complex internal structure, with more than one chromosome (DNA molecule) in the nucleus. Eucaryotic cells have a true nuclear membrane and contain mitochondria ,endoplasmic reticulum ,golgi apparatus and a variety of specialized organelles.

Recently ,it has become obvious that the situation is even more complicated. Evidence suggests that a common or universal ancestor gave rise to three distinctive branches of life: eucaryotes, eubacteria (or "true" bacteria), and archaebacteria. The ability to sequence the genes of whole organisms will have a great impact on our understanding of how these families evolved and are related.

Viruses cannot classifies under any of these categories, as they are not free-living organisms.