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  • 7/11/2014 Lesson 2: Classification

    http://water.me.vccs.edu/courses/ENV108/Lesson2_print.htm 1/23

    Lesson 2:Classification

    Objective

    In this lesson we will answer the following question:

    How are microorganisms classified?

    Reading Assignment

    Read the online lecture.

    Lecture

    General Classification

    Introduction

    This lesson is concerned with classification, also known as taxonomy, which is the arrangement

    of organisms into related groups. In this lesson, we will explain the categories into which

    microorganisms can be placed - bacteria, algae, fungi, protozoa, and viruses. In addition, we willbriefly consider a few larger organisms such as rotifers and worms. But before we consider the

    different types of microorganisms, you need to understand how scientists classify all livingorganisms.

    Categories

    Taxonomists place every organism in the world into a series of categories, such as those shown

    below. These categories are based on relationships, with closely related organisms placed in the

    same category.

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    As you can see, kingdom is the most general category used to describe an organism. A cat is inthe kingdom Animalia, also known as the animal kingdom. A variety of other organisms such as

    worms, insects, and snails are also in the animal kingdom. By saying that cats and snails are in thesame kingdom, we are saying that they are more closely related to each other than either is related

    to, for example, a fern in the plant kingdom.

    Each category below kingdom narrows down the types of characteristics which an organism has. The phylum Chordata, for example, includes only animals with backbones, while the class

    Mammalia contains animals with backbones which also have hair and feed their young with milk.

    The narrowest category is species, which is a group of organisms that have similar traits and caninterbreed. Scientists usually refer to a certain species of organism using its scientific name, which

    consists of both its genus and species names with the genus name capitalized and with both namesitalicized. For example, the scientific name of the domestic cat is Felis catus, the scientific name of

    humans is Homo sapiens, and the scientific name of the organism which causes giardiasis isGiardia lamblia.

    In addition to the categories shown on the pyramid above, there are a few other categories whichyou may come in contact with. Subspecies, strain, and variety are all terms used to refer to

    categories smaller than species. For example, the grizzly bear is a subspecies of the brown bear. In microbiology, we often talk about different strains of bacteria, some of which can cause disease

    and some of which cannot.

    Microorganism Classification

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    The chart above shows how microorganisms are related. The three most general groups into whichthe organisms are placed are prokaryotes, eukaryotes, and non-living organisms. We will explain

    what each of these categories mean in a later section. For now, you should just be aware thatprokaryotes are more primitive organisms than eukaryotes. Only bacteria are prokaryotes; the rest

    of the organisms considered in this course are either eukaryotes or viruses.

    Prokaryotes

    Introduction

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    Prokaryotes are organisms which do not contain nuclei or membrane-bound organelles. (Nuclei

    and organelles are both cell parts which we will define in a later section.) All prokaryotes are

    unicellular, which means that each organism is made up of only one cell.

    Another trait common to all prokaryotes is their small size - a typical cell is only about 2 um long.

    A micrometer, abbreviated as um and sometimes known as a micron, is equal to one millionth of

    a meter. It would take about 13,000 prokaryotes lying end to end to stretch the length of oneinch. Under a light microscope, bacteria are so small that they are usually visible only as tiny dots.

    Although there are two kingdoms which contain prokaryotes (Eubacteria and Archaebacteria), all

    prokaryotes are commonly known as bacteria. In the past, some prokaryotes have been calledblue-green algae, but these organisms are now known as cyanobacteria.

    Importance

    Bacteria are present in large numbers in raw wastewater, in biological treatment plants, in plant

    effluent, in natural waters, and throughout our environment. In the wastewater treatment plant, they

    form part of the slime on trickling filters and on the discs of rotating biological contactors. They arealso present in activated sludge.

    Bacteria are heterotrophs, meaning that they get their food from eating other organisms or from

    eating organic matter. (In contrast, organisms like plants which make their own food are known asautotrophs.) As a result, bacteria are important to the wastewater operator since the bacteria are

    able to digest a large amount of the waste in wastewater. On the other hand, some bacteria get

    their food from living inside organisms such as humans, in which case they can cause disease.

    Cell Structure

    A cell is the fundamental unit of all life. In the case of unicellular organisms, a cell is the body of the

    organism. In the case of multicellular organisms (organisms which consist of more than one cell),the cell is the building block from which the organism's body is made.

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    The diagram above illustrates a typical bacterial cell. As with every other kind of cell, a membrane

    serves as a sac holding the parts of the cell together. The membrane also regulates what passesinto and out of the cell.

    Inside the membrane, the cell is filled with a fluid known as cytoplasm. Floating in the cytoplasm

    are various organelles (subcellular structures with specific functions.) We have only illustrated afew of the most important organelles. Notice that the the DNA, which contains the genetic material

    of the cell, is floating freely in a mass within the cell. In addition to the main mass of DNA, the

    bacterial cell contains plasmids, which are small loops of DNA which can be transferred to otherbacteria, or in some cases into other organisms. Ribosomes are the sites of protein synthesis.

    Outside the membrane, most bacteria are surrounded by two other layers. The first of these, the

    cell wall, is a rigid layer made up of proteins, polysaccharides, and lipids. The cell wall gives thebacterium a set shape. Outside the cell wall is the capsule, a gelatinous slime layer which allows

    the bacterium to attach to surfaces and also protects the bacterium. In the treatment plant, bacterial

    capsules are responsible for clumping the organisms into flocs, or aggregations, which can settle out

    of water. In order for disinfecting agents such as chlorine to be effective, they must penetrate thisprotective slime layer.

    The bacterium can also have various appendages. Pili are hollow, hair-like structures which allow

    the bacterium to attach to other cells. Flagella are longer projections which can move and pushthe bacterium from place to place.

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    Endospores

    Some bacteria are able to survive in harsh environments by forming endospores. Endospores aresmall spores which develop asexually inside the bacterial cell. An endospore consists of the

    bacterium's DNA surrounded by a protective cell wall. Once the endospore has formed, the

    parent cell bursts open and releases the endospore.

    An endospore is able to survive in very harsh environments because it is in a dormant state and

    does not attempt to eat, grow, and reproduce. Bacteria typically form endospores when they

    encounter an undesirable pH, electrolyte content, amount of food, or amount of oxygen in theenvironment. Once the environmental conditions improve, the endospore is able to germinate and

    turn back into a growing bacterial cell.

    Classification

    There are thousands of species of bacteria on earth, many of which have not yet been identified.

    When attempting to classify a bacterium, a variety of characteristics are used, including visual

    characteristics and laboratory tests.

    Some bacteria can be identified through a simple visual perusal. First, the operator considers the

    appearance of the bacterial colony (a group of the same kind of bacteria growing together, often

    on a petri dish.) The operator also views individual bacteria under a microscope, considering their

    shape, groupings, and features such as the number and location of flagella.

    A variety of laboratory techniques can be used to narrow down the identity of a bacterial species if

    a visual survey is not sufficient. The operator can stain the bacteria using a gram stain or an acid-

    fast stain. The bacteria can be cultured on a specific medium which promotes the growth of certain

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    species, as in the membrane filter method of testing for coliform bacteria. Other tests can detectbacterial by-products, while yet more advanced tests act