Lesson 5:


Bacterial Shapes and 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.  Bacteria are simple, unicellular organisms. Most are free-living organisms, but a few require animal or plant hosts for survival. Bacteria absorb nutrients from their environments, excrete waste products, and secrete various toxins that help them invade tissues. Bacteria have no enclosed nucleus. Their chromosomal material is in the form of a large loop, packed into the cytoplasm of the cell.

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 species, as in the membrane filter method of testing for coliform bacteria.  Other tests can detect bacterial by-products, while yet more advanced tests actually analyze the DNA of the bacteria. 

In water microbiology, the primary focus is on bacteria of the family Enterobacteriaceae. These include:


**pathogens (all or part of genus)

Bacterial Shapes

Bacteria are classified based on major observable features:

Cultural classification - the culture media and environmental conditions which support optimal growth (ex. with or without oxygen, incubation temperature).

Microscopic examination - used to examine staining characteristics and cell shape. The principle stain used is the Gram stain where a cell exhibits either a positive (deep purple) or negative (red) reaction. Bacterial cell shapes include:

Spheres (cocci)
Coils (spirochetes)
Rods (bacilli)
Spirals (spirilla)


These exist as chains, clusters, pairs, tetrads, singles or other configurations.


Characterization of metabolism - when similar gram stain characteristics are noted, physiological characteristics are used, based on the fact that the genetic makeup of a cell reflects its ability to utilize and metabolize nutrients in the environment. Microorganisms are grown in the presence of a specific nutrient substance, or substrate, and examined to determine what chemical change took place. For example, the breakdown of starch or the fermentation of glucose to produce acid and gas are often used to separate bacterial species. The type of metabolism, aerobic, anaerobic, or facultative anaerobic, is also an important classification tool.

Chemical characterization - involves breaking the microorganism apart cell membrane and nuclear structures.

Genetic characterization - DNA determination, PCR technology.


The most basic method used for identifying bacteria is based on the bacterium's shape and cell arrangement.  This section will explain the three morphological categories which all bacteria fall into - cocci, bacilli, and spirilla.  You should keep in mind that these categories are merely a way of describing the bacteria and do not necessarily refer to a taxonomic relationship. The most common shapes of bacteria include rod, cocci (round), and spiral forms. Cellular arrangements occur singularly, in chains, and in clusters. Some species have one to numerous projections called flagella enabling the bacteria to swim, making them motile organisms.


Cocci (or coccus for a single cell) are round cells, sometimes slightly flattened when they are adjacent to one another.  Cocci bacteria can exist singly, in pairs (as diplococci ), in groups of four (as tetrads ), in chains (as streptococci ), in clusters (as stapylococci ), or in cubes consisting of eight cells (as sarcinae .)


Bacilli (or bacillus for a single cell) are rod-shaped bacteria.  Since the length of a cell varies under the influence of age or environmental conditions, you should not use cell length as a method of classification for bacillus bacteria.  Like coccus bacteria, bacilli can occur singly, in pairs, or in chains.  Examples of bacillus bacteria include coliform bacteria , which are used as an indicator of wastewater pollution in water, as well as the bacteria responsible for typhoid fever. 


Spirilla (or spirillum for a single cell) are curved bacteria which can range from a gently curved shape to a corkscrew-like spiral.  Many spirilla are rigid and capable of movement.  A special group of spirilla known as spirochetes are long, slender, and flexible.



Gram Stain Procedure

The most fundamental technique for classifying bacteria is the gram stain, developed in 1884 by Danish scientist Cristian Gram. It is called a differential stain because it differentiates among bacteria and can be used to distinguish among them, based on differences in their cell wall.

In this procedure, bacteria are first stained with crystal violet, then treated with a mordant - a solution that fixes the stain inside the cell. The bacteria are then washed with a decolorizing agent, such as alcohol, and counterstained with safranin, a light red dye. The walls of gram-positive bacteria (ie. Staphylococcus aureus) have more peptidoglycans (the large molecular network of repeating disaccharides attached to chains of four or five amino acids) than do gram-negative bacteria. Thus, gram-positive bacteria retain the original violet dye and cannot be counterstained.

Gram-negative bacteria (ie. Escherichia coli) have thinner walls, containing an outer layer of lipopolysaccharide, which is disrupted by the alcohol wash. This permits the orignial dye to escape, allowing the cell to take up the second dye, or counterstain. Thus, gram-positive bacteria stain violet, and gram-negative bacteria stain pink. The gram stain works best on young, growing populations of bacteria, and can be inconsistent in older populations maintained in the laboratory.




Although we think of respiration as breathing, respiration is actually the process by which organisms break down organic substances (such as sugars) to produce energy.  All living organisms must perform some kind of respiration. 

In many cases, the chemical process of respiration requires oxygen, although some organisms are able to carry out respiration in the absence of oxygen.  This page will explain the three types of respiration found in microorganisms, as well as how these types of respiration affect the wastewater treatment plant. 

Aerobic Respiration

Aerobic respiration is respiration in the presence of oxygen.  Most multicellular organisms and many microorganisms produce their energy using aerobic respiration.  In aerobic respiration, sugars are broken down in the presence of oxygen to produce carbon dioxide, water, and energy.  Without oxygen, aerobic microorganisms are unable to produce energy and quickly die. 

Anaerobic Respiration

Other microorganisms are able to survive in environments which lack oxygen by performing anaerobic respiration , sometimes known as fermentation .  Like aerobic respiration, anaerobic respiration breaks down sugars and releases energy.  However, anaerobic respiration is typically slower and less efficient than aerobic respiration.   In addition, anaerobic respiration involves chemicals other than oxygen and carbon dioxide. 

The chemicals used and produced during anaerobic respiration vary from microorganism to microorganism.  Some anaerobic microorganisms use sulfate (SO42-) during respiration and produce hydrogen sulfide (H2S.)  Other microorganisms use nitrate (NO3-), producing nitrite (NO2-), nitrous oxide (NO), or nitrogen gas (N2 ).  Yet other microorganisms are able to use hydrogen gas (H2 ), producing methane (CH4 ) or acetic acid (CH3COOH-) as the byproduct. 

Anaerobic reactions generally lead to more offensive end products than those produced during aerobic respiration.  For example, hydrogen sulfide is very reactive and smells like rotten eggs even at low concentrations.  Hydrogen sulfide can combine with the organic end products of anaerobic respiration to form the dark-colored, odorous substances which are characteristic of anaerobic (also known as septic ) conditions. 

Facultative Anaerobic Respiration

Many microorganisms are either obligate aerobes or obligate anaerobes.  That is, those which perform aerobic respiration will die if the oxygen content of their environment drops too low.  In contrast, those which perform anaerobic respiration will die if they are brought in contact with oxygen. 

The final type of microorganisms - facultative anaerobes - are able to perform either aerobic respiration or anaerobic respiration depending on the oxygen content of their environment.  Since aerobic respiration is more efficient, facultative anaerobes will perform aerobic respiration if there is oxygen present in their environment.  However, in the absence of oxygen, these organisms simply switch over to anaerobic respiration.  Coliform bacteria are a well-known example of facultative anaerobic microorganisms. 

In the Treatment Plant

In most wastewater treatment processes, operators attempt to maintain an environment suitable for aerobic respiration.  By maintaining an aerobic environment the operators prevent the bad smells associated with septic environments and also maintain a higher speed of waste digestion.  Aerobic processes are most common in biological wastewater treatment systems, including the activated sludge process, trickling filters, and many oxidation ponds. 

Since aerobic microorganisms use up oxygen as they break down waste, it is often necessary to aerate (add air to) the wastewater to maintain an aerobic environment.  Aeration may be achieved by blowing air into the water or (as in the trickling filter) by allowing water to run through the air. 

Despite the advantages of aerobic systems, some wastewater treatment processes are designed to be anaerobic.  Both anaerobic digesters and septic tanks are wholly anaerobic environments.  Since these systems house obligate anaerobic microorganisms, exposing anaerobic digestion systems to oxygen even for a short period of time can seriously affect the systems' ability to function. 

Some systems, through accident or design, can function both aerobically and anaerobically.  Although oxidation ponds are generally aerobic, bottom deposits and stagnant pockets in the ponds often become anaerobic.  On a trickling filter's slime layer, aerobic and anaerobic zones may occur within millimeters of each other, with the surface layers being aerobic and the deeper layers being anaerobic.

Facultative anaerobic microorganism species are very important in many wastewater treatment processes since they area able to perform in both aerobic and anaerobic environments.  However, facultative anaerobic microorganisms can cause problems when  they begin to respire anaerobically, producing unpleasant byproducts.  In general, facultative anaerobic species usually begin performing anaerobic reactions when the dissolved oxygen levels of their environment fall below about 0.5 mg/L for several hours.  This condition is rarely met in aeration tanks unless equipment failure occurs, but keeping sludge in the final clarifiers for an extended period of time can lead to anaerobic conditions.  In addition, conditions of low flow or elevated temperature can result in anaerobic conditions. 

Part 3: Types of Bacteria