43 Introduction to microbiology

Welcome to the wonderful world of microbiology!

So. What is microbiology? If we break the word down it translates to ‘the study of small life’, where the small life refers to microorganisms or microbes. But who are the microbes? And how small are they?

Generally microbes can be divided into two categories: the cellular microbes (or organisms) and the acellular microbes (or agents). In the cellular camp we have the bacteria, the archaea, the fungi, and the protists (a bit of a grab bag composed of algae, protozoa, slime molds, and water molds). Cellular microbes can be either unicellular, where one cell is the entire organism, or multicellular, where hundreds, thousands or even billions of cells can make up the entire organism. In the acellular camp, we have the viruses and other infectious agents, such as prions and viroids.

The history of microbiology discovery and research

The small size of microbes hindered their discovery. It is hard to get people to believe that their skin is covered with billions of small creatures, if you cannot show it to them. ‘Seeing is believing’, that is what I always say. Or someone says that.

In microbiology, there are two people that are given the credit for the discovery of microbes. Or at least providing the proof of their discovery, both around the same time period:

Robert Hooke (1635-1703)

Robert Hooke was a scientist who used a compound microscope, or microscope with two lenses in tandem, to observe many different objects. He made detailed drawings of his observations, publishing them in the scientific literature of the day, and is credited with publishing the first drawings of microorganisms. In 1665 he published a book by the name of Micrographia, with drawing of microbes such as fungi, as well as other organisms and cell structures. His microscopes were restricted in their resolution, or clarity, which appeared to limit what microbes he was able to observe.

Antony van Leeuwenhoek (1632-1723)

Antony van Leeuwenhoek was a Dutch cloth merchant, who also happened to dabble in microscopes. He constructed a simple microscope (which has a single lens), where the lens was held between two silver plates. Apparently he relished viewing microbes from many different sample types – pond water, fecal material, teeth scrapings, etc. He made detailed drawings and notes about his observations and discoveries, sending them off to the Royal Society of London, the scientific organisation of that time. This invaluable record clearly indicates that he saw both bacteria and a wide variety of protists. Some microbiologists refer to van Leeuwenhoek as the “Father of Microbiology,” because of his contributions to the field.

Characteristics of microbes

Obviously microbes are small. The traditional definition describes microbes as organisms or agents that are invisible to the naked eye, indicating that one needs assistance in order to see them. That assistance is typically in the form of a microscope. The only problem with that definition is that there are microbes that you can see without a microscope. Not well, but you can see them. It would be easy to dismiss these organisms as non-microbes, but in all other respects they look/act/perform like other well-studied microbes (who follow the size restriction).

So, the traditional definition is modified to describe microbes as fairly simple agents/organisms that are not highly differentiated, meaning even the multicellular microbes are composed of cells that can act independently– there is no set division of labor. If you take a giant fungus and chop half the cells off, the remaining cells will continue to function unimpeded. Versus if you chopped half my cells off, well, that would be a problem. Multicellular microbes, even if composed of billions of cells, are relatively simple in design, usually composed of branching filaments.

It is also acknowledged that research in the field of microbiology will require certain common techniques, largely related to the size of the quarry. Because microbes are so small and there are so many around, it is important to be able to isolate the one type that you are interested in. This involves methods of sterilisation, to prevent unwanted contamination, and observation, to confirm that you have fully isolated the microbe that you want to study.

Microbe size

Since size is a bit of theme in microbiology, let us talk about actual measurements. How small is small? The cellular microbes are typically measured in micrometres (µm). A typical bacterial cell (let us say E. coli) is about 1 µm wide by 4 µm long. A typical protozoal cell (let us say Paramecium) is about 25 µm wide by 100 µm long. There are 1000 µm in every millimetre, so that shows why it is difficult to see most microbes without assistance.

When we talk about the acellular microbes we have to use an entirely different scale. A typical virus (let us say influenza virus) has a diameter of about 100 nanometres (nm). There are 1000 nanometres in every micrometre, so that shows why you need a more powerful microscope to see a virus.

Classification and naming of microbes

Classification of organisms, or the determination of how to group them, continually changes as we acquire new information and new tools of assessing the characteristics of an organism. Currently all organisms are grouped into one of three categories or domains: Bacteria, Archaea, and Eukarya. The Three Domain Classification is based on ribosomal RNA (rRNA) sequences and widely accepted by scientists today as the most accurate current portrayal of organism relatedness.

Bacteria

The Bacteria domain contains some of the best known microbial examples (E. coli, anyone?). Most of the members are unicellular (but not all!), most members lack a nucleus or any other organelle, most members have a cell wall with a particular substance known as peptidoglycan (not found anywhere else but in bacteria!), they have 70S ribosomes, and humans are intimately familiar with many members, since they are common in soil, water, our foods, and our own bodies. All Bacteria are considered microbes.

Archaea

Archaea is a relatively new domain, since these organisms used to be grouped with the bacteria. There are some obvious similarities, since they are mostly (but not all!) unicellular, cells lack a nucleus or any other organelle, they have 70S ribosomes, and all Archaea are microbes. But they have completely different cell walls that can vary markedly in composition (but notably lack peptidoglycan and might have pseudomurien instead). In addition, their rRNA sequences have shown that they are not closely related to Bacteria at all.

Eukarya

The Eukarya Domain includes many non-microbes, such as animals and plants, but there are numerous microbial examples as well, such as fungi, protists, slime molds, and water molds. The eukaryotic cell type has a nucleus, as well as many organelles, such as mitochondria or an endoplasmic reticulum. They have 80S ribosomes and are commonly found as unicellular or multicellular.

Viruses

Viruses are not part of the Three Domain Classification, since they lack ribosomes and therefore lack rRNA sequences for comparison. They are classified separately, using characteristics specific to viruses. Viruses are typically described as “obligate intracellular parasites,” a reference to their strict requirement for a host cell in order to replicate or increase in number. These acellular entities are often agents of disease, a result of their cell invasion.

Binomial Nomenclature

When referring to the actual scientific name assigned to an organism, it is important to follow convention, so it is clear to everyone that you are referring to the scientific name. A scientific name is composed of a genus and a species, where the genus is a generic name and the species is specific. The species name, once assigned, is permanent for the organism, while the genus can change if new information becomes available.

Structure and morphology of bacteria, archaea and eukaryotic cells

Cell structure

Traditionally, cellular organisms have been divided into two broad categories, based on their cell type. They are either prokaryotic or eukaryotic. In general, prokaryotes are smaller, simpler, with a lot less stuff, which would make eukaryotes larger, more complex, and more cluttered. The crux of their key difference can be deduced from their names: “karyose” is a Greek word meaning “nut” or “center,” a reference to the nucleus of a cell. “Pro” means “before,” while “Eu” means “true,” indicating that prokaryotes lack a nucleus (“before a nucleus”) while eukaryotes have a true nucleus.

Cell Morphology

Cell morphology is a reference to the shape of a cell. It might seem like a trivial concept but to a cell it is not. The shape dictates how that cell will grow, reproduce, obtain nutrients, move, and it’s important to the cell to maintain that shape to function properly. Cell morphology can be used as a characteristic to assist in identifying particular microbes. It is important to note that cells with the same morphology are not necessarily related. Bacteria tend to display the most representative cell morphologies (Figure 9.3).

There are additional shapes seen for bacteria, and an even wider array for the archaea, which have even been found as star or square shapes. Eukaryotic microbes also tend to exhibit a wide array of shapes, particularly the ones that lack a cell wall such as the protozoa.

Cell Size

Cell size, just like cell morphology, is not a trivial matter either, to a cell. There are reasons why most archaeal/bacterial cells are much smaller than eukaryotic cells. Much of it has to do with the advantages derived from being small. These advantages relate back to the surface-to-volume ratio of the cell, a ratio of the external cellular layer in contact with the environment compared to the liquid inside. This ratio changes as a cell increases in size. Let us look at a 2 μm cell in comparison with a cell that is twice as large at 4 μm.

The surface-to-volume ratio of the smaller cell is 3, while the surface-to-volume ratio of the larger cell decreases to 1.5. Think of the cell surface as the ability of the cell to bring in nutrients and let out waste products. The larger the surface area, the more possibilities exist for engaging in these activities. Based on this, the larger cell would have an advantage. Now think of the volume as representing what the cell has to support. As the surface-to-volume ratio decreases, the larger cell will struggle to bring in the nutrients necessary to support the cell’s activities at a rapid rate, such as growth and reproduction, despite the larger surface area. Thus, small cells grow and reproduce faster than larger cells, despite having a smaller surface area. This also means that they evolve faster over time, giving them more opportunities to adapt to environments.

Keep in mind that the size difference (bacterial/archaeal cells = smaller, eukaryotic cells = larger) is on average. A typical bacterial/archaeal cell is a few micrometres in size, while a typical eukarytotic cell is about 10x larger. There are a few monster bacteria that fall outside the norm in size and still manage to grow and reproduce very quickly. One such example is Thiomargarita namibiensis, which can measure from 100-750 μm in length, compared to the more typical 4 μm length of E. coli. T. namibiensis manages to maintain its rapid reproductive rate by producing very large vacuoles or bubbles that occupy a large portion of the cell. These vacuoles reduce the volume of the cell, increasing the surface-to-volume ratio. Other very large bacteria utilise a ruffled membrane for their outer surface layer. This increases the surface area, which also increase the surface-to-volume ratio, allowing the cell to maintain its rapid reproductive rate.

Cell Components

All cells (bacterial, archaeal, eukaryotic) share four common components:

• Cytoplasm – cytoplasm is the gel-like fluid that fills each cell, providing an aqueous environment for the chemical reactions that take place in a cell. It is composed of mostly water, with some salts and proteins.
• DNA – deoxyribonucleic acid or DNA is the genetic material of the cell, the instructions for the cell’s abilities and characteristics. This complete set of genes, referred to as a genome, is localised in an irregularly-shaped region known as the nucleoid in bacterial and archaeal cells, and enclosed into a membrane-bound nucleus in eukaryotic cells.
• Ribosomes – the protein-making factories of the cell are the ribosomes. Composed of both RNA and protein, there are some distinct differences between the ones found in bacteria/archaea and the ones found in eukaryotes, particularly in terms of size and location. The ribosomes of bacteria and archaea are found floating in the cytoplasm, while many of the eukaryotic ribosomes are organised along the endoplasmic reticulum, a eukaryotic organelle. Ribosomes are measured using the Svedberg unit, which corresponds to the rate of sedimentation when centrifuged. Bacterial/archaeal ribosomes have a measurement of 70S as a sedimentation value, while eukaryotic ribosomes have a measurement of 80S, an indication of both their larger size and mass.
• Cell Membrane – one of the outer boundaries of every cell is the cell membrane. A plasma membrane can be found elsewhere as well, such as the membrane that bounds the eukaryotic nucleus, while the term cell membrane refers specifically to this boundary of the cell proper. The plasma membrane separates the cell’s inner contents from the surrounding environment. While not a strong layer, the plasma membrane participates in several crucial processes for the cell, particularly for bacteria and archaea, which typically only have the one membrane:
  • Acts as a semi-permeable barrier to allow for the entrance and exit of select molecules. It functions to let in nutrients, excrete waste products, and possibly keep out dangerous substances such as toxins or antibiotics.
  • Performs metabolic processes by participating in the conversion of light or chemical energy into a readily useable form known as ATP. This energy conservation involves the development of a proton motive force (PMF), based on the separation of charges across the membrane, much like a battery.
  • “Communicates” with the environment by binding or taking in small molecules that act as signals and provide information important to the cell. The information might relate to nutrients or toxin in the area, as well as information about other organisms.

Eukaryotes have numerous additional components called organelles, such as the nucleus, the mitochondria, the endoplasmic reticulum, the Golgi apparatus, etc (Figure 9.6). These are all membrane-bound compartments that house different activities for the cell. Because each structure is bounded by its very own plasma membrane, it provides the cell with multiple locations for membranous functions to occur.

Plasma Membrane Structure

When talking about the details of the plasma membrane, bacteria and eukaryotes share the same basic structure, while archaea have marked differences.

The plasma membrane is often described by the fluid-mosaic model, which accounts for the movement of various components within the membrane itself (Figure 9.7). The general structure is explained by the separation of individual substances based on their attraction or repulsion of water. The membrane is typically composed of two layers (a bilayer) of phospholipids, which form the basic structure. Each phospholipid is composed of a polar region that is hydrophilic (“water loving”) and a non-polar region that is hydrophobic (“water fearing”). The phospholipids will spontaneously assemble in such a way as to keep the polar regions in contact with the aqueous environment outside of the cell and the cytoplasm inside, while the non-polar regions are sequestered in the middle, much like the jelly in a sandwich.

The phospholipids themselves are composed of a negatively-charged polar head which is a phosphate group, connected by a glycerol linkage to two fatty acid tails. The phosphate group is hydrophilic while the fatty acid tails are hydrophobic. While the membrane is not considered to be particularly strong, it is strengthened somewhat by the presence of additional lipid components, such as the steroids in eukaryotes and the sterol-like hopanoids in bacteria. Embedded and associated with the phospholipid bilayer are various proteins, with myriad functions. Proteins that are embedded within the bilayer itself are called integral proteins while proteins that associate on the outside of the membrane are called peripheral proteins. Some of the peripheral proteins are anchored to the membrane via a lipid tail, and many associate with specific integral proteins to fulfill cellular functions. Integral proteins are the dominant type, representing about 70-80% of the proteins associated with a plasma membrane, while the peripheral proteins represent the remaining 20-30%.

Link to learning: Review the structure of the cell membrane

The amount of protein composing a plasma membrane, in comparison to phospholipid, differs by organism. Bacteria have a very high protein to phospholipid ratio, around 2.5:1, while eukaryotes exhibit a ratio of 1:1, at least in their cell membrane. But remember that eukaryotes have multiple plasma membranes, one for every organelle. The protein to phospholipid ratio for their mitochondrial membrane is 2.5:1, just like the bacterial plasma membrane, providing additional evidence for the idea that eukaryotes evolved from a bacterial ancestor.

Knowledge check