Microorganisms

What are microorganisms?

Let's start by looking at the definition of a microorganism.

Microorganisms were long suspected to exist, but their formal discovery was made in 1673 when Dutch scientist Antoine Philips van Leeuwenhoek confirmed their existence using an early microscope consisting of only a single lens.

This makes Leeuwenhoek one of the two "fathers of microbiology" along with Louis Pasteur, who also made numerous discoveries, including pasteurization.

Characteristics of microorganisms

Microorganisms are impressively diverse, some of their main characteristics are:

• They include single- and multi-celled organisms, both prokaryotes and eukaryotes can be microorganisms. They can be bacteria, archaea, fungi, or protists.
• We can only see up to 100 micrometres (µm) with our bare eyes, so organisms smaller than this size are considered microorganisms (Fig. 1).
• Microorganisms are found in every ecosystem and can also be closely associated with many multicellular organisms.

Fig. 1: Microorganisms come in a range of sizes, yet none of them are visible with just the naked eye. A bacteria can have a size of about 1 μm.

Microorganisms and their function

Microorganisms serve a wide variety of functions, depending on their type and their location. Some of them, like bacteria, can play beneficial and harmful roles inside other living organisms, depending on species and strain. But they also play a vital role in the maintenance of the environment.

Let's have a closer look at some microorganisms' functions:

1. Decomposition: microorganisms break down dead organic matter such as plant material and animal remains, releasing nutrients back into the soil. Microorganisms also play a crucial role in nutrient cycling: they take part in the nitrogen, phosphorus, and sulfur biogeochemical cycles. They help to convert these nutrients into forms that can be used by plants and other organisms.

2. Oxygen production: protists like microscopic algae are a vital source of oxygen for our planet. It is estimated that over 50% of our oxygen is available due to the conversion of carbon dioxide to oxygen by microscopic algae!

3. Fermentation: microorganisms such as yeast and bacteria are used in the production of many foods and beverages, including bread, cheese, beer, and yoghurt.

4. Bioremediation: some microorganisms have the ability to break down toxic pollutants in the environment, such as oil spills or industrial waste. This process, known as bioremediation, is a current interesting area of reascan help to clean up contaminated sites and restore ecosystems.

Types of microorganisms

As stated previously, microorganisms are generally considered to be bacteria, archaea, fungi, and protists (Fig. 2).

Fig. 2: Microorganisms include prokaryotes (bacteria and archaea) and eukaryotes (protists and fungi). The archaea are not depicted in this image.

Bacteria

Bacteria are single-celled prokaryotic microorganisms that can live freely or in association with a host and are omnipresent within our environment. When bacteria are said to be omnipresent, it means that they are present in virtually every habitat on Earth, from the soil to the ocean to within our bodies. Bacteria even inhabit seemingly inhospitable environments, such as within the hot soil in and near volcanoes and in radioactive waste.

Bacteria play a vital role in our environment and within our bodies. The presence of bacteria is essential for all other life on Earth.

• Bacteria are both decomposers and producers - they decompose dead organic matter and waste into inorganic matter rich in nutrients, thus allowing plants to grow. These plants then feed herbivores, which in turn feed carnivores.
• Inside and on animals, including humans, bacteria can be found as part of the microbiome, playing vital roles such as aiding digestion. In fact, disruption of the microbiome is believed to play a role in developing specific syndromes and diseases.
  • While most bacteria are harmless or beneficial to humans, some can cause illness, disease, and even death. These are known as pathogenic bacteria.

Fig. 3: Scanning electron micrograph of methicillin-resistant Staphylococcus aureus bacteria (yellow) and a dead human white blood cell (red).

Throughout human history, some of these pathogenic bacterial species have been responsible for human mortality on a massive scale. This was particularly true during the pre-antibiotic era when diseases like tuberculosis and plague killed millions.

Archaea

Archaea are another type of single-celled prokaryotic organism and, until relatively recently, were believed to be another kind of bacteria known as archaebacteria. This is due to the many similarities that archaea and bacteria share.

In addition to being single-celled prokaryotes, archaea are also believed to be some of the earliest living organisms. They can survive in extreme environments, such as deep-sea hydrothermal vents that may exceed 212° F!

So, what are the differences between the two? Well, archaea tend to have genes that more closely resemble those of eukaryotic organisms, and archaea have cell walls that do not contain peptidoglycan, a polysaccharide that forms the cell wall in bacterial species.

Unlike bacteria, archaea are also not currently known to be pathogenic, meaning there are no diseases that are known to be caused by archaea, at least not yet.

Fungi

Fungi are eukaryotic organisms that can be microscopic or visible. Perhaps the fungi you are most familiar with are mushrooms since they are visible to the naked eye (and, sometimes, edible)!

Despite the physical appearance of mushrooms, fungi are not plants and are, instead, members of a separate biological kingdom unique from animals and plants. For our purposes, we are only interested in microscopic fungi, known as microfungi.

Most microfungi have a hyphal structure, which can be observed as the white, fuzzy mold growing on old food products.

Unfortunately, some microfungi species can be dangerous to humans. Among these pathogenic microfungi are those that cause benign conditions like athlete's foot and yeast infections. However, other conditions can be fatal, such as mucormycosis, caused by a black fungus of the order Mucorales. Infections by pathogenic microfungi are treated with antifungals.

Fig. 5: A penicillin poster from World War II. Penicillin was the first antibiotic ever developed and saved many lives. Source: Wiki Commons, Public Domain

Protists

Protists are mostly microscopic, single-celled organisms, including algae species, amoebas, ciliates, slime molds, and more. Protists appear to be a very diverse group of organisms, and protist taxonomy is mainly in a state of flux due to continually changing classifications and discoveries.

Protists can be autotrophic, producing their own energy through photosynthesis, or heterotrophic, consuming other organisms to meet their energy requirements.

Despite the changing classifications and general lack of clarity regarding protist taxonomy, protist species are of significant interest to humans for positive and negative reasons.

Fig. 6: Scanning electron micrograph of the protozoan Giardia lamblia during cell division. The two daughter organisms will become separate individuals when division is finished.

Examples of microorganisms

Lastly, let's look at specific examples of microorganisms from each type - bacteria, archaea, fungi, and protists. First up, let's look at a few of the more well-known pathogenic bacteria.

• Escherichia coli: Commonly referred to as E. coli, most strains are harmless residents of our bodies, but some are pathogenic and can cause severe diarrheal illness.

• Mycobacterium tuberculosis: The causative agent of tuberculosis, which usually causes pulmonary disease, but can affect many parts of the body, including the lymph nodes and the gastrointestinal tract.

• Borrelia burgdorferi: The causative agent of Lyme disease, which is transmitted to humans via bites from infected ticks.

• Vibrio cholerae: The causative agent in cholera, which is a potentially life-threatening diarrheal disease most common in developing countries.

• Staphylococcus aureus: While often harmless (around 30% of humans carry it on their skin), it can be pathogenic and can cause a wide variety of illnesses, from pneumonia to sepsis.

Next, let's look at some examples of archaea species.

• Methanobrevibacter smithii: archaea species responsible for producing methane in human flatulence! M. smithii plays a role in the digestion of polysaccharides within the human gut.

• Saccharolobus solfataricus: This species is known to be an "extremophile", which means it can survive in "extreme" environments. It was first identified within the Solfatara volcano in Italy (1980).

• Nitrosopumilus maritimus: This species plays an essential role in ammonia oxidation and is abundant in seawater.

The following are some notable species of microfungi.

• Candida albicans: Though often a harmless commensal fungus of the human gastrointestinal tract, it can also be pathogenic and is the most common cause of yeast infections and oral thrush.

• C. auris: This species of Candida can cause severe and life-threatening infections in humans. C. auris is an emerging public health concern, particularly given that it is resistant to most antifungals.

• Penicillium chrysogenum: This is the Penicillium species complex that is used to create the antibiotic penicillin.

Lastly, the following is a notable species of protist.

• Giardia duodenalis or lamblia: The protist species responsible for giardiasis, a common parasitic illness characterized by gastrointestinal symptoms, principally diarrhea and abdominal pain. G. duodenalis is typically spread via contaminated food or water.

Now, I hope that you feel more confident in your understanding of microorganisms!