7.1: Microbe classification

Biotech Focus

Extremophiles are microorganisms that thrive in extreme conditions where most other life forms would perish. Traditionally, these hardy microbes are found in environments like deep-sea hydrothermal vents, Antarctic ice, or highly acidic hot springs. However, recent studies have revealed a surprising habitat for certain extremophiles: common household appliances. Household appliances such as dishwashers, washing machines, and even coffee makers create unique microenvironments that can mimic some extreme conditions. Dishwashers, for instance, generate high temperatures, rapid temperature shifts, and fluctuating pH levels from detergents—all challenging environments that some extremophiles can endure. These extremophiles, adapted to the challenging conditions of household appliances, hold significant potential for biotechnological innovation. They could be used in many domains, for example, to produce enzymes that could withstand extreme conditions, or to develop methods for sustainable waste management, demonstrating how even the most commonplace settings can contribute to groundbreaking science.

To know more about the study, read The Microbiome of Things: Appliances, Machines, and Devices Hosting Artificial Niche-Adapted Microbial Communities

Introduction

Microbes are microscopic organisms (i.e. microbes) that are too small to be seen by the naked eye. They include bacteria, archaea, fungi, but also viruses. Such a broad definition means that many different types of microbes exist, with different structures, sizes and metabolism. Despite their small size, microbes play critical roles in natural ecosystems. They are also invaluable tools in biotechnology.

Learning Objectives

Microbes are an incredibly important part of biotechnology. At the end of this section, you will be able to:

• Distinguish between prokaryotic and eukaryotic cells, including listing their common structures and how they differ
• List the major microbes used in biotechnology
• Describe the basic morphology of bacterial cells and some of their major structures, including the cell wall
• Explain the "extremophile" nature of archaea
• Describe some basic viral structures

Prokaryotes vs Eukaryotes

All living things are made of one or more cells. Two general types of cells can be found: prokaryotic (lacking a nucleus) and eukaryotic (possessing a nucleus). Prokaryotic organisms are unicellular, meaning they are made of one cell only (Figure \(\PageIndex{1}\)). In contrast, eukaryotic organisms can be unicellular, such as yeast, or multicellular, such as humans.

Figure \(\PageIndex{1}\): Methicillin-resistant Staphylococcus aureus. A scanning electron micrograph shows two methicillin-resistant Staphylococcus aureus (MRSA) bacterial cells (colorized orange) interacting with a human neutrophi (gray). Note the difference in size between the smaller two bacterial cells and the much larger neutrophil (eukaryotic). (Methicillin-Resistance Staphylococcus aureus, by NIAID, CC BY 2.0)

Both prokaryotes and eukaryotes share the same basic elements:

1. a cytoplasm: a gel-like substance mainly composed of water, proteins and salts
2. a cell membrane: a phospholipid bilayer that surrounds the cytoplasm
3. one or more chromosomes: an organized form of DNA; the number is specific to the species
4. ribosomes: a non-membranous organelle used for protein synthesis

However, they also differ in many ways. Table \(\PageIndex{1}\) below lists some of these differences.

Table \(\PageIndex{1}\): Prokaryotes vs. Eukaryotes

Feature	Prokaryotes	Eukaryotes
Nucleus	No	Yes
DNA organization	DNA in the form of a circular chromosome known as a genophore	DNA in the form of circular or linear chromosomes; multiple chromosomes found within the nucleus
Membrane-bound organelles	No	Yes (mitochondria, ER, Golgi, lysosomes, peroxisomes, vacuoles, chloroplasts etc....)
Cell division mechanism(s)	Binary fission, budding (asexual reproduction)	Binary fission, budding, mitosis, and meiosis
Cell wall composition	Peptidoglycans (bacteria), pseudopeptidoglycans (archaea)	Cellulose (plant cells), chitin (fungal cells), no cell wall in animals cells
Ribosome composition	70S: 30S and 50S subunits	80S: 40S and 60S subunits
Examples	bacteria, archaea	fungi, plants, animals

Microbial Biotechnology: Cell Types

Microbial biotechnology is the use of microbes for industrial, environmental, and pharmaceutical applications. Over the years, advances in genetic engineering, molecular biology, and bioinformatics have expanded the scope of microbial biotechnology, allowing us to harness these organisms for innovations in a wide range of areas such as agriculture, medicine, bioenergy, and environmental management. What microbes are used in biotechnology is dependent upon the application. For example, bacteria are widely used in biotechnology due to their rapid growth and the ability to manipulate their genetic material easily.

The microbes used in biotechnology are:

1. Bacteria: single-celled prokaryotic organisms that lack a nucleus and membrane-bound organelles
2. Yeast: single-celled eukaryotic organisms that are classified as fungi
3. Archaea: single-celled prokaryotic organisms that are genetically distinct from bacteria
4. Viruses: small, infectious organisms that can only replicate inside of a host cell

Bacteria

Bacteria are the oldest and most diverse form of life and comprise the domain Bacteria. They can be found in many shapes and sizes depending on the bacterial species (Figure \(\PageIndex{2}\)).

The most common bacterial shapes are:

1. coccus: spherical shape (plural = cocci), e.g., Streptococcus mutans
2. bacillus: rod shape (plural = bacilli), e.g., Esherichia coli (E.coli)

While these two are the most common shapes seen, there are additional bacterial shapes including spiral shaped (or spirillum), stalked forms, filamentous shapes, and a comma-shaped cell called vibrio.

Figure \(\PageIndex{2}\): Common bacterial shapes. Left: the spherical bacterial cell is called coccus (plural: cocci). Center: the rod shaped cell is called bacillus (plural: bacilli). Right: the bent rod shaped cell is called vibrio. (Electron microscopy image credits: Left: Betsy Crane; Center: NIAID; Right: Janice Haney Carr; all images are public domain)

Bacterial species can also be characterized by the arrangement of their cells (Figure \(\PageIndex{3}\)). For example, they can found as single cells, in pairs (diplo), in chains (strepto) or in clusters (staphylo). The names of bacteria often reflects their shapes and arrangement, such as the genus Staphylococcus (spherical cells arranged in clusters).

Figure \(\PageIndex{3}\): Bacterial cell arrangements. Left: cells can be arranged in pairs. Cocci found in pairs are called diplococci (top), bacilli in pairs are called diplobacilli (bottom). Center: cells can be arranged in chains. Cocci grouped as a chain are called streptococci, bacilli in chains are called streptobacilli. Right: only cocci can be arranged in clusters and are called staphylococci. (Bacterial Cell Arrangements by Kareen Martin, CC BY 4.0)

The genome of most bacteria is a circular chromosome, called a genophore. Because bacteria lack a nucleus, the bacterial chromosome is found in a region of the cytoplasm called the nucleoid. In addition to the bacterial chromosome, some bacteria have pieces of extra-chromosomal DNA called plasmids. A plasmid is a small, circular double-stranded piece of DNA that replicates independently from the bacterial chromosome and can be passed on from one bacterium to another bacterium. While the genes found in a plasmid are not necessary for the normal metabolism of the bacteria, they confer advantageous traits, such as antibiotic resistance. Plasmids are a valuable tool in molecular biology and genetics, they can be easily manipulated and used as vector to transfer and express genes into a host organism. They can be used to study the effect of the product of a gene or to create genetically modified organism. For more about the bacterial chromosome and plasmids, go to Chapter 3.1 DNA Structure. The bacterial genome can easily be altered either by exposing them to physical or chemical mutagens. They also have the ability to acquire DNA from their environment. Because of these properties, bacteria constitute an invaluable tool in biotechnology.

Although both bacteria and eukaryotic cells possess ribosomes that are responsible for the synthesis of proteins, the bacterial ribosome is smaller and simpler than their eukaryotic counterpart. Prokaryotic ribosomes are called 70S ribosomes, whereas eukaryotic ribosomes are called 80S ribosomes. The "S" is short for Svedberg unit and it is a measure of how fast a particle settles when being centrifuged. The sedimentation rate of a particle depends on a combination of characteristics, such as size, shape, and density. The 70S ribosome indicates that this particle sediments slower that the eukaryotic 80S ribosome, which is due to its smaller size. Prokaryotic ribosomes not only differ from eukaryotic ones in size, but also in their overall structure and composition. These differences make prokaryotic ribosomes sensitive to a wide range of antibiotics and allow for the treatment of bacterial infections without damaging eukaryotic cells.

Most bacteria are surrounded by a cell wall composed of a complex polymer called peptidoglycan (Figure \(\PageIndex{4}\)). Peptidoglycan is composed of repeating disaccharide units. The two sugars of this unit are called N-acetyl glucosamine (NAG) and N-acetyl muramic acid (NAM). The NAM monomer within the disaccharide is modified by the addition of 5 to 6 amino acids (i.e., "peptido"). The NAG/NAM disaccharides link together to form long chains of sugars (i.e. "glycan" ) that crosslink to one another through the peptides. The peptidoglycan-rich cell wall forms a rigid layer that protects and maintains the shape of the bacterium. Numerous antibiotics are effective against bacteria through their ability to affect the assembly or integrity of the peptidoglycan cell wall.

Figure \(\PageIndex{4}\): Peptidoglycan structure. The cell wall of a bacterium is made of peptidoglycan, an alternating series of sugars called N-acetyl glucosamine or NAG (G, green circles) and N-acetyl muramic acid or NAM (M, blue circles). The NAM sugar is modified through the attachment of several peptides (small circles). Cross-linking between the peptides (peptide X-links, shown with red arrows) produces a rigid mesh-like structure that protects the bacteria. (Peptidoglycan Structure by Patricia Zuk, CC BY 4.0; adapted from Peptidoglycan membrane by Bradleyhintze, CC0 1.0)

The bacterial cell wall can be used to classify bacteria as either gram-positive or gram-negative, a classification technique that is named after the Gram staining method. Gram-positive cell walls consist of a thick peptidoglycan layer that is readily stained through Gram staining. Gram-positive bacteria will be dark purple in color (Figure \(\PageIndex{5}\)). In contrast, the gram-negative cell wall consists of a thin peptidoglycan layer sandwiched between the plasma membrane of the bacterial cell and an outer membrane. This outer membrane prevents the staining of the cell wall and gram-negative bacteria are pink in color (the color of the Safranin counterstain) (Figure \(\PageIndex{5}\)). The outer membrane is a phospholipid bilayer studded with fat and sugar components, called lipopolysaccharides (LPS) (Figure \(\PageIndex{5}\)). The lipopolysaccharides can be released from the cell wall and contribute to the pathogenicity of the bacteria.

 

 

Figure \(\PageIndex{5}\): Gram-positive and gram-negative bacteria. Left image: A micrograph of gram-positive cocci (purple circles) and gram-negative bacilli (pink rods). (Gram stain by Y tambe, CC BY-SA 3.0)
Right image: The cell wall composition of gram-positive bacteria (left) is a thick peptidoglycan layer over the plasma membrane (i.e. cytoplasmic membrane). Gram-negative bacteria (right) have a thinner peptidoglycan layer found in between the cytoplasmic membrane and an outer membrane. The outer membrane is a phospholipid bilayer studded with lipopolysaccharides. (Cell wall composition by Malihe Mehdizadeh Allaf and Hassan Peerhossaini, CC BY-SA 4.0)

Bacteria divide rapidly, mainly through binary fission. In binary fission, the bacteria will duplicate its genetic material and partition it into two daughter cells. Many bacteria divide every 20 minutes. Hence, with the population doubling every 20 minutes, millions of identical cells can be produced in a short period of time. Compare this with the 24 hours doubling time of eukaryotic cells, and it is obvious why bacteria are a favorite organisms in biotechnology.

Archaea

Archaea are a group of single-celled microorganisms that make up the domain, Archaea. They are similar in appearance to bacteria but are genetically and biochemically distinct, with unique evolutionary histories. Archaea thrive in a wide range of environments, including some of the most extreme on Earth, such as hot springs, deep-sea hydrothermal vents, and highly acidic or saline habitats. This ability to survive in extreme conditions is due to their specialized cell membranes and enzymes, which allow them to maintain stability and function. Unlike bacteria, archaea have distinct metabolic pathways and can utilize a variety of energy sources, including methane, sulfur, and hydrogen, making them key players in global nutrient cycles.

Despite their microscopic size, archaea are critical to many ecological processes and have potential applications in biotechnology due to their resilience and unique biochemistry. Their enzymes, known as extremozymes, are particularly valuable in industrial processes that require extreme conditions, such as high temperatures, high salinity, or extreme pH levels. For instance, thermostable DNA polymerases from archaea are widely used in PCR (polymerase chain reaction) which requires using cycles with very high temperatures. Archaea are also used in bioremediation, where they help break down pollutants in harsh environments, and in biofuel production, where their metabolic pathways can be harnessed to produce methane or hydrogen. The resilience and adaptability of archaea make them promising candidates for innovations in biotechnology, including drug development, waste management, and sustainable energy solutions.

Yeast

Yeast are single-celled eukaryotic organisms belonging to Domain Eukarya, Kingdom Fungi. Yeast thrive in a variety of environments, including those that are moist and warm. They grow rapidly in aqueous environments and have been extensively studied for their metabolic processes. Yeast is widely used in biotechnology due to its versatility and ease of manipulation. Dating back several millennia., yeast has been employed in the production of bread, beer, and wine through fermentation - a biological process that use microbes, like yeast, to convert sugars (e.g. glucose) into energy (i.e. ATP). Nowadays, yeast is also used in many different applications. They are used to produce renewable fuels, like bioethanol, through fermentation. Yeast are used to produce enzymes for industrial applications. The ability of yeast to efficiently express foreign genes and its well-characterized genetics make it a powerful tool in the development of pharmaceuticals, like insulin and vaccines.

Virus

Viruses are microscopic infectious agents that can infect all life forms; bacteria, archaea, animals, plants, and fungi. Even though a virus has both genetic material and protein components, it is not a living organism. It is unable to self-replicate and relies on the cellular biochemistry of the host cell it has infected. This makes a virus an obligate parasite, or an organism that is required to infect a living cell.

The key features of viruses are (Figure \(\PageIndex{6}\)):

1. Genetic material: The genetic information of a virus is either DNA or RNA, in either single stranded or double stranded forms. The nucleic acid content of a virus determines how they replication and can be used to classify them. The viruses that carry DNA are called DNA viruses (e.g. Herpesvirus) whereas those carrying RNA are called RNA viruses (Coronavirus, HIV). The size of viral genome depends on the type of virus. Some viruses contain enough genetic material to make only a few proteins; others code up to 100 proteins. The smaller the genome, the more viral copies can be made by a host cell. In order to replicate, a virus needs to infect a cell and so its genome can be copied. Once in the host cell, it will "hijack" the host's cellular machinery. What aspects of the host cell is used depends on whether the genome is single-stranded or doubled-stranded DNA or RNA. For example, a DNA virus will use the host's DNA polymerase to replicate its genome, followed by host cell transcription and translation. In contrast, RNA viruses have no need of DNA polymerases but will use host cell ribosomes for protein translation.
2. Capsid: The capsid is a protein shell that surround the viral genome. The capsid protects the genome from the environment, plays a role in binding the host cell, permits its entry into the host cell, and assists in viral assembly following replication. The protein subunits of the capsid are known as capsomeres. The way these capsomeres assemble determines the shape of the virus. For example, many viruses are icosahedral, a shape made of 20 identical triangular faces. Others viruses have a helical capsid, such as the Ebola virus.
3. Envelope: The envelope is not found in all viruses. When it is present, the envelope is composed of a phospholipid bilayer that is derived from the host cell. The envelope forms around the virus, when it exists the host cell. As a result of this process, some of the proteins of the host cell membrane will be found embedded within the envelope. These proteins aid in recognition by host cells and facilitate their entry. Viruses with an envelope are called "enveloped" viruses; those lacking an envelope are often called "naked" viruses.
4. Surface proteins: Surface proteins can be found embedded in either the capsid or the envelope (if present). Those embedded in the envelope are glycoproteins - proteins that have been modified through the addition of short sugar monomers. Most of these proteins are spike-like in shape and are called spike proteins. Spike proteins help in viral attachment and entry by binding to receptors at the surface of a cell. They also play a role in evading the host's immune system. Surface proteins found embedded in the capsid are known as capsid proteins. Capsid proteins serve as attachment proteins that interact directly with receptors on the host cell's surface. Viral surface proteins are critical for the specificity of the virus, allowing certain viruses to bind and enter only a particular type of cell found in a certain species. While most viruses are highly specific, some viruses may cross the barrier species in a process called "spillover". These viruses are called zoonotic viruses. Zoonotic viruses originate in other animals (e.g. bats, birds, pigs) but adapt to infect humans, sometimes leading to endemics or pandemics. The SARS outbreak of 2002-2003 is an example of a zoonotic virus that originated in bats and cats and made the jump to humans.

Figure \(\PageIndex{6}\): Enveloped and non-enveloped viruses. Top image: the non-enveloped virus is surrounded by a capsid made of individual capsomeres (blue spheres) that assemble to give the capsid its shape. The capsid surrounds the viral genome (shown in orange). Surface proteins can be found embedded in the capsid (not shown). Bottom image: the enveloped virus has a viral genome and a capsid like the non-enveloped virus. However, the capsid is surrounded by an phospholipid bilayer called the envelope. Envelope proteins (shown in red and yellow) can be found embedded in the envelope. (Enveloped and Non-enveloped Viruses by Patricia Zuk, CC BY 4.0)

Viruses have made major contributions to biotechnology. Viruses are critical to the development of vaccines that train the immune system to recognize and fight infections. They can be used as cloning vectors to introduce foreign genes into host organisms, like bacteria. They have been used in gene therapy to introduce functional genes to specific cell types in order to treat diseases, such as sickle-cell anemia. Viruses called oncolytic viruses have been engineered to infect and destroy cancer cells, while leaving normal cells unaffected. Modified plant viruses can be used as vectors to introduce foreign genes into plant cells in order to create genetically-engineered plants with beneficial traits, such as increased resistance to pests, diseases, or environmental stresses. The future of viral biotechnology is likely to include personalized medicine with custom-designed viruses or vaccines, synthetic viruses to target specific diseases, and improved gene editing tools using viral systems.

Key Concepts

Microbial biotechnology is the use of microbes for industrial, environmental, and pharmaceutical applications. Some important concepts to remember are:

• all living things are made of cells
• there are two types of cells: prokaryotic and eukaryotic
• prokaryotic and eukaryotic cells have DNA in the form of chromosomes, a cytoplasm, ribosomes, and a plasma membrane
• additional features like the presence of a nucleus distinguish eukaryotic cells from prokaryotic cells
• the microbes used in microbial biotechnology include prokaryotic cells (e.g. bacteria and archaea), eukaryotic cells (e.g. yeast), and viruses
• bacteria and archaea are single-celled prokaryotic cells found in Domain Bacteria and Domain Archaea, respectively
• bacteria can be classified using several approaches, including cell shape, cell arrangement and gram staining
• the cell wall of bacteria is made of peptidoglycan, long chains of NAG and NAM sugars that crosslink for rigidity and strength
• gram-positive bacteria have a thick layer of peptidoglycan in their cell wall; the peptidoglycan is stained by the gram stain
• gram-negative bacteria have a thin peptidoglycan layer found in between the cell membrane and an outer membrane; the outer membrane prevents staining by the gram stain
• archaea are found in extreme environments
• yeast are single-celled eukaryotic cells found in Domain Eukarya
• yeast have several uses in biotechnology, including fermentation and genetic engineering
• viruses are non-living, infectious agents that require host cells for their replication
• viruses are made of a nucleic acid genome (DNA or RNA), a capsid, and surface proteins; some viruses may also have a envelope

Glossary

Archaea – a domain of single-celled microorganisms that are genetically distinct from bacteria and eukaryotes, often found in extreme environments

Asexual reproduction – a mode of reproduction in microbes where offspring arise from a single parent, without genetic recombination

Bacillus – a rod-shaped bacterium

Bacteria – single-celled prokaryotic microbes that can be found in diverse environments and classified on parameters like cell shape and gram stain

Binary fission – a common asexual reproduction method in bacteria where a single "parent" cell splits into two identical "daughter" cells

Budding - an asexual reproduction strategy where a small "bud" detaches itself from the "parent" cell, followed by maturation

Capsid – a structure that surrounds and protect the viral genome

Coccus – a spherical-shaped bacterium

Domain - the largest group used to classify organisms; all life can be classified into three domains (Bacteria, Archaea, Eukarya)

Diplo - a pair of bacterial cells joined together; e.g. "diplococcus" - a pair of spherical bacteria joined together

Eukaryote – an organism whose cells contain a nucleus and membrane-bound organelles, including fungi, plants and animals

Extremophile – a microorganism that thrives in extreme conditions, such as high temperatures, acidity, or salinity

Fungi – a kingdom of eukaryotic microorganisms, including yeasts and molds, that obtain nutrients through decomposition

Genophore - the bacterial chromosome

Gram staining – a differential staining technique used to classify bacteria as Gram-positive (purple) or Gram-negative (pink) based on cell wall composition

Host – an organism that provides a habitat or nutrients for a microbe, including pathogens and symbionts

Lipopolysaccharide (LPS) - a component of the outer membrane of gram-negative bacteria; plays a role in immune response and toxicity

Outer membrane - a structure made of phospholipids and lipopolysacchardies found on the outside of the cell wall of Gram-negative bacteria

Peptidoglycan – a polymer found in bacterial cell walls, providing structural strength; used to distinguish gram-positive from gram-negative bacteria

Plasmid – a small, circular DNA molecule found in bacteria that can carry antibiotic resistance genes and other traits

Spirillum – a spiral-shaped bacterium

Staphylo - a cluster of bacterial cells joined together; "staphylococcus" - a chain of spherical bacteria joined together

Strepto - a chain of bacterial cells joined together; "streptobacilli" - a chain of rod-shaped bacteria joined together

Vaccine – a biological preparation that stimulates an immune response against a microbe

Virus – a non-living infectious agent composed of nucleic acids contained in a protein coat; requires a host cell to replicate