Learn key DAT concepts related to archaebacteria, eubacteria, protists, fungi, and viruses, plus practice questions and answers

Microbes for the DAT banner — everything you need to know about microbes for the dat

Part 1: Introduction to microbes

Microbes, short for microorganisms, are microscopic organisms which include several kingdoms: archaebacteria, eubacteria, protista, fungi, and viruses. We will review each kingdom in detail in this guide. Understanding microbes for the DAT is crucial for answering questions related to topics such as microbial classification, characteristics, pathogenicity, transmission, infection, reproduction and much more. Utilize this guide to familiarize yourself with key concepts related to microbes in preparation for the DAT, and test what you’re learning with DAT-style practice questions and answers at the end.

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Part 2: Taxonomy

Taxonomy is the science of categorizing and classifying biological organisms and structures. There are eight taxonomic categories. Listed from most broad to most specific, they are domain, kingdom, phylum, class, order, family, genus, species. A helpful mnemonic to remember the order of taxonomy from most broad to most specific is “King Phillip Came Over For Great Soup.'' Feel free to create your own helpful mnemonics as well!

The six kingdoms include archaea, eubacteria, protista, fungi, plantae, animalia. The largest classification of life is known as a domain which encompasses multiple kingdoms. The three-domain system is a taxonomic classification system that groups together all cellular life into three domains, which are archaebacteria, eubacteria, and eukarya.

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Part 3: Prokaryotes

Prokaryote is a term that includes all organisms from domains (eu)bacteria and archaea (bacteria). Prokaryote is a perfect term to describe these organisms as it directly translates to “before nucleus,” “pro” meaning before and “karyon” meaning nucleus. Prokaryotes were earth’s earliest life forms, and as the name implies, organisms from this classification lack a nucleus. Kingdom Monera is an outdated kingdom that no longer exists, but had grouped together domains archaea and bacteria. Although both archaea and bacteria lack nuclei and membrane-bound organelles, they each belong to their own separate domain and therefore cannot belong to the same kingdom. Additionally, domain archaea is more closely related to eukarya than domain bacteria is, so archaea and bacteria were split into separate kingdoms.

Common characteristics among all prokaryotes include having no membrane-bound nucleus, but a nucleoid region which is composed of genetic material (DNA). Prokaryotic bacteria often contain plasmids, which are extrachromosomal circular DNA distinct from the cell’s chromosomal DNA. Unlike eukaryotes, in prokaryotic cells, transcription and translation occurs simultaneously within the cytoplasm. Additionally, prokaryotes have cell walls for protection and structural support, no membrane-bound organelles, no telomeres or telomerase protein, and all are haploid. Haploid means that these cells contain only one set of chromosomes, a result of reproducing asexually.

All prokaryotes’ ribosomes are built in the nucleoid region and consist of the same material as eukaryotic ribosomes, rRNA, and proteins. However, prokaryotic ribosomes’ size is 70S (as opposed to 80S eukaryotic ribosomes) and composed of two ribosomal subunits, a 50S ribosomal subunit and a 30S ribosomal subunit. The shape and structure of ribosomes in bacteria and archaea differ, but the 70S size remains the same.

Prokaryotes contain pili and flagella, but never cilia. Pili are short, hair-like projections found on the surface of some bacteria. They serve various functions including:

Attachment: pili help bacteria attach to surfaces, such as host cells or other bacteria
Conjugation: bacteria exchange genetic material between one another in the form of plasmids which contributes to genetic diversity and antibiotic resistance
Motility: certain types of pili enable bacteria to move across surfaces or through liquid environments via a process called twitching motility

Flagella are whip-like structures found on the surface of some cells, particularly bacteria, that help them move. They act like tiny propellers, spinning to push the cell forward through liquid environments. Prokaryotic and eukaryotic cells can both have flagella, however with differing characteristics. Prokaryotic flagella are small and simple structures, made up of flagellin proteins, have rotatory motion, and are proton driven. Whilst eukaryotic flagella are larger, more complex structures, made up of tubulin dimer proteins. They operate in a bending motion and are ATP driven.

a) Archaebacteria

Archaea are single-celled organisms similar to bacteria but with some eukaryotic traits. The term “archaea" translates to “ancient.” The first ever archaea found produced methane and were thought to have played a large role in primitive earth’s atmosphere. Archaea have cell walls composed of polysaccharides and possess ether-linked cell membranes. Unlike bacteria, their DNA contains histone proteins and sometimes contains introns. They are extremophiles, meaning they can withstand harsh environmental conditions such as extreme temperatures, pressure, salinity, radiation, or pH levels. Archaea are only able to reproduce asexually via a process known as binary fission, explained in the next section.

b) Bacterial morphology

Like archaea, bacteria are single-celled organisms. The prefix “eu” in eubacteria translates to “true,” because eubacteria fit the initial thoughts of what scientists viewed as bacteria. Bacteria have cell walls made up of peptidoglycan and ester-linked membrane lipids. Their DNA does not contain histone proteins, nor introns and therefore spliceosomes do not exist in bacteria cells because there are no introns for them to splice out.

Bacteria can be classified according to their shape. The common shapes of bacteria are shown below:

**FIGURE 1:** BACTERIA CAN BE ROUND (COCCI), ROD-SHAPED (BACILLI), OR SPIRAL-SHAPED (SPIRILLI)

c) Gram-positive and gram-negative

The peptidoglycan cell wall of bacteria is a combination of glycoproteins and glycolipids. Glycoproteins are proteins linked to carbohydrate chains and glycolipids are lipids linked to carbohydrate chains. Gram staining is a test done on bacteria to observe the amount of peptidoglycan in their cell walls. In the test, a counterstain is applied that causes the bacteria to turn either purple or pink depending on the type of bacteria it is.

Gram staining shows us if the bacteria is gram-positive or gram-negative bacteria. Gram-positive bacteria stains purple from a counterstain and has one cell membrane with a small periplasmic space between the membrane and the thick peptidoglycan cell wall layer. Gram-positive bacteria contain a structural component known as teichoic acids, which are acid polysaccharides that connect the cell membrane to the cell wall. Gram-negative bacteria stains pink from the counterstain and has two membranes. The inner and outer cell membranes have a large periplasmic space dividing them that contains periplasmic gel and a thin peptidoglycan cell wall layer. The outer cell membrane of gram-negative bacteria is composed of lipopolysaccharides (LPS) and proteins. LPS in the outer cell membrane of gram-negative bacteria secrete endotoxins, bacterial toxins that are released when gram-negative bacteria is destroyed. Both gram-negative and positive bacteria secrete exotoxin bacterial toxins.

**FIGURE 2:** GRAM-POSITIVE VERSUS GRAM-NEGATIVE STAINING

All bacteria cells are surrounded by a capsule, this is considered a virulence factor since it enhances bacteria’s ability to survive and cause disease by preventing the phagocytosis (cellular eating) of bacteria by other cells such as immune cells. The capsule also prevents desiccation and helps prokaryotes cling to surfaces. Capsules sometimes occur in archaea but are rare.

d) Bacterial metabolism

Another key way to classify bacteria is by their oxygen requirements for metabolism. Anaerobes are bacteria that do not need oxygen for metabolism, whereas aerobes do require oxygen. Within these groups, there are various types of bacteria based on their specific relationship with oxygen.

Obligate anaerobes must avoid oxygen because it is toxic to them. Aerotolerant anaerobes, while also engaging only in anaerobic metabolism, are not harmed by the presence of oxygen. Conversely, obligate aerobes need oxygen to survive and metabolize. There are also facultative anaerobes and facultative aerobes, which prefer one type of metabolism (e.g., with oxygen) but can switch to the other (e.g., without oxygen) when necessary. The diagram below illustrates where different types of bacteria are likely to be found in a culture medium with oxygen present at the surface.

**FIGURE 3:** LOCATION OF BACTERIA IN A CULTURE MEDIUM WITH OXYGEN PRESENT

e) Bacterial reproduction

Bacterial reproduction can occur asexually or sexually. Bacterial asexual reproduction occurs via binary fission. Binary fission allows cell growth, DNA replication, and cell division to occur simultaneously in prokaryotes. As a result, binary fission allows for rapid reproduction. These steps occur separately and one at a time in eukaryotic cells, which makes reproduction much slower. Binary fission results in daughter cells that are genetically identical to the parent cell, resulting in no genetic diversity among offspring.

Binary fission happens quickly, leading to exponential growth in bacteria. However, this exponential growth is preceded by the lag phase, during which bacteria adapt to their new environment. During the log phase, bacteria grow rapidly, but limited resources eventually cause the population to stabilize in the stationary phase. The final stage is the death phase, which occurs when resources are depleted. This growth cycle demonstrates the increase and decrease in bacterial numbers over time. Bacterial growth exemplifies a positive feedback loop, where the formation of more bacteria accelerates further reproduction until resources are exhausted and growth ceases.

In adverse environmental conditions, bacteria cells produce endospores, which are non-reproducing and possess tough inner and outer coat structures that force bacteria into a dormant state to be able to endure the harsh environment. Once environmental conditions become favorable again bacteria is able continue normal growth and reproduction.

As for sexual reproduction, bacteria are able to increase genetic diversity among its population via horizontal gene transfer, in which genes are passed within the same generation. Conversely, vertical gene transfer is when genes are passed to the next generation, from parent to offspring, as us humans do when reproducing.

There are three types of horizontal gene transfer that bacteria cells can undergo: conjugation, transformation, and transduction.

Conjugation is when genetic material is passed from an F+ to F- bacteria cell via the pili, making both cells into F+ bacteria cells and increasing genetic diversity among bacteria within the same generation. F+ bacteria is bacteria cells that possess the F plasmid which allows them to produce pilis. F- bacteria is bacteria cells that lack the F plasmid and thus cannot produce pilis. Plasmids are DNA independent of bacteria’s single circular chromosome, and the plasmids involved in conjugation are R factors. R factors contain antibiotic resistant genes. A pili is a cytoplasmic bridge that occurs between bacterial cells during conjugation. The process of conjugation is simple, an F+ bacteria cell forms a pili to an F- bateria and transfers an F plasmid to the F- bacteria. Genetic diversity increases by genetic material being passed within the F plasmid, and both bacteria cells are now F+ bacteria.
Transformation is when bacteria increases genetic diversity within the generation by incorporating environmental DNA into their genome. Bacteria cells can only undergo transformation if they are competent, meaning they are able to intake extracellular DNA. Electroporation is done in a lab. It is the process which makes bacteria cells competent by charging their cell membrane with a brief electrical pulse.
Transduction is when genetic material is passed to other bacteria cells via virus particles. A bacteriophage is a type of virus that infects bacteria. A bacteriophage begins by infecting a bacterial host cell and enters the lysogenic life cycle. Favorable environmental conditions allow the bacteriophage to enter the lytic life cycle and create new phage particles which contain the bacterial host’s DNA. Eventually, the abundance of phage particles causes the bacterial cell to lyse and the particles can infect other bacteria cells. The bacterial DNA which the viral phage particles contain is also transferred to the new host cell’s genome. This is how transduction horizontally increases genetic diversity among bacteria.

FIGURE 6: TRANSDUCTION, TRANSFORMATION, AND CONJUGATION — **FIGURE 6:** TRANSDUCTION, TRANSFORMATION, AND CONJUGATION

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Microbes for the DAT

Learn key DAT concepts related to archaebacteria, eubacteria, protists, fungi, and viruses, plus practice questions and answers

Table of Contents

Part 1: Introduction to microbes

Part 2: Taxonomy