Prokaryotes

A prokaryote is a type of cell that does not have any nucleus or membrane-bound organelles. Prokaryotes include two of the three domains of life: Eubacteria (often just called bacteria) and Archaeabacteria (often just called archaea). Archaea, as their name suggests, are thought to be more ancient of the two groups. Archaea have also not yet been found to be pathogenic - that is, able to cause disease - in any other organism. The other group, bacteria, are more familiar to most people and include human pathogens as well as many bacteria that are beneficial to humans and/or important in environmental processes. Some archaea and bacteria reside in the human gut microbiome and are important for proper digestion, vitamin synthesis, and other processes.

Prokaryotic cells divide by a process called binary fission. It is similar to eukaryotic division, with the exception that DNA replication leads directly to cytokinesis (splitting of cell membrane), with no agglomeration into chromosomes first.

Prokaryotes are the most primitive forms of life, so they are immensely important in evolution. While they are far less complex than eukaryotic organisms like eukaryotic algae, protozoa, fungi, plants, and animals, they are still some of the most common life forms. They are continuing to evolve now, developing resistance to antibiotic drugs and rendering them useless.
Bacteria

Bacteria are single-celled, prokaryotic microorganisms. Some bacteria are beneficial to humans while others are pathogenic, but a majority of bacteria are harmless to humans. Pathogenic bacteria are responsible for a variety of diseases including strep throat and tetanus. Bacteria originate from the single-celled organisms that were the first to inhabit the Earth.

Bacteria, despite their small size and simple nature, have an immense impact on human society. Negatively, they have caused epidemics and pandemics, like cholera outbreaks seen in Europe up until the early 20th century, and in less developed countries in modern times. In more recent years, humans have helped to make drug-resistant strains of bacteria. Humans have brought about these stronger bacteria by using only a small amount of antibiotics, for related or unrelated purposes. This small exposure enables the bacteria to develop resistance or even immunity to larger amounts of the drug.

However, bacteria have also impacted society in a positive way. The first artificial life created was a bacterium. Also, bacteria are being studied to determine what may have been the origin of life on Earth, as well as for extraterrestrial life - they are the most likely candidates for this. Outside of science, bacteria are used in industry to create many familiar products, and some plants have nitrogen-fixing bacteria. Motile bacteria may utilize rotating flagella to move, or they may secrete slime to slide around like a slug. Bacteria may also be non-motile.

Bacterial cell shapes

Bacteria may assume many different shapes. Some of the most common morphologies include spherical, rod-shaped, and spiral. Spherical bacteria are called cocci (singular:coccus) and include bacterial genera such as Staphylococcus, Streptococcus, and Pneumococcus. Rod-shaped bacteria are called bacilli (singular: bacillus), and include bacterial genera such as Bacillus (confusingly, Bacillus also refers to a genus of bacteria), Escherichia (including the famous E. coli), Lactobacillus, Rhizobium, Streptobacillus, and many more. Spiral bacteria include the rigid, corkscrew- or helix-shaped spirilla (singular: spirillum) such as Campylobacter, Helicobacter, and Spirllium (again, the shape is the same name as the genus) as well as the longer, thinner, and more flexible spirochetes (e.g., Borellia, Leptospira, andTreponema). Other bacteria have more complex cell shapes, such as club-shaped (e.g., Cornyebacterium; sometimes, this shape is described as cornyeform after the genus) or comma-shaped (e.g., Vibrio, Bdellovibrio; sometimes, this shape is called a vibrio after the genus). In addition, some bacteria are pleomorphic, meaning they do not have a fixed cell shape but instead alter their morphology in response to environmental conditions.

Beyond possessing different cell shapes, bacterial cells may display various different arrangements. For example, Streptococcus bacteria form linear arrangements of cocci, and Streptobacillus bacteria form linear arrangements of rods. Staphylococcus bacteria are cocci form clustered arrangements. Diplococci are arranged as pairs of cocci, tetrads form a 2 x 2 square arrangement of cocci, and the genus Sarcina assumes a 2 x 2 x 2 cuboidal arrangement of cocci.

Gram staining

Gram staining is a common microbiological technique used to classify bacteria on the basis of their cell wall structure. The method was developed by the Danish bacteriologist Hans Christian Gram in 1884. Because Gram staining yields different results for two different groups of bacteria (Gram-positive and Gram-negative bacteria), it is a type of differential stain (as opposed to a simple stain). The procedure for Gram staining involves first heat-fixing bacteria (so that the bacteria are able to hold the primary stain and keep the bacteria in place) before sequentially treating them with four different reagents:

1) A cationic (i.e., positively charged) primary stain (often crystal violet, which stains cells purple, or methylene blue) that is taken up by both Gram-positive and Gram-negative bacteria. Cells are usually incubated with the dye for at least 1 minute. In an aqueous solution, crystal violet disassociates into CV+ and Cl- ions. These ions penetrate through the cell wall and CV+ associates with negatively charged functional groups in bacterial cell walls.

2) A mordant (usually Gram's iodine solution) containing anions that complex with the positively charged primary stain inside of Gram-positive cell walls, preventing easy removal of the primary stain when cells are washed with a decolorizer. The mordant essentially acts as a trapping agent for the primary dye, and cells are usually incubated for at least one minute before rinsing off any excess mordant.

3) A decolorizer (often ethanol or acetone) used to wash the primary stain off the surface of Gram-negative bacteria, which cannot remove any primary stain molecules that were fixed inside Gram-positive cell walls by the mordant. Alcohol dissolves the outer membrane of Gram-negative bacteria, effectively removing any primary stain on Gram-negative cells, while the primary stain remains trapped in the thick cell walls of Gram-positive cells.

4) A counterstain (often safranin, basic fuchsin, or carbol fuchsin; all of which stain cells red/ pink). The counterstain stains both Gram-positive and Gram-negative cells, but is not visible on Gram-positive cells due to the darker color of the primary stain. This procedure results in Gram-positive bacteria being stained purple, while Gram-negative bacteria stain red/ pink color.
Gram-positive vs. Gram-negative bacteria

Typically, Gram-positive bacteria produce exotoxins and are susceptible to phenol disinfectants. They retain the blue-purple color of crystal violet in Gram staining because of their thicker walls of peptidoglycan. Unlike Gram-negative bacteria, they lack the periplasmic space between the cytoplasmic and outer membranes because Gram-positive bacteria lack an outer membrane. Certain types of Gram-positive bacilli, most importantly Lactobacilli (used in milk and dairy products), cannot form spores.

Gram-negative bacteria have thinner walls of peptidoglycan and two membranes and periplasmic space between them. Because of the safranin counterstain, they become red-pink after Gram staining. There are many Gram-negative aerobic (oxygen-using) bacteria.

Generally, it is more difficult to kill Gram-negative bacteria with antibiotics due to their more complex cell membrane structure.
Limitations of Gram staining

Gram staining is not always an effective technique for classifying some types of bacteria, namely acid-fast bacteria. Acid-fast bacteria usually stain weakly Gram-negative or Gram-variable. They are similar to Gram-negative bacteria in that they both have thinner layers of peptidoglycan comprising the cell wall as well as an outer lipid membrane coating the cell wall (Note: this outer membrane is in addition to the bilayer beneath the cell wall that constitutes the cytoplasmic membrane, which all types of bacteria have). While Gram-negative bacteria contain an outer phospholipid bilayer rich in lipopolysaccharide, acid-fast bacteria have a much more complex layer beyond their cell walls. Directly above the peptidoglycan cell wall is an arabinogalactan (a type of structural polysaccharide) layer, which is covalently bound to a layer of mycolic acids that comprise the inner leaflet of the outermost lipid bilayer. The outer leaflet of the outermost acid-fast lipid bilayer contains free mycolic acids, phospholipids, and glycolipids. This outer layer also contains surface proteins and porin proteins that span the outer membrane, allowing transport of specific small molecules in and out of the cell.

Some bacteria can assume growth forms in which they lack cell walls. Bacteria that lack cell walls are called L-form or L-phase bacteria and always stain Gram-negative due to the absence of a cell wall, although L-form bacteria may arise from either Gram-negative or Gram-positive bacteria.

Additionally Gram staining yields widely varying results when performed on Archaea. Many Archaea stain Gram-negative while others stain Gram-positive, and Gram staining results do not meaningfully align with phylogenetic relationships across different Archaea.
Horizontal Gene Transfer
Mechanisms of Horizontal Gene Transfer

Conjugation: A bacterium can transfer some of it's own DNA into other bacteria via pilus. This is seen with penicillin binding proteins, where a bacterium with the protein can give it to another bacterium.

Transduction: A bacteriophage infects a bacterium, and takes some of its DNA after replication. The replicated bacteriophages infect other bacteria, inserting the previous bacteria's DNA into another bacteria.

Transformation: After the process of lysis or death, a bacterium can take some of the of DNA fragments that were left behind of the other dead bacteria.
Bacterial motility
Motility structures and composition

Bacterial flagella are made of helical filaments made of a protein called flagellin. Bacterial flagella are rotary motors that can rotate clockwise or counter-clockwise.
There are differences in flagella structure between gram-positive and gram-negative bacteria. Gram-positive bacteria have 2 protein rings present in the peptidoglycan cell wall and plasma membrane that act as bearings for the shaft of the flagellum. Gram-negative bacteria have 4 of these basal protein rings instead: the L ring in the outer lipopolysaccharide layer, the P ring in the peptidoglycan cell wall, the M ring in the plasma membrane, and the S ring which is directly attached to the cytoplasm.
Most bacterial flagella are driven by chemiosmosis (protons) rather than ATP hydrolysis. Some species have flagella that are driven by a sodium-pump (e.g., some Vibrio species)

Flagellar Arrangements

Monotrichous: Only one flagellum, on one pole of the cell. Ex: Vibrio cholera

Amphitrichous: A single flagellum on each pole of the cell. Ex: Alcaligenes faecalis

Cephalotrichous: More than one flagella on each pole of the cell. Sometimes no distinction is made between this an "amphitrichous" flagellar arrangements.
A: Monotrichous B: Amphitrichous C: Lophotrichous D: Peritrichous

Lophotrichous: More than one flagella on one pole of the cell. Ex: Helicobacter pylori

Peritrichous: Many flagella are distributed across the surface of the cell and are not necessarily localized to the poles of the cells. Ex: Escherichia Coli

Atrichous: Lacking flagella entirely. Ex: Lactobacillus delbrueckii

Archaea

Archaea (Domain Archaea) are a group of single-celled, prokaryotic microorganisms that were once thought to be bacteria due to their similar size and appearance under the microscope. Archaea were first identified as a separate domain of life The evolutionary origin of archaea (singular: archaeon) remains to be fully deciphered; however, archaea and eukaryotes are thought to share a common ancestors because of their many similarities. Phylogenetic analyses suggest that early eukaryotes arose from an ancestor that was a part of a group of archaea called the Asgard archaea, specifically the lineage Heimdallarchaeota. Evidence for the archaeal origin of eukaryotes include the presence of several key proteins involved in eukaryotic processes called eukaryotic signature proteins in the Heimdallarchaeota. Some of these eukaryotic signature proteins are involved in complex processes such as the cytoskeleton and membrane remodeling. Unlike bacteria, no species of archaea are known to form spores.

Many archaea are extremophiles, meaning they live in extreme environments that would pose major challenges for many other organisms (e.g., very hot, cold, acidic, salty, etc.). The first archaea to be discovered were extremophiles, and because few other organisms are able to withstand the harsh conditions, there is a relative abundance of these organisms in extreme environments While there are also many archaea that are mesophiles, which prefer moderate environmental conditions, the prevalence of archaea in extreme environments some extent, this

Archaea are involved in the carbon and nitrogen cycles, assist in digestion, and can be used in sewage treatment.

Archaea, especially methanogens like Methanobrevibacter smithii, play important roles in the human gut microbiome. For instance, methanogen metabolism regulates the concentration of H2 gas in the intestines, which promotes the production of short-chain fatty acids (SCFAs) by bacteria. In turn, SCFAs are involved in different metabolic pathways that are relevant to cardio-metabolic diseases like obesity, insulin resistance, and type 2 diabetes.

Interestingly, archaea are not known to cause any diseases in humans or in any other organisms. It remains to be discovered if the archaea constitute an entirely non-pathogenic Domain of organisms.