Prokaryotes: Bacteria and Archaea

Prokaryotes, encompassing Bacteria and Archaea, are single-celled organisms characterized by their simple cellular structure, metabolic diversity, and rapid reproduction. They play crucial roles in ecosystems, including nutrient cycling and primary production, and have significant medical and industrial relevance.

The Earth formed approximately 4.6 billion years ago, with early life appearing around 3.8 billion years ago. Early Earth conditions included bombardment by asteroids, high temperatures, high atmospheric pressure, and no atmospheric oxygen. Stromatolites, layered structures formed by photosynthetic prokaryotes, provide fossil evidence of early life dating back 3.5 billion years.

Prokaryotes are defined by their relatively simple, single-celled structure. They have a plasma membrane, cytoplasm, and ribosomes, similar to eukaryotes, but lack membrane-bound organelles. The genome is arranged in a single, circular DNA chromosome. Prokaryotes reproduce asexually via binary fission, a rapid process that allows for quick population growth. Horizontal gene transfer enables prokaryotes to acquire DNA from other bacteria, the environment, or viruses, facilitating the spread of genes like antibiotic resistance.

Bacteria and Archaea, while both prokaryotes, differ in several key characteristics. Bacteria have cell walls containing peptidoglycan, whereas Archaea lack peptidoglycan. Their RNA polymerases also differ in complexity, and Archaea share some characteristics with Eukarya such as DNA packaging with histone proteins. Archaea are thought to be more closely related to eukaryotes than to bacteria.

Identifying new prokaryotic species is challenging due to their small size, slow growth, and presence in extreme environments. Metagenomics, which involves sequencing all the DNA in an environmental sample, offers a valuable approach for identifying new species.

Prokaryotes are ubiquitous and can thrive in diverse habitats, including extreme environments. Some prokaryotes exhibit symbiosis, living in close association with other organisms. Extremophiles are adapted to extreme conditions such as high salinity, pH, pressure, or temperature. The human microbiome is a community of prokaryotes, fungi, viruses, and protists living in and on the human body. It is estimated that the number of prokaryotic cells in and on our body is greater than the number of human cells and this microbiome is essential for our health, affecting digestion and disease resistance.

Prokaryotes exhibit significant morphological diversity, varying in size, shape, and cell wall composition. Common cell shapes include coccus (sphere), bacillus (rod), and spirillum/spirochaete (spiral). Cell arrangements can be described as diplo (pair), strepto (chain), and staphylo (cluster). Bacteria have peptidoglycan in their cell walls, which differ in morphology. Gram-positive bacteria have a thick layer of peptidoglycan, while Gram-negative bacteria have a thin layer of peptidoglycan surrounded by an outer phospholipid bilayer containing lipopolysaccharides. Gram staining differentiates between these types of bacteria.

Prokaryotes exhibit a wide range of metabolic diversity. All living organisms require ATP (energy) and a carbon source. Phototrophs obtain energy from sunlight, while chemotrophs obtain energy from chemicals. Autotrophs fix carbon (synthesize their own C-C compounds) from simple molecules like CO2, while heterotrophs absorb C-C compounds from the environment. Based on these criteria, organisms can be categorized as photoautotrophs, chemoautotrophs, photoheterotrophs, or chemoheterotrophs.

Prokaryotes play crucial roles in ecosystems. Photoautotrophic prokaryotes, such as cyanobacteria, are primary producers. Chemoheterotrophic prokaryotes are decomposers, breaking down organic matter and returning nutrients to the environment. Some prokaryotes fix nitrogen, converting atmospheric nitrogen into ammonia, which can be used by plants. Early photosynthetic prokaryotes performed non-oxygenic photosynthesis, but the evolution of oxygenic photosynthesis by cyanobacteria led to the “oxygen revolution”, increasing oxygen levels in the atmosphere.

Prokaryotes have practical uses in molecular biology, biochemistry research, the food industry, and bioremediation. E. coli is widely used in genetic engineering. The CRISPR-Cas system, found in bacteria, is used for gene editing research. Some bacteria are used in the production of dairy products. Bioremediation uses bacteria and archaea to clean sites polluted with organic solvents.

Some bacteria are pathogenic, possessing toxins that damage host cells or alter their function. Some species can form biofilms, colonies that coat surfaces and can contaminate medical devices and contribute to tooth decay. Antibiotics are molecules that kill or inhibit bacterial reproduction, but bacterial resistance to antibiotics has evolved and is a growing problem.

Key bacterial lineages include Proteobacteria, Chlamydias, Spirochaetes, Cyanobacteria, and Gram-positive bacteria. Cyanobacteria perform oxygenic photosynthesis and fix nitrogen. Proteobacteria are gram-negative bacteria involved in the nitrogen cycle and causing diseases. Chlamydias are endosymbionts that live inside host cells and can cause chlamydia. Spirochaetes have a corkscrew shape and cause syphilis and Lyme disease. Gram-positive bacteria include Firmicutes and Actinobacteria. Firmicutes are common in the human gut and are used to ferment milk in yogurt and cheese. Actinobacteria can cause tuberculosis and leprosy and produce many antibiotics.

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