There are three main nutrient cycles that bacteria use. They are the carbon cycle, nitrogen cycle, and sulfur cycles.  In the carbon cycle, CO2 is removed from the atmosphere by photosynthesis of land plants and return through the respiration of land animals. The nitrogen cycle is an essential element for life and includes nitrogen fixation and denitrification. During nitrogen fixation nitrogen in the atmosphere is converted into ammonium. During denitrification, NO3- is reduced to N2, NO, or N2O. During the sulfur cycle mineralization of organic sulfur into inorganic form occurs, followed by the oxidation of hydrogen sulfide. Then sulfate is reduced into sulfide, and the sulfide in incorporated into organic materials.

Humans have a large impact on microbial nutrient cycles by adding and removing components of the of the cycles in large amounts. CO2 is responsible for global warming. It has increased in the atmosphere by 40% since the industrial revolution. Human impact on nitrogen cycles includes the production of nitrogenous fertilizers. These fertilizers create a nitrogen amount equivalent to the amount of fixed nitrogen entering the biosphere.

Crenarchaeota has the distinction of including microbial species with the highest known growth temperatures of any organisms. Although they are microscopic, single-celled organisms, they flourish under conditions which would quickly kill most “higher” organisms. As a rule, they grow best between 80° and 100°C (100°C = 212°F, the boiling point of water at sea level), and several species will not grow below 80°C. Several species also prefer to live under very acidic conditions in dilute solutions of hot sulfuric acid. Approximately 15 genera are known, and most of the hyperthermophilic species have been isolated from marine or terrestrial volcanic environments, such as hot springs and shallow or deep-sea hydrothermal vents. Recent analyses of genetic sequences obtained directly from environomental samples, however, indicate the existence of low temperature Crenarchaeota, which have not yet been cultivated.

Korarchaeota is a phylum of hyperthermophilic Archaea that branches closest to the archaeal root. The Korarchaeota were originally discovered by microbial community analysis of ribosomal RNA genes from environmental samples of a hot spring in Yellowstone National Park. No pure cultures from this phylum have been isolated yet, but the sequenced 16S ribosomal RNA genes belong to organisms that branch near the root of the archaeal phylogenetic tree. Stable enrichment mixed cultures, containing Korarchaeota identifiable by in situ hybridization, have been grown at thermophilic conditions in the laboratory.

Nanoarchaeota is a phylum of very small parasitic Archaea that branches closest to the root of the archaeal phylogentic tree. Cells of Nanoarchaeum, the only genus in this phylum, are small coccoids that live as parasites, or possibly as symbionts, of the crenarchaeota Ignicoccus. Cells of Nanoarchaeum are about 0.4 μm in diameter and replicate only when attached to the surface of Ignicoccus. Nanoarchaeum is hyperthermophilic, with an optimal growth of about 90°C. The metabolism of Nanoarchaeum is unknown, but its host is an autotroph, growing with H2 as electron donor and elemental sulfur as electron acceptor. Isolates from Nanoarchaeum have been obtained from submarine hydrothermal vents as well as terrestrial hot springs. The genome of Nanoarchaeum is only 0.49 Mbp, the smallest genome known. It lacks identifiable genes for most known metabolic functions, including the synthesis of monomers, such as aminoacids, nucleotides, and coenzymes.

Thaumarchaeota represent a unique phylum within the domain Archaea that embraces ammonia-oxidizing organisms from soil, marine waters, and hot springs as well as many lineages represented only by environmental sequences from virtually every habitat that has been screened. All cultivated Thaumarchaeota perform the first step in nitrification. They live under autotrophic conditions and fix CO2, but some are dependent on the presence of other bacteria or small amounts of organic material. Different from bacterial ammonia oxidizers, all cultivated Thaumarchaeota are adapted to comparably low amounts of substrate (ammonia) and inhabit not only moderate but also extreme environments, such as hot springs and acidic soils. All cultivated strains contain tetraether lipids with crenarchaeol, a Thaumarchaeota-specific core lipid.

Euryarchaeota is one of the four phyla of the domain Archaea. Euryarchaeota comprises a physiologically diverse group of Archaea: all known methanogens, extreme halophilic Archaea, hyperthermephile​s such as Thermococcus and Pyrococcus, most acidophilic-thermophilic prokaryotes including Picrophilus and the thermophilic-acidophilic cell wall-less Thermoplasma. A large number of Euryarchaeota produce methane (CH4) as an integral part of their metabolism (see methanogens). It is considered a very ancient metabolism due to the unique set of enzymes involved. The extreme halophilic Archaea are a diverse group of Euryarchaea that inhabit highly saline environments.

Horizontal gene transfer is any process in which an organism transfers genetic material to another cell that is not its offspring. Vertical transfer occurs when an organism receives genetic material from its ancestor such as from its parent or a species from which it evolved.

Horizontal gene transfer is common among bacteria, even very distantly related ones. For example, this process is thought to be a significant cause of increased drug resistance; when one bacterial cell acquires resistance, it can quickly transfer the resistance genes to many species. Also enteric bacteria appear to exchange genetic material with each other within the gut in which they live.

DNA replication uses proteins and enzymes, each of which plays a important role during the process. One of the key players is the enzyme DNA polymerase, which adds nucleotides one by one to the growing DNA chain that are complementary to the template strand. The addition of nucleotides requires energy; this energy is obtained from the nucleotides that have three phosphates attached to them, similar to ATP which has three phosphate groups attached. When the bond between the phosphates is broken, the energy released is used to form the phosphodiester bond between the incoming nucleotide and the growing chain. In prokaryotes, three main types of polymerases are known: DNA pol I, DNA pol II, and DNA pol III. DNA pol III is the enzyme required for DNA synthesis; DNA pol I and DNA pol II are primarily required for repair.

Translation is decoding mRNA to build a polypeptide (chain of amino acids). In an mRNA, the instructions for building a polypeptide come in groups of three nucleotides called codons. These relationships between mRNA codons and amino acids are known as the genetic code. Initiation is when the ribosome gets together with the mRNA and the first tRNA so translation can begin. Elongation is when amino acids are brought to the ribosome by tRNAs and linked together to form a chain. Termination is the finished polypeptide is released to go and do its job in the cell.

Transcription is the first step in gene expression. Information from a gene is used to construct a functional product. This could be something like a protein. The goal of transcription is to make a RNA copy of a gene’s DNA sequence. For a protein-coding gene, the RNA copy, also called the transcript, carries the information needed to build a polypeptide (protein or protein subunit). It occurs in the cytoplasm. There is no definite phase for it to take place in. A single RNA polymerase synthesizes all three types.