Metallic archaea were an artificially modified subculture of single-celled organisms called archaea created by Code Talker. They had various abilities, mostly involving the metabolism and manipulation of metals.
Code Talker first began work on the metallic archaea during the Cold War. Since the ground beneath the Navajo nation was rich with uranium ore that could be utilized in nuclear weaponry, the U.S. government set up countless mines on their land and sent the Navajo people there to work. Many were irradiated because of their close contact with uranium and became sick and died. Around this time, Code Talker discovered microbes that could "eat" uranium, and he believed he could use them to cleanse the Navajo of the irradiation. However, the research's required funding was much too high. Nobody was willing to invest in his research but Skull Face. Skull Face put Code Talker to research the microbes' potential in nuclear weaponry rather than uranium clean-up, holding the Navajo people hostage to force Code Talker to abandon his old work and move on.
In his time working under Skull Face, Code Talker created a metallic offspring of pure archaea that subsisted on metals rather than organic matter, dubbing it "metallic archaea." The uranium strain of metallic archaea were quickly used in the production of Metal Gear Sahelanthropus and other XOF projects. During this time Code Talker also created other variants of the archaea that could be used as a weapon on its own, which was to later be heavily utilized by the Parasite Unit.
The technology spread relatively slowly, eventually landing in the hands of Huey Emmerich and assisting in the creation of his exo-legs, using more docile forms of metallic archaea to increase the exo-legs' reaction speed and enable him to lock and release his joints at will. He also was nearly on the receiving end of metallic archaea by Ocelot during an interrogation session, destroying his glasses and threatening to destroy his exo-legs next, eventually resulting in Huey divulging the location of Metal Gear as being at OKB Zero. Despite this, however, Ocelot eventually placed the needle right behind one of Huey's kneecaps anyways, forcing him to keep his leg up.
Uranium enrichment archaea
Uranium enrichment archaea was first discovered by Code Talker in 1973. The archaea metabolized uranium-235, producing weapons-grade enriched uranium. This process was similar to how plants fractionate carbon isotopes when conducting photosynthesis. They were placed inside of Metal Gear Sahelanthropus to allow it to activate a nuclear self-destruct, and they were also inactive inside the yellowcake recovered by Venom Snake in Central Africa. They were required to be stored inside of yellowcake to survive and were normally kept dormant inside, similarly to baker's yeast.
The objectively much more dangerous corrosive archaea quickly oxidized metals, feeding off the energy in the electrons they received from the process. This strain had an orange or brown color similar to smoke or cinders. The Parasite Unit was equipped with machetes infused with this corrosive archaea, allowing them to burn and corrode whatever their blades came in contact with for extra damage. Certain members of the Parasite Unit also stored corrosive archaea under their parasitic skin and could release it to incapacitate machinery and vehicles. For example, these corrosive archaea were used against Venom Snake when he attempted to escape Central Africa with Code Talker in a chopper, a large cloud of them almost instantly rusting over their entire aircraft and causing it to crash at Nova Braga Airport. Metal Gear Sahelanthropus was also equipped with blades similar to the Parasite Unit's that could function either as flexible whips or rigid swords, as well as grenades containing the archaea to deploy corrosive clouds that would render other machinery useless.
The nuclear bombs Skull Face planned to spread around the world were equipped with a fail safe to make sure his buyers wouldn't turn the weapons on him. The detonator would be destroyed using corrosive archaea and render the nuke useless, so no detonation was possible unless Skull Face disengaged the lock.
Alternatively, a more tame and less destructive kind of these archaea could be used to make better and faster mechanisms, increasing a machine's reaction speed and allowing them to lock and release their individual joint parts at will, almost like a living creature.
The Mist and Armor subdivisions of the Parasite Unit were also equipped with a unique strain of metallic archaea which they could use to turn people into the zombie-like puppet soldiers. It is unexplained how this strain functioned.
Behind the scenes
The metallic archaea are a minor yet important element in Metal Gear Solid V: The Phantom Pain.
The metallic archaea are thematically very similar to the nanomachines from later in the Metal Gear series, being a small yet potentially incredibly dangerous scientific creation with a wide variety of uses.