Autotrophic bacteria synthesize all their cell constituents using carbon dioxide as the carbon source. The most common pathways for synthesizing organic compounds from carbon dioxide are the reductive pentose phosphate (Calvin) cycle, the reductive tricarboxylic acid cycle, and the acetyl-CoA pathway. The Calvin cycle, elucidated by American biochemist Melvin Calvin, is the most widely distributed of these pathways, operating in plants, algae, photosynthetic bacteria, and most aerobic lithoautotrophic bacteria. The key step in the Calvin cycle is the reaction of ribulose 1,5-bisphosphate with carbon dioxide, yielding two molecules of 3-phosphoglycerate, a precursor to glucose. This cycle is extremely expensive for the cell in terms of energy, such that the synthesis of one molecule of glyceraldehyde-3-phosphate requires the consumption of nine molecules of ATP and the oxidation of six molecules of the electron donor, the reduced form of nicotinamide adenine dinucleotide phosphate (NADPH). Autotrophic behavior depends on the ability of the cell to carry out photosynthetic or aerobic respiratory metabolism, which are the only processes able to deliver sufficient energy to maintain carbon fixation.

The aerobic nonphotosynthetic lithoautotrophs are those bacteria that not only use carbon dioxide as their sole carbon source but also generate energy from inorganic compounds (electron donors) with oxygen as an electron acceptor. These bacteria are taxonomically diverse and are usually defined by the electron donor that they use. For example, Nitrosomonas europaea oxidizes ammonia (NH₄⁺) to nitrite, and Nitrobacter winogradskyi oxidizes nitrite to nitrate. Thiobacillus oxidizes thiosulfate and elemental sulfur to sulfate, and A. ferrooxidans oxidizes ferrous ions to the ferric form. This diverse oxidizing ability allows A. ferrooxidans to tolerate high concentrations of many different ions, including iron, copper, cobalt, nickel, and zinc. All of these types of bacteria appear to be obligate lithotrophs and are unable to use organic compounds to a significant degree. Carbon monoxide (CO) is oxidized to carbon dioxide by Oligotropha carboxidovorans, and hydrogen gas (H₂) is oxidized by Alcaligenes eutrophus and, to a lesser degree, by many other bacteria.

Metabolic energy is made available from the oxidation of these electron donors in basically the same way as that used by respiring heterotrophs, which transfer electrons from an organic molecule to oxygen. As electrons are passed along the electron transport chain to oxygen, a proton gradient is generated across the cell membrane. This gradient is used to generate molecules of ATP. Other reactions present in lithoautotrophs are those used for the removal of electrons from the inorganic donor and for carbon dioxide fixation.

Phototrophic metabolism

Life on Earth is dependent on the conversion of solar energy to cellular energy by the process of photosynthesis. The general process of photosynthesis makes use of pigments called chlorophylls that absorb light energy from the Sun and release an electron with a higher energy level. This electron is passed through an electron transport chain, with the generation of energy by formation of a proton gradient and concomitant ATP synthesis. The electron ultimately returns to the chlorophyll. This cyclic reaction path can fulfill the energy needs of the cell. For the cell to grow, however, the Calvin cycle of carbon dioxide fixation must be activated, and electrons must be transferred to the cofactor NADP to form NADPH, which is needed in large amounts for the operation of the cycle. Thus, phototrophic cell growth requires that a source of electrons be available to replace the electrons that are consumed during biosynthetic reactions.

Photosynthetic organisms are divided into two broad groups according to the nature of the source of these electrons. One group includes the higher plants, eukaryotic algae, and the cyanobacteria (blue-green algae); these organisms contain the pigment chlorophyll a and use water as their electron source in reactions that generate oxygen. It is thought that by 1.8 billion years ago predecessors of the cyanobacteria had produced enough oxygen globally to begin to allow for the development of higher forms of life. Oxygen-evolving photosynthesis requires the action of two separate light-absorbing systems to raise the energy of the electrons from water to a level high enough for their transfer to NADP. Thus, two distinct photoreaction centers are present in these organisms, one for the oxygen-generating reaction and the other for the cyclic process for energy generation. In the cyanobacteria, both photoreaction centers contain chlorophyll a. Their photosynthetic apparatus also contains other light-absorbing pigments that serve as antennae to capture light energy and transfer it to the reaction centers. Cyanobacterial antennae include additional molecules of chlorophyll a, which transfer energy to the cyclic reaction center, and phycobilisomes, which are protein pigments that absorb light of short, high-energy wavelengths and transmit this energy to the oxygen-evolving reaction center. In almost all cyanobacteria, the photosynthetic apparatus is contained in an extensive intracellular system of flattened membranous sacs, called thylakoids, the outer surfaces of which are studded with regular arrays of phycobilisome granules. This arrangement, in which pigment aggregates exist on the thylakoid surfaces, is called a photosystem.

Other photosynthetic bacteria contain only a single type of reaction center with a different pigment, called bacteriochlorophyll, which absorbs light of long, low-energy wavelengths. These organisms require an electron donor other than water and do not release oxygen. The green bacteria (Chlorobiaceae) and purple sulfur bacteria (Chromatiaceae) use elemental sulfur, sulfide, thiosulfate, or hydrogen gas as electron donor, whereas the purple nonsulfur bacteria use electrons from hydrogen or organic substrates. These bacteria require anaerobic conditions for photosynthetic activity. The photosystem in green bacteria is related to photosystem I of higher plants, whereas that in purple bacteria is related to photosystem II, which provides some indication of an evolutionary trail from bacteria to plants (see photosynthesis: The process of photosynthesis: the light reactions).