The actions of microorganisms help extract carbon from non-living sources and make the carbon available to living organisms. The cycling of carbon by microorganisms, including a variety of bacteria and fungi, occurs in aquatic habitats.Soil microbes can break down plant organic matter to carbon dioxide or convert it to dissolved organic carbon (DOC) compounds. This leads either to long-term carbon storage, because DOC can bind to soil particles, or to the release of carbon back to the atmosphere as carbon dioxide. As microorganisms help break down organic matter, they release essential nutrients and carbon dioxide into the soil, fix nitrogen and help transform nutrients into mineral forms that plants can use through a process by mineralization.

Bacteria play such a large role in the carbon cycle, for they consume organic material, such as organic wastes, decaying plants and animals, etc. There are also autotrophic bacteria, which provide carbon-based nourishment to themselves and the ecosystem. Soil microbes can break down plant organic matter to carbon dioxide or convert it to dissolved organic carbon (DOC) compounds. This leads either to long-term carbon storage, because DOC can bind to soil particles, or to the release of carbon back to the atmosphere as carbon dioxide. Microorganisms and fungi break down wood and return carbon to the biogeochemical cycles. If these organisms become absent, carbon would accumulate in the wood, where it could not be recycled into the environment. The fixation of nitrogen is dependent on microorganisms mostly through biological nitrogen fixation. Many microorganisms can assimilate CO2as sole carbon source and convert it into valuable products and microbial CO2 fixation techniques have been attracting much attention for reducing greenhouse gases and subsequent production of value-added products. In the carbon cycle, microorganisms have many roles and some include the following: fungi are decomposers in the soil, algae are photosynthetic and some use carbon dioxide as a source of carbon and convert it to organic material, cyanobacteria fix carbon dioxide and produce oxygen during photosynthesis. Microbes are involved in many processes, including the carbon and nitrogen cycles, and are responsible for both using and producing greenhouse gases such as carbon dioxide and methane. Microbes can have positive and negative responses to temperature, making them an important component of climate change models. Carbon is transferred from the atmosphere to soil via 'carbon-fixing' autotrophic organisms, mainly photosynthesising plants and also photo- and chemoautotrophic microbes that synthesise atmospheric carbon dioxide (CO2) into organic material. A type of bacteria called cyanobacteria also use carbon dioxide to grow, as do green algae and single-celled organisms called diatoms. In both cyanobacteria and photosynthetic organisms, the process of converting carbon dioxide gas into an organic building block is called carbon fixation. Soil microbes can break down plant organic matter to carbon dioxide or convert it to dissolved organic carbon (DOC) compounds. This leads either to long-term carbon storage, because DOC can bind to soil particles, or to the release of carbon back to the atmosphere as carbon dioxide.