Microbial ecology is the relationship of microorganisms with one another and with their environment. It concerns the three major domains of life — Eukaryota, Archaea, and Bacteria — as well as viruses. Microorganisms, by their omnipresence, impact the entire biosphere. They are present in virtually all of our planet's environments, including some of the most extreme, from acidic lakes to the deepest ocean, and from frozen environments to hydrothermal vents.
Microbes, especially bacteria, often engage in symbiotic relationships (either positive or negative) with other organisms, and these relationships affect the ecosystem. One example of these fundamental symbioses are chloroplasts, which allow eukaryotes to conduct photosynthesis. Chloroplasts are considered to be endosymbiotic cyanobacteria, a group of bacteria that are thought to be the origins of aerobic photosynthesis. Some theories state that this invention coincides with a major shift in the early earth's atmosphere, from a reducing atmosphere to an oxygen-rich atmosphere. Some theories go as far as saying that this shift in the balance of gasses might have triggered a global ice-age known as the Snowball Earth.
They are the backbone of all ecosystems, but even more so in the zones where light cannot approach and thus photosynthesis cannot be the basic means to collect energy. In such zones, chemosynthetic microbes provide energy and carbon to the other organisms.
Other microbes are decomposers, with the ability to recycle nutrients from other organisms' waste poducts. These microbes play a vital role in biogeochemical cycles. The nitrogen cycle, the phosphorus cycle and the carbon cycle all depend on microorganisms in one way or another. For example, nitrogen which makes up 78% of the planet's atmosphere is "indigestible" for most organisms, and the flow of nitrogen into the biosphere depends on a microbial process called fixation.
Microbial resource management
Biotechnology may be used alongside microbial ecology to address a number of environmental and economic challenges. Managing the carbon cycle to sequester carbon dioxide and prevent excess methanogenesis is important in mitigating global warming, and the prospects of bioenergy are being expanded by the development of microbial fuel cells. Microbial resource management advocates a more progressive attitude towards disease, whereby biological control agents are favoured over attempts at eradication. Fluxes in microbial communities must be better characterized for this field's potential to be realised.