Environmental Microbiology focuses on microbial properties and processes that define the structure and function of natural and man-made ecosystems. Since the flow of energy and matter through the environment is often governed by microbial activities, it is essential to understand, predict and leverage them, to both address and avoid environmental problems. Water is a key media through which energy and elements are transported within and between ecosystems, and it is also a conduit for the transport of anthropogenic materials and waste. Because microorganisms are the primary living constituents of aquatic ecosystems and mediate globally important processes, we focus on environmental microbiology

Microbial ecology
Microbial ecology is the ecology of microorganisms: their relationship 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. Microbial life plays a primary role in regulating biogeochemical systems in virtually all of our planet's environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine. As a consequence of the quantitative magnitude of microbial life (Whitman and coworkers calculated 5.0×1030 cells, eight orders of magnitude greater than the number of stars in the observable universe) microbes, by virtue of their biomass alone, constitute a significant carbon sink. Aside from carbon fixation, microorganisms’ key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling. The immensity of microorganisms’ production is such that, even in the total absence of eukaryotic life, these processes would likely continue unchanged.
While microbes have been studied since the seventeenth-century, this research was from a primarily physiolocal perspective rather than an ecological one. Martinus Beijerinck invented the enrichment culture, a fundamental method of studying microbes from the environment. He is often incorrectly credited with framing the microbial ecology idea that "everything is everywhere, but, the environment selects," which was stated by Lourens Baas Backing. Sergei Winogradsky was one of the first researchers to attempt to understand microorganisms outside of the medical context—making him among the first students of microbial ecology and environmental microbiology—discovering chemosynthesis, and developing the Winogradsky column in the process.
Beijirnck and Windogradsky, however, were focused on the physiology of microorganisms, not the microbial habitat or their ecological interactions. Modern microbial ecology was launched by Robert Hungate and coworkers, who investigated the rumen ecosystem. The study of the rumen required Hungate to develop techniques for culturing anaerobic microbes, and he also pioneered a quantitative approach to the study of microbes and their ecological activities that differentiated the relative contributions of species and catabolic pathways.
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 gases 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 products. 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.
Due to the high level of horizontal gene transfer among microbial communities, microbial ecology is also of importance to studies of evolution.
Microbial resource management

Biotechnology may be used alongside microbial ecology to address a number of environmental and economic challenges. For example, molecular techniques such as community fingerprinting can be used to track changes in microbial communities over time or assess their biodiversity. 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 have to be better characterized for this field's potential to be realized. In addition, there are also clinical implications, as marine microbial symbioses are a valuable source of existing and novel antimicrobial agents, and thus offer another line of inquiry in the evolutionary arms race of antibiotic resistance, a pressing concern for researchers.

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