Microbial ecology (or environmental microbiology) 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, nose, and mouth. As a consequence of the quantitative magnitude of microbial life (calculated as 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.
History
While microbes have been studied since the seventeenth-century, this research was from a primarily physiological perspective rather than an ecological one. For instance, Louis Pasteur and his disciples were interested in the problem of microbial distribution both on land and in the ocean. Martinus Beijerinck invented the enrichment culture, a fundamental method of studying microbes from the environment. He is often incorrectly credited with framing the microbial biogeographic idea that "everything is everywhere, but, the environment selects", which was stated by Lourens Baas Becking. 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.
Beijerinck 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.
Progress in microbial ecology has been tied to development of new technologies. The measurement of biogeochemical process rates in nature was driven by the availability of radioisotopes beginning in the 1950s. For example, 14CO2 allowed analysis of rates of photosynthesis in the ocean (ref). Another significant breakthrough came in the 1980s, when microelectrodes sensitive to chemical species like O2 were developed. These electrodes have a spatial resolution of 50–100 μm, and have allowed analysis of spatial and temporal biogeochemical dynamics in microbial mats and sediments.
Although measuring biogeochemical process rates could analyze what processes were occurring, they were incomplete because they provided no information on which specific microbes were responsible. It was long known that ‘classical’ cultivation techniques recovered fewer than 1% of the microbes from a natural habitat. However, beginning in the 1990s, a set of cultivation-independent techniques have evolved to determine the relative abundance of microbes in a habitat. Carl Woese first demonstrated that the sequence of the 16S ribosomal RNA molecule could be used to analyze phylogenetic relationships. Norm Pace took this seminal idea and applied it to analyze ‘who's there’ in natural environments. The procedure involves (a) isolation of nucleic acids directly from a natural environment, (b) PCR amplification of small subunit rRNA gene sequences, (c) sequencing the amplicons, and (d) comparison of the those sequences to a database of sequences from pure cultures and environmental DNA. This has provided tremendous insights into the diversity present within microbial habitats. However, it does not resolve how to link specific microbes to their biogeochemical role. Metagenomics, the sequencing of total DNA recovered from an environment, can provide insights into biogeochemical potential, whereas metatranscriptomics and metaproteomics can measure actual expression of genetic potential but remains more technically difficult.