The great plate count anomaly. Counts of cells obtained via cultivation
are orders of magnitude lower than those directly observed under the
microscope. This is because microbiologists are able to cultivate only a
minority of naturally occurring microbes using current laboratory
techniques, depending on the environment.[1]
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.[2]
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.[3][4] 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[5][6]) microbes, by virtue of their biomass alone, constitute a significant carbon sink.[7] Aside from carbon fixation, microorganisms' key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling.[8] The immensity of microorganisms' production is such that, even in the total absence of eukaryotic life, these processes would likely continue unchanged.[9]
History
While microbes have been studied since the seventeenth-century, this research was from a primarily physiological perspective rather than an ecological one.[10] For instance, Louis Pasteur and his disciples were interested in the problem of microbial distribution both on land and in the ocean.[11] 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.[12] 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.[13]:644Beijerinck and Windogradsky, however, were focused on the physiology of microorganisms, not the microbial habitat or their ecological interactions.[10] 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.[10]
Roles
Microorganisms are the backbone of all ecosystems, but even more so in the zones where photosynthesis is unable to take place because of the absence of light. 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.[14] The nitrogen cycle, the phosphorus cycle, the sulphur cycle and the carbon cycle all depend on microorganisms in one way or another. For example, the nitrogen gas which makes up 78% of the earth's atmosphere is unavailable to most organisms, until it is converted to a biologically available form by the microbial process of nitrogen fixation.
Due to the high level of horizontal gene transfer among microbial communities,[15] microbial ecology is also of importance to studies of evolution.[16]
Symbiosis
Microbes, especially bacteria, often engage in symbiotic relationships (either positive or negative) with other microorganisms or larger organisms. Although physically small, symbiotic relationships amongst microbes are significant in eukaryotic processes and their evolution.[17][18] The types of symbiotic relationship that microbes participate in include mutualism, commensalism, parasitism,[19] and amensalism,[20] and these relationships affect the ecosystem in many ways.Mutualism
Mutualism in microbial ecology is a relationship between microbial species and between microbial species and humans that allow for both sides to benefit.[21] One such example would be syntrophy, also known as cross-feeding,[20] which is clearly shown in Methanobacterium omelianskii. Although initially thought of as one microbial species, this system is actually two species - an S organism and Methabacterium bryantii. The S organism provides the bacterium with the H2, which the bacterium needs in order to grow and produce methane.[17][22] The reaction used by the S organism for the production of H2 is endergonic (and so thermodynamically unfavored) however, when coupled to the reaction used by Methabacterium bryantii in its production of methane, the overall reaction becomes exergonic.[17] Thus the two organisms are in a mutualistic relationship which allows them to grow and thrive in an environment, deadly for either species alone. Lichen is an example of a symbiotic organism.[22]Amensalism
Amensalism (also commonly known as antagonism) is a type of symbiotic relationship where one species/organism is harmed while the other remains unaffected.[21] One example of such a relationship that takes place in microbial ecology is between the microbial species Lactobacillus casei and Pseudomonas taetrolens.[23] When co-existing in an environment, Pseudomonas taetrolens shows inhibited growth and decreased production of lactobionic acid (its main product) most likely due to the byproducts created by Lactobacillus casei during its production of lactic acid.[24] However, Lactobacillus casei shows no difference in its behaviour, and such this relationship can be defined as amensalism.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 has to be better characterized for this field's potential to be realised.[25] 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.[26]In built environment and human interaction
Microbes exist in all areas, including homes, offices, commercial centers, and hospitals. In 2016, the journal Microbiome published a collection of various works studying the microbial ecology of the built environment.[27]A 2006 study of pathogenic bacteria in hospitals found that their ability to survive varied by the type, with some surviving for only a few days while others survived for months.[28]
The lifespan of microbes in the home varies similarly. Generally bacteria and viruses require a wet environment with a humidity of over 10 percent.[29] E. coli can survive for a few hours to a day.[29] Bacteria which form spores can survive longer, with Staphylococcus aureus surviving potentially for weeks or, in the case of Bacillus anthracis, years.[29]
In the home, pets can be carriers of bacteria; for example, reptiles are commonly carriers of salmonella.[30]
S. aureus is particularly common, and asymptomatically colonizes about 30% of the human population;[31] attempts to decolonize carriers have met with limited success[32] and generally involve mupirocin nasally and chlorhexidine washing, potentially along with vancomycin and cotrimoxazole to address intestinal and urinary tract infections.[33]
