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Microbial ecology

From Wikipedia, the free encyclopedia

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]
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]

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  • Microbial Ecology (MBI 475/575)
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  • Professor Margaret McFall-Ngai - Environmental Microbiology Annual Lecture 2016
  • Our ancient microbial self: the evolutionary ecology of the microbiome | Christina Warinner
  • UTS Science in Focus: Marine Microbes: The Ocean's Lifeblood?


>> DR. RACHAEL MORGAN-KISS: In addition to the opportunity within our laboratory for research for our undergraduates and graduates, we have integrated our Antarctic samples into a new course in microbial ecology. The students within this course are senior undergraduates and graduate students and they will be working directly with the samples we've collected from Antarctica. So they will have the opportunity to learn top-level molecular biology techniques as well as the ability to cultivate uncultivate-able or difficult to culture microorganisms from an extreme environment. This is really exciting for the students who ... of course, not all of them have the possibility to go to Antarctica ... They learn new techniques and this work is novel. Nobody has ever worked with these samples before, and so the students are aware of that ... that they're really on the cutting edge of designing science projects on samples which have never been studied before. >> DR. ANNETTE BOLLMANN: We taught them molecular techniques. That includes DNA isolation, PCR and sequencing. And we will, in the next weeks, still teach them how to evaluate those data, and that is a big part of the class is also the data evaluation rather than just obtaining data. In addition, we will teach them how to cultivate microorganisms and how to inoculate growth experiments, experiments where they test how they grow, under which conditions, and then how also to evaluate the data from those experiments. I think this class offers to the students a very unique possibility because they learn really cutting-edge background science, theoretical knowledge. We incorporate a lot of really recent publications into our lectures and so on. And then they will use that knowledge and transfer it to the lab. They develop their own research projects for the lab. They then do research with the newest techniques and the evaluation of the data. The benefit is that the students work on samples that are very unique. It is a big benefit, of course, for us because they are very, very excited about the opportunity they have. We are very excited about giving them the opportunity. And they will learn modern techniques, microbial ecology on really these unique Antarctic samples.



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]:644

Beijerinck 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]


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]


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 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 (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]


Some metals, particularly copper and silver, have antimicrobial properties. Using antimicrobial copper-alloy touch surfaces is a technique which has begun to be used in the 21st century to prevent transmission of bacteria.[34] Silver nanoparticles have also begun to be incorporated into building surfaces and fabrics, although concerns have been raised about the potential side-effects of the tiny particles on human health.[35]

See also


  1. ^ Hugenholtz, P. (2002). "Exploring prokaryotic diversity in the genomic era". Genome Biology. 3 (2): reviews0003.reviews0001–reviews0003.reviews0001. doi:10.1186/gb-2002-3-2-reviews0003. PMC 139013. PMID 11864374.
  2. ^ Barton, Larry L.; Northup, Diana E. (9 September 2011). Microbial Ecology. Wiley-Blackwell. Oxford: John Wiley & Sons. p. 22. ISBN 978-1-118-01582-7. Retrieved 25 May 2013.
  3. ^ Bowler, Chris; Karl, David M.; Colwell, Rita R. (2009). "Microbial oceanography in a sea of opportunity". Nature. 459 (7244): 180–4. Bibcode:2009Natur.459..180B. doi:10.1038/nature08056. PMID 19444203.
  4. ^ Konopka, Allan (2009). "What is microbial community ecology?". The ISME Journal. 3 (11): 1223–30. doi:10.1038/ismej.2009.88. PMID 19657372.
  5. ^ Whitman, W. B.; Coleman, DC; Wiebe, WJ (1998). "Prokaryotes: The unseen majority". Proceedings of the National Academy of Sciences. 95 (12): 6578–83. Bibcode:1998PNAS...95.6578W. doi:10.1073/pnas.95.12.6578. JSTOR 44981. PMC 33863. PMID 9618454.
  6. ^ "number of stars in the observable universe - Wolfram|Alpha". Retrieved 2011-11-22.
  7. ^ Reddy, K. Ramesh; DeLaune, Ronald D. (15 July 2004). Biogeochemistry of Wetlands: Science and Applications. Boca Raton: Taylor & Francis. p. 116. ISBN 978-0-203-49145-4. Retrieved 25 May 2013.
  8. ^ Delong, Edward F. (2009). "The microbial ocean from genomes to biomes". Nature. 459 (7244): 200–6. Bibcode:2009Natur.459..200D. doi:10.1038/nature08059. PMID 19444206.
  9. ^ Lupp, Claudia (2009). "Microbial oceanography". Nature. 459 (7244): 179. Bibcode:2009Natur.459..179L. doi:10.1038/459179a. PMID 19444202.
  10. ^ a b c Konopka, A. (2009). "Ecology, Microbial". Encyclopedia of Microbiology. pp. 91–106. doi:10.1016/B978-012373944-5.00002-X. ISBN 978-0-12-373944-5.
  11. ^ Adler, Antony; Dücker, Erik (2017-04-05). "When Pasteurian Science Went to Sea: The Birth of Marine Microbiology". Journal of the History of Biology. 51: 1–27. doi:10.1007/s10739-017-9477-8. ISSN 0022-5010.
  12. ^ De Wit, Rutger; Bouvier, Thierry (2006). "'Everything is everywhere, but, the environment selects'; what did Baas Becking and Beijerinck really say?". Environmental Microbiology. 8 (4): 755–8. doi:10.1111/j.1462-2920.2006.01017.x. PMID 16584487.
  13. ^ Madigan, Michael T. (2012). Brock biology of microorganisms (13th ed.). San Francisco: Benjamin Cummings. ISBN 9780321649638.
  14. ^ Fenchel, Tom; Blackburn, Henry; King, Gary M. (24 July 2012). Bacterial Biogeochemistry: The Ecophysiology of Mineral Cycling (3 ed.). Boston, Mass.: Academic Press/Elsevier. p. 3. ISBN 978-0-12-415974-7. Retrieved 25 May 2013.
  15. ^ McDaniel, L. D.; Young, E.; Delaney, J.; Ruhnau, F.; Ritchie, K. B.; Paul, J. H. (2010). "High Frequency of Horizontal Gene Transfer in the Oceans". Science. 330 (6000): 50. Bibcode:2010Sci...330...50M. doi:10.1126/science.1192243. PMID 20929803.
  16. ^ Smets, Barth F.; Barkay, Tamar (2005). "Horizontal gene transfer: Perspectives at a crossroads of scientific disciplines". Nature Reviews Microbiology. 3 (9): 675–8. doi:10.1038/nrmicro1253. PMID 16145755.
  17. ^ a b c L., Kirchman, David (2012). Processes in microbial ecology. Oxford: Oxford University Press. ISBN 9780199586936. OCLC 777261246.
  18. ^ López-García, Purificación; Eme, Laura; Moreira, David (2017-12-07). "Symbiosis in eukaryotic evolution". Journal of Theoretical Biology. The origin of mitosing cells: 50th anniversary of a classic paper by Lynn Sagan (Margulis). 434 (Supplement C): 20–33. doi:10.1016/j.jtbi.2017.02.031.
  19. ^ I., Krasner, Robert (2010). The microbial challenge : science, disease, and public health (2nd ed.). Sudbury, Mass.: Jones and Bartlett Publishers. ISBN 978-0763756895. OCLC 317664342.
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  23. ^ García, Cristina; Rendueles, Manuel; Díaz, Mario (September 2017). "Synbiotic Fermentation for the Co-Production of Lactic and Lactobionic Acids from Residual Dairy Whey". Biotechnology Progress. 33 (5): 1250–1256. doi:10.1002/btpr.2507. PMID 28556559.
  24. ^ I., Krasner, Robert (2010). The microbial challenge : science, disease, and public heatlh (2nd ed.). Sudbury, Mass.: Jones and Bartlett Publishers. ISBN 9780763756895. OCLC 317664342.
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This page was last edited on 4 October 2018, at 07:59
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