User:Estevezj/sandbox/microbialecology

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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.[1]

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.[2][3] As a consequence of the quantitative magnitude of microbial life (Whitman and coworkers calculated 5 × 10 30 cells, eight orders of magnitude greater than the number of stars in the observable universe [4][5] ) microbes, by virtue of their biomass alone, constitute the single largest carbon sink.[6] Aside from carbon fixation, microorganisms’ key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling.[7] The immensity of microorganisms’ production is such that, even in the total absence of eukaryotic life these processes would likely continue unchanged.[8]

History[edit]

While microbes have been studied since the seventeenth-century, this research was from a primarily physiolocal perspective rather than an ecological one.[9] 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 Becking.[10] 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.[11]

Beijirnck and Windogradsky, however, were focused on the physiology of microorganisms, not the microbial habitat or their ecological interactions.[9] 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.[9]

Principles of microbial ecology[edit]

Who, what, where?

Diversity[edit]

The great plate count anomaly. Counts of cells obtained via cultivation are orders of magnitude lower than those directly observed via microscope. This is because microbiologists are able to cultivate only 1% of microbes using current techniques.[12]

Metabolic diversity[edit]

  • Metabolic redundancy

Phylogenetic diversity[edit]

  • Bottom-up control

Abundance[edit]

Microbial biomass[edit]

Population levels and catalytic activity[edit]

Vollenweider model[edit]

Distribution[edit]

Spatial scales[edit]

Ecosystem types[edit]

Evolution[edit]

Symbiosis[edit]

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.

Diversity[edit]

Roles[edit]

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.[6] 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,[13] microbial ecology is also of importance to studies of evolution.[14]

Biogeochemical catalysis[edit]

Microbial resource management[edit]

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.[15] 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.[16]

Methods[edit]

Descriptive[edit]

In situ[edit]

Microcosms[edit]

Model laboratory systems[edit]

  • Lab rats

Omics approaches[edit]

Theoretical[edit]

See also[edit]

References[edit]

  1. ^ Ogilvie, LA; Hirsch, PR (editor) (2012). Microbial Ecological Theory: Current Perspectives. Caister Academic Press. ISBN 978-1-908230-09-6. {{cite book}}: |author= has generic name (help)CS1 maint: multiple names: authors list (link)
  2. ^ Bowler, C. (2009). "Microbial oceanography in a sea of opportunity". Nature. 458 (7244): 180–184. doi:10.1038/nature08056. PMID 19444203. S2CID 4426467. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)(subscription required)
  3. ^ Konopka, Allan (November 2009). "What is microbial community ecology?". The ISME Journal. 3 (11): 1223–1230. doi:10.1038/ismej.2009.88. ISSN 1751-7370. PMID 19657372. S2CID 7213233. Retrieved 2011-02-27.
  4. ^ Whitman, William B.; Coleman, David C.; Wiebe, William J. (1998-06-09). "Prokaryotes: the unseen majority". Proceedings of the National Academy of Sciences of the United States of America. 95 (12): 6578–6583. doi:10.1073/pnas.95.12.6578. ISSN 0027-8424. PMC 33863. PMID 9618454.
  5. ^ "number of stars in the observable universe - Wolfram". Retrieved 2011-11-22. {{cite web}}: Text "Alpha" ignored (help)
  6. ^ a b Fenchel, Tom (1998). Bacterial biogeochemistry : the ecophysiology of mineral cycling (2nd ed.). San Diego: Academic Press.
  7. ^ DeLong, Edward F. (May 2009). "The microbial ocean from genomes to biomes". Nature. 459 (7244): 200–206. doi:10.1038/nature08059. hdl:1721.1/69838. ISSN 0028-0836. PMID 19444206. S2CID 205216984.(subscription required)
  8. ^ Lupp, Claudia (May 2009). "Microbial oceanography". Nature. 459 (7244): 179. doi:10.1038/459179a. PMID 19444202. S2CID 205046443.(subscription required)
  9. ^ a b c Konopka, A. (2009). "Ecology, Microbial". In Moselio Schaechter (ed.) (ed.). Encyclopedia of Microbiology (Third ed.). Oxford: Academic Press. pp. 91–106. ISBN 978-0-12-373944-5. Retrieved 2013-01-12. {{cite book}}: |editor= has generic name (help)
  10. ^ de Wit R, Bouvier T. (2006). "Everything is everywhere, but, the environment selects'; what did Baas Becking and Beijerinck really say?". Environmental Microbiology. 8 (4): 755–758. doi:10.1111/j.1462-2920.2006.01017.x. PMID 16584487. Retrieved 2008-09-16.
  11. ^ Madigan, Michael T. (2012). Brock biology of microorganisms (13th ed.). San Francisco: Benjamin Cummings. ISBN 9780321649638.
  12. ^ Staley, J. T.; Konopka, A. (1985). "Measurement of in Situ Activities of Nonphotosynthetic Microorganisms in Aquatic and Terrestrial Habitats". Annual Review of Microbiology. 39: 321–346. doi:10.1146/annurev.mi.39.100185.001541. PMID 3904603.
  13. ^ McDaniel, Lauren D.; Young, Elizabeth; Delaney, Jennifer; Ruhnau, Fabian; Ritchie, Kim B.; Paul, John H. (2010-10-01). "High Frequency of Horizontal Gene Transfer in the Oceans". Science. 330 (6000): 50. doi:10.1126/science.1192243. PMID 20929803. S2CID 45402114.(subscription required)
  14. ^ Smets, B. F (2005). "Horizontal gene transfer: perspectives at a crossroads of scientific disciplines". Nature Reviews Microbiology. 3 (9): 675–678. doi:10.1038/nrmicro1253. PMID 16145755. S2CID 2265315. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)(subscription required)
  15. ^ W. Verstraete (May 2007). "Microbial ecology and environmental biotechnology". The ISME Journal. 1 (1): 4–8. doi:10.1038/ismej.2007.7. PMID 18043608. S2CID 3340578.{{cite journal}}: CS1 maint: date and year (link)(subscription required)
  16. ^ Ott, J. (2005). "Marine Microbial Thiotrophic Ectosymbioses". Oceanography and Marine Biology. 42: 95–118.
  17. ^ Hugenholtz, P. (2002). "Exploring prokaryotic diversity in the genomic era". Genome Biology. 3 (2): reviews0003.reviews0001. doi:10.1186/gb-2002-3-2-reviews0003. PMC 139013. PMID 11864374.{{cite journal}}: CS1 maint: unflagged free DOI (link)

External links[edit]

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