Rare biosphere

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Rare biosphere refers to diverse rare species of bacteria, adapted to environmental conditions that are not common today.

Microbial ecosystems[edit]

Schematic of the microbial loop.

Changes in the biodiversity of an ecosystem, whether marine or terrestrial, may affect its efficiency and function. Climate change or other anthropogenic perturbations can decrease productivity and disrupt global biogeochemical cycles. The possible ramifications of such changes are not well characterized or understood, and up to a point redundancy in an ecosystem may protect it from disruption.[1]

The dynamics of microbial ecosystems are tightly coupled to biogeochemical processes.[2] For example, in the marine microbial loop, bacteria decompose organics and recycle nutrients such as nitrogen for other organisms such as phytoplankton to use.[2] A reduction in recycled nitrogen would limit the production rate of phytoplankton, in turn limiting the growth of grazers, with effects throughout the food web and nitrogen cycle. To gauge such effects, a base line of microbial diversity is needed.

DNA sequencing[edit]

Recent use of high-throughput sequencing techniques, pioneered by Dr. Mitchell Sogin of the Marine Biological Laboratory, has broadened the scope of biodiversity, with the discovery of the rare biosphere.[3] Previous attempts to characterize in situ abundance have been made through pure culture and molecular techniques.[4] Pure culture providing a very narrow picture of some of the rarer species present, <1-5% of bacteria present.[4] Molecular techniques, such as Sanger sequencing, resulting in a much broader scope but highlighting the more abundant species present.[5][6] Neither technique captures all of the diversity present. Alternatively high throughput sequencing, “tag sequencing”, divides unique rRNA tag sequences into operational taxonomic units (OTUs) based upon similarities in mitochondrial-encoded cytochrome oxidases.[3] Both Sanger, shot gun sequencing, and tag sequencing organize sequences into OTUs.[5] However, it is the resolution that tag sequencing provides that sets it apart, resulting from the increased efficiency in serial analysis.[5] This efficiency increase is made possible through the use of internal primer sequences resulting in restriction digest overhanging sequences.[5] Though OTUs provide a means of distinguishing the possible number of phylogenetic groups, it is not possible to deduce phylogenetic relationships based upon OTU’s. Tags associated with OTUs must be cross-referenced with gene banks, in order for tags to be phylotyped and relationships established.[3]

The result of tag sequencing has been to produce orders of magnitude larger estimates of OTUs present in ecosystems, producing a long tail on species abundance curves.[7][6] This long tail accounts for less than .1% of the abundant species in a particular ecosystem. At the same time it represents thousands of populations accounting for most of the phylogenetic diversity in an ecosystem. This low-abundance high-diversity group is the rare biosphere. Using this method, Sogin et al.’s study of microbial diversity in North Atlantic deep water produced an estimate of 5266 different taxa.[3] This is particularly dramatic considering that previous studies employing more traditional PCR cloning techniques have resulted in estimates of up to 500.[6]

Ecological role[edit]

Considering their low abundance, members of the rare biosphere may represent ancient and persistent taxa.[3] As these less abundant species are limited in number viral infection, and ultimately death by lysis, is unlikely.[6] Viruses depend on high concentrations of hosts to persist. Additionally being less abundant implies limited growth, and on the smaller end of the cell size spectrum.[6] This limits the likelihood of death by ingestion, as grazers prefer larger more active microbes. As well it is important to note that just because these taxa are “rare” now does not mean that under previous conditions in our planet’s history they were “rare”.[3] These taxa could be have been episodically abundant, resulting in global changes in biogeochemical cycles.[3] Essentially this requires microbial ecologists to change their perspective on how microbial interactions function on evolutionary time scales.[3]

On that note, rare today does not mean rare tomorrow. Given the persistence of these taxa under the right conditions they have the potential to dominate, and become the more abundant taxa.[3] The occurrence of such conditions may occur on many temporal scales. It may be possible that some rare taxa dominate only during anomalous years, such as during El Niño.[4] While, a four-year study by Brown et al. in species abundance in a single marine ecosystem found that some taxa were undetectable during some months and accounted for a couple percent of the total abundance other months.[8] Indicating that a change in abundance may occur on a seasonal scale. Recent global climate change may provide some of these rare taxa with the conditions necessary to increase in abundance. Even in their low abundance taxa belonging to the rare biosphere may be affecting global biogeochemical cycles. For example, most of nitrogen fixation was attributed to Trichodesmium and abundant cyanobacterium. However, more recent evidence implicates that the rare minority may be responsible for fixing more cumulative Nitrogen than the abundant majority.[4]

A subtle and less direct manner these populations may be affecting ecosystems, in terms of biodiversity and biogeochemical cycles, is by acting as an unlimited source of genetic diversity and material.[4][3] How microbial communities present resilience after environmental perturbation or catastrophe and how closely a closely related species may present unique and novel genetic attributes compared to near relatives, are topics of much discussion and investigation.[3] The rare biosphere could be a seed bank, transferring genes resulting in fitter recombinants that rise to become the dominant majority.[3] Until now this group has been overlooked entirely, and may be the answer to many longstanding questions concerning microbial ecology and genetics.

Biogeography and distribution[edit]

There is some debate concerning the distribution of taxa within the rare biosphere. Taxa within this group at a given site may be in the process of dispersal.[4][7] Studies in the Arctic seabed identified thermophilic bacteria, arriving through mechanisms of dispersal, that could not be metabolically active.[7] Once these populations, such as the thermophilic bacteria in the Arctic, reach a suitable niche they will again become metabolically active and increase in abundance. This requires that one view these populations as non-discrete, not endemic to any one particular body of water.[7] Rather view populations as continuous throughout the oceans. Alternatively, studies suggest that given the biogeography of rare taxa the idea of the rare biosphere being the product of dispersal seems unlikely.[9] Galand et al. completed a study in the Arctic Ocean on the biogeography of the rare biosphere and found that between parcels of water within that ocean the rare biosphere presented a large amount of diversity.[9] Suggesting that populations within the rare biosphere experience evolutionary forces specific to the location they are found such as selection, speciation, and extinction.[9] Asserting that water masses have physical boundaries resulting in highly evolved and divergent taxa between rare biospheres from different locations.[9] Also, given the fact that many rare taxa cannot be identified in gene banks, it seems unlikely that they abundant elsewhere.[9] Though this statement is difficult to validate, due to the extreme under sampling of marine ecosystems.[5]


  1. ^ Gitay, Habiba; Suárez, Avelino; Dokken, David Jon; Watson, Robert T., eds. (April 2002). Climate Change and Biodiversity: IPCC Technical Paper V (PDF) (Report). Intergovernmental Panel on Climate Change.
  2. ^ a b Kirchman, David L., ed. (2008). Microbial Ecology of the Oceans (2nd ed.). Hoboken: John Wiley & Sons. ISBN 0470281839.
  3. ^ a b c d e f g h i j k l Sogin, M. L.; Morrison, H. G.; Huber, J. A.; Welch, D. M.; Huse, S. M.; Neal, P. R.; Arrieta, J. M.; Herndl, G. J. (31 July 2006). "Microbial diversity in the deep sea and the underexplored "rare biosphere"". Proceedings of the National Academy of Sciences. 103 (32): 12115–12120. doi:10.1073/pnas.0605127103.
  4. ^ a b c d e f Fuhrman, Jed A. (14 May 2009). "Microbial community structure and its functional implications". Nature. 459 (7244): 193–199. doi:10.1038/nature08058.
  5. ^ a b c d e Heidelberg, Karla B.; Gilbert, Jack A.; Joint, Ian (September 2010). "Marine genomics: at the interface of marine microbial ecology and biodiscovery". Microbial Biotechnology. 3 (5): 531–543. doi:10.1111/j.1751-7915.2010.00193.x. PMC 2948669.
  6. ^ a b c d e Pedros-Alío, C. (12 January 2007). "ECOLOGY: Dipping into the Rare Biosphere". Science. 315 (5809): 192–193. doi:10.1126/science.1135933.
  7. ^ a b c d Patterson, D. J. (17 September 2009). "Seeing the Big Picture on Microbe Distribution". Science. 325 (5947): 1506–1507. doi:10.1126/science.1179690.
  8. ^ Brown, Mark V.; Schwalbach, Michael S.; Hewson, Ian; Fuhrman, Jed A. (September 2005). "Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series". Environmental Microbiology. 7 (9): 1466–1479. doi:10.1111/j.1462-2920.2005.00835.x.
  9. ^ a b c d e Galand, P. E.; Casamayor, E. O.; Kirchman, D. L.; Lovejoy, C. (17 December 2009). "Ecology of the rare microbial biosphere of the Arctic Ocean" (PDF). Proceedings of the National Academy of Sciences. 106 (52): 22427–22432. doi:10.1073/pnas.0908284106.

Further reading[edit]

  • American Society for Microbiology (3 March 2017). "Importance of rare microbial species is much greater than you think". Science Daily. Retrieved 22 August 2017.
  • Reid, Ann; Buckley, Merry (2011). The Rare Biosphere (Report). Based on a colloquium convened by the American Academy of Microbiology on April 27–29, 2009 in San Francisco, CA. American Academy of Microbiology. |access-date= requires |url= (help)
  • Bachy, Charles; Worden, Alexandra Z. (April 2014). "Microbial Ecology: Finding Structure in the Rare Biosphere". Current Biology. 24 (8): R315–R317. doi:10.1016/j.cub.2014.03.029.
  • Corinaldesi, Cinzia (11 March 2015). "New perspectives in benthic deep-sea microbial ecology". Frontiers in Marine Science. 2. doi:10.3389/fmars.2015.00017.
  • Jousset, Alexandre; Bienhold, Christina; Chatzinotas, Antonis; Gallien, Laure; Gobet, Angélique; Kurm, Viola; Küsel, Kirsten; Rillig, Matthias C; Rivett, Damian W; Salles, Joana F; van der Heijden, Marcel G A; Youssef, Noha H; Zhang, Xiaowei; Wei, Zhong; Hol, W H Gera (10 January 2017). "Where less may be more: how the rare biosphere pulls ecosystems strings". The ISME Journal. 11 (4): 853–862. doi:10.1038/ismej.2016.174.
  • Kallmeyer, Jens; Wagner, Dirk (2013). Microbial Life of the Deep Biosphere. Berlin: de Gruyter. ISBN 9783110370676.
  • Lynch, Michael D. J.; Neufeld, Josh D. (2 March 2015). "Ecology and exploration of the rare biosphere". Nature Reviews Microbiology. 13 (4): 217–229. doi:10.1038/nrmicro3400.
  • Linnaeus University (4 July 2017). "Fungi are key players of the deep biosphere". Science Daily. Retrieved 22 August 2017.
  • Marine Biological Laboratory (2 September 2006). "Ocean microbe census discovers diverse world of rare bacteria". Science Daily. Retrieved 22 August 2017.
  • Nogales, Balbina; Lanfranconi, Mariana P.; Piña-Villalonga, Juana M.; Bosch, Rafael (March 2011). "Anthropogenic perturbations in marine microbial communities". FEMS Microbiology Reviews. 35 (2): 275–298. doi:10.1111/j.1574-6976.2010.00248.x.
  • Orcutt, Beth N.; LaRowe, Douglas E.; Biddle, Jennifer F.; Colwell, Frederick S.; Glazer, Brian T.; Reese, Brandi Kiel; Kirkpatrick, John B.; Lapham, Laura L.; Mills, Heath J.; Sylvan, Jason B.; Wankel, Scott D.; Wheat, C. Geoff (2013). "Microbial activity in the marine deep biosphere: progress and prospects". Frontiers in Microbiology. 4. doi:10.3389/fmicb.2013.00189.
  • Suttle, Curtis (April 2005). "The viriosphere: the greatest biological diversity on Earth and driver of global processes". Environmental Microbiology. 7 (4): 481–482. doi:10.1111/j.1462-2920.2005.803_11.x.