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United States Department of Agriculture

Agricultural Research Service

Title: Identifying the Fundamental Units of Bacterial Diversity: A Paradigm Shift to Incorporate Ecology into Bacterial Systematics)

Author
item Koeppel, Alexander
item Perry, Elizabeth
item Sikorski, Johannes
item Krizanc, Danny
item Warner, Andrew
item Ward, David
item Rooney, Alejandro - Alex
item Brambilla, Evelyne
item Connor, Nora
item Ratcliff, Rodney
item Nevo, Eviatar
item Cohan, Frederick

Submitted to: Proceedings of the National Academy of Sciences
Publication Type: Peer reviewed journal
Publication Acceptance Date: 1/10/2008
Publication Date: 2/19/2008
Citation: Koeppel, A., Perry, E., Sikorski, J., Krizanc, D., Warner, A., Ward, D.M., Rooney, A.P., Brambilla, E., Connor, N., Ratcliff, R.M., Nevo, E., Cohan, F.M. 2008. Identifying the Fundamental Units of Bacterial Diversity: A Paradigm Shift to Incorporate Ecology into Bacterial Systematics. Proceedings of the National Academy of Sciences. 105(7):2504-2509.

Interpretive Summary: In this paper, we describe a new method for identifying the number of ecologically distinct populations of bacteria present in various environmental and clinical samples. Identifying how many such populations exist within a particular clinical or environmental sample is of the utmost importance for agriculture, public health, and human and veterinary medicine, as these distinct populations represent different species that must each be treated with a unique control or monitoring strategy.

Technical Abstract: How many ecologically distinct populations of bacteria are in a natural community, who are they, and what differences allow them to coexist or perform different ecosystem functions? These central questions of bacterial ecology and systematics require a method to consistently demarcate, from the vast and diverse set of bacterial cells within a natural community, the groups playing ecologically distinct roles. In principle, surveys of sequence diversity can be used to demarcate bacteria into ecologically distinct groups forming irreversibly separate evolutionary lineages (ecotypes), but bacterial systematics has yet to provide a general method for doing so. Here we propose and test a conceptual framework, based on the evolutionary dynamics of bacterial populations, for using sequence data to estimate the number of ecotypes within a natural community and to identify them. The power of this ‘community phylogeny’ approach to demarcate ecotypes was demonstrated through analysis of Bacillus in ‘Evolution Canyon’ of the Negev Desert, Synechococcus in Yellowstone hot springs, and Legionella pneumophila from clinical and environmental samples. Within each system, community phylogeny identified numerous putative ecotypes, each predicted to have a history of coexistence with other such groups as an ecologically distinct lineage. Several such groups were corroborated independently as ecologically distinct through ecological data. Ecotypes demonstrated in this way to have a history of coexistence based on sequence analysis, as well as a prognosis for future coexistence based on ecological distinctness, can be considered the fundamental units of bacterial evolution, ecology, and systematics. Community phylogeny offers the first glimpse of rates of ecotype formation and ‘periodic selection’ events (which purge the diversity within ecotypes) in nature, allowing for tests of how a taxon’s history and lifestyle might determine its evolutionary rates.

Last Modified: 8/24/2016
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