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BIOLOGICAL SCIENCES / ECOLOGY
Genome dynamics in a natural archaeal population
Departments of *Environmental Science, Policy, and Management and ||Earth and Planetary Science, University of California, Berkeley, CA 94720; and ¶Department of Energy Joint Genome Institute, Walnut Creek, CA 94598
Edited by James M. Tiedje, Michigan State University, East Lansing, MI, and approved November 30, 2006 (received for review June 9, 2006)
Evolutionary processes that give rise to, and limit, diversification within strain populations can be deduced from the form and distribution of genomic heterogeneity. The extent of genomic change that distinguishes the acidophilic archaeon Ferroplasma acidarmanus fer1 from an environmental population of the same species from the same site, fer1(env), was determined by comparing the 1.94-megabase (Mb) genome sequence of the isolate with that reconstructed from 8 Mb of environmental sequence data. The fer1(env) composite sequence sampled 
92% of the isolate genome. Environmental sequence data were also analyzed to reveal genomic heterogeneity within the coexisting, coevolving fer1(env) population. Analyses revealed that transposase movement and the insertion and loss of blocks of novel genes of probable phage origin occur rapidly enough to give rise to heterogeneity in gene content within the local population. Because the environmental DNA was derived from many closely related individuals, it was possible to quantify gene sequence variability within the population. All but a few gene variants show evidence of strong purifying selection. Based on the small number of distinct sequence types and their distribution, we infer that the population is undergoing frequent genetic recombination, resulting in a mosaic genome pool that is shaped by selection. The larger genetic potential of the population relative to individuals within it and the combinatorial process that results in many closely related genome types may provide the basis for adaptation to environmental fluctuations.
Archaea | Ferroplasma | population genomics | recombination
Present address: Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093.
Present address: Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139.
Present address: Department of Microbiology, University of Illinois, Urbana, IL 61801.
The authors declare no conflict of interest.
This article is a PNAS direct submission.
Data deposition: Accession numbers for the community genomic data are AADL01000000 and AADL00000000. The Ferroplasma acidarmanus fer1 genome data associated with this study have been deposited in the GenBank database (accession no. AABC05000000).
This article contains supporting information online at www.pnas.org/cgi/content/full/0604851104/DC1.
Alpers, C. N., Nordstrom, D. K., Verosub, K. L., Helm, C. M. (1999) Geological Society of America Cordilleran Section Centennial Meeting, Abstracts with Programs, Vol. 31, No. 6, p. A-33 (abstr).
**To whom correspondence should be addressed. E-mail: jill{at}eps.berkeley.edu
© 2007 by The National Academy of Sciences of the USA
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