Searching for species in haloarchaea

doi:10.1073/pnas.0706358104

Searching for species in haloarchaea

*Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269-3125;
^†Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS, Canada B3H 1X5; and
^‡Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom

Contributed by W. Ford Doolittle, July 10, 2007 (received for review June 1, 2007)

Abstract

Prokaryotic (bacterial and archaeal) species definitions and the biological concepts that underpin them entail clustering (cohesion) among individuals, in terms of genome content and gene sequence similarity. Homologous recombination can maintain gene sequence similarity within, while permitting divergence between, clusters and is thus the basis for recent efforts to apply the Biological Species Concept in prokaryote systematics and ecology. In this study, we examine isolates of the haloarchaeal genus Halorubrum from two adjacent ponds of different salinities at a Spanish saltern and a natural saline lake in Algeria by using multilocus sequence analysis. We show that, although clusters can be defined by concatenation of multiple marker sequences, barriers to exchange between them are leaky. We suggest that no nonarbitrary way to circumscribe “species” is likely to emerge for this group, or by extension, to apply generally across prokaryotes. Arbitrary criteria might have limited practical use, but still must be agreed upon by the community.

Footnotes

^§To whom correspondence should be addressed. E-mail: ford{at}dal.ca
Author contributions: R.T.P. designed research; R.T.P., O.Z., K.S., and D.M. performed research; R.T.P., O.Z., E.J.F., and W.F.D. analyzed data; and R.T.P., O.Z., E.J.F., and W.F.D. wrote the paper.
The authors declare no conflict of interest.
Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. AM777162–AM777382 and AM777425–AM777776).
This article contains supporting information online at www.pnas.org/cgi/content/full/0706358104/DC1.
Abbreviations:

BSC,

Biological Species Concept;

HR,

homologous recombination;

ST,

sequence type;

MLSA,

multilocus sequence analysis;

SLV,

single locus variant.