Abstract
The Halobacteria are known to engage in frequent gene transfer and homologous recombination. For stably diverged lineages to persist some checks on the rate of between lineage recombination must exist. We surveyed a group of isolates from the Aran-Bidgol endorheic lake in Iran and sequenced a selection of them. Multilocus Sequence Analysis (MLSA) and Average Nucleotide Identity (ANI) revealed multiple clusters (phylogroups) of organisms present in the lake. Patterns of intein and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) presence/absence and their sequence similarity, GC usage along with the ANI and the identities of the genes used in the MLSA revealed that two of these clusters share an exchange bias toward others in their phylogroup while showing reduced rates of exchange with other organisms in the environment. However, a third cluster, composed in part of named species from other areas of central Asia, displayed many indications of variability in exchange partners, from within the lake as well as outside the lake. We conclude that barriers to gene exchange exist between the two purely Aran-Bidgol phylogroups, and that the third cluster with members from other regions is not a single population and likely reflects an amalgamation of several populations.
Highlights
Besides an obligate requirement for high concentrations of NaCl, a unifying trait of Halobacteria—a class within the archaeal phylum Euryarchaeota, is their propensity for horizontal gene transfer (HGT) (Legault et al, 2006; Rhodes et al, 2011; Nelson-Sathi et al, 2012; Williams et al, 2012)
HGTs from bacterial lineages into the Halobacteria occurred before their last common ancestor and brought respiration and nutrient transport genes that transformed them from a methanogen to their current aerobic heterotrophic state (NelsonSathi et al, 2012)
Measurements of frequency across the breadth of halobacterial diversity indicates no absolute barrier to homologous recombination; rather between relatives, there is a log-linear decay in recombination frequency relative to phylogenetic distance (Williams et al, 2012)
Summary
Besides an obligate requirement for high concentrations of NaCl, a unifying trait of Halobacteria (often referred to colloquially as the haloarchaea)—a class within the archaeal phylum Euryarchaeota, is their propensity for horizontal gene transfer (HGT) (Legault et al, 2006; Rhodes et al, 2011; Nelson-Sathi et al, 2012; Williams et al, 2012). HGTs from bacterial lineages into the Halobacteria occurred before their last common ancestor and brought respiration and nutrient transport genes that transformed them from a methanogen to their current aerobic heterotrophic state (NelsonSathi et al, 2012). The study of recombination frequency among this class has been utilized to address population genetics questions that address whether they are clonal (i.e., linked alleles at different loci) or “sexual” in the sense that alleles at different loci are randomly associated. Within phylogroups where genetic diversity was less than one percent divergent for protein coding genes, alleles at different loci were randomly associated whereas between phylogroups they were not (Papke et al, 2007) indicating haloarchaea are highly sexual. Measurements of frequency across the breadth of halobacterial diversity indicates no absolute barrier to homologous recombination; rather between relatives, there is a log-linear decay in recombination frequency relative to phylogenetic distance (Williams et al, 2012)
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