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Intragenomic Heterogeneity and Intergenomic Recombination among Haloarchaeal rRNA Genes. Yan Boucher, 2004.More than one copy of rRNA operons, which code for both the small-subunit (SSU) and large-subunit (LSU) rRNA, are often found in prokaryotes . It is generally assumed that all rRNA operons within a single cell are almost identical . A notable exception is the extremely halophilic archaeal genus Haloarcula, most species of which are known to harbor highly divergent rRNA operons that differ at  5%
of the nucleotide positions in the SSU gene and at 1 to 2% of the
nucleotide positions in the LSU gene . We report that such
intragenomic heterogeneity is not unique to Haloarcula, as
high levels of intragenomic sequence variation have been observed for
the SSU genes of two other genera of extreme halophiles,
Halosimplex and Natrinema . To investigate this in detail,
the two rRNA operons of Halosimplex carlsbadense and the four
operons of Natrinema sp . strain XA3-1 were cloned and
completely sequenced . The SSU and LSU genes of H . carlsbadense
show the highest levels of intragenomic heterogeneity observed so far
in archaea (6.7 and 2.6%) . The operons of Natrinema sp . strain
XA3-1 have additional unusual characteristics, such as identical
internal transcribed spacers, while one of four SSU genes is 5%
divergent and all LSU genes differ from each other by 0.9 to 1.9% .
The heterogeneity among the Natrinema sp . strain XA3-1 LSU
genes is localized in hot spots, and one of these regions is shown to
be the result of a recombination event with a distantly related
halophile . This is the first example of interspecies recombination
between rRNA genes in archaea, and the recombination occurred over
one of the largest phylogenetic distances ever reported for such an
event . We suggest that intragenomic heterogeneity of rRNA operons is
an ancient and stable trait in several lineages of the
Halobacteriales . The impact of this phenomenon on the taxonomy of
extremely halophilic archaea is discussed .
Issues in Pharmacokinetics and Pharmacodynamics of Anti-Infective Agents: Distribution in Tissue. Markus Müller, 2004. Autoinducer 2 Production by Streptococcus gordonii DL1 and the Biofilm Phenotype of a luxS Mutant Are Influenced by Nutritional Conditions. David S. Blehert, 2003.The luxS gene, present in many bacterial genera, encodes the autoinducer 2 (AI-2) synthase . AI-2 has been implicated in bacterial signaling, and this study investigated its role in biofilm formation by Streptococcus gordonii, an organism that colonizes human tooth enamel within the first few hours after professional cleaning . Northern blotting and primer extension analyses revealed that S . gordonii luxS is monocistronic . AI-2 production was dependent on nutritional conditions, and maximum AI-2 induction was detected when S . gordonii was grown in the presence of serum and carbonate . In planktonic cultures, AI-2 production rose sharply during the transition from exponential to stationary phase, and the AI-2 concentration peaked approximately 4 h into stationary phase . An S . gordonii luxS mutant that did not produce AI-2 was constructed by homologous recombination . Complementation of the mutant by insertion of an intact luxS gene into the chromosome in tandem with the disrupted gene restored AI-2 production to a level similar to that of the wild-type strain . In planktonic culture, no growth differences were observed between the mutant and wild-type strains when five different media were used . However, when grown for 4 h as biofilms in 25% human saliva under flow, the luxS mutant formed tall microcolonies that differed from those formed by the wild-type and complemented mutant strains . Biofilms of the luxS mutant exhibited finger-like projections of cells that extended into the flow cell lumen . Thus, the inability to produce AI-2 is associated with altered microcolony architecture within S . gordonii biofilms formed in saliva during a time frame consistent with initial colonization of freshly cleaned enamel surfaces . Geographical Variation in Ribotype Profiles of Escherichia coli Isolates from Humans, Swine, Poultry, Beef, and Dairy Cattle in Florida. Troy M. Scott, 2003.Waters impacted by fecal pollution can exact high risks to human health and can result in financial losses due to closures of water systems used for recreation and for harvesting seafood . Identifying the sources of fecal pollution in water is paramount in assessing the potential human health risks involved as well as in assessing necessary remedial action . Recently, various researchers have used the ribotyping method to identify sources of bacterial indicators (Escherichia coli and enterococci) in environmental waters . While these studies have identified genotypic differences between human- and animal-derived indicators that are capable of differentiating organisms isolated from humans and various animal hosts, most have focused on organisms collected from a confined geographic area and have not addressed the question of whether these ribotype profiles are watershed specific or if they can be applied universally to organisms from other geographic locations . In this study, E . coli isolates were obtained from humans, beef cattle, dairy cattle, swine, and poultry from locations in northern, central, and southern Florida and were subjected to ribotyping analysis . The intent was to determine (i) if ribotype profiles are capable of discriminating the source of E . coli at the host species level and (ii) if the resulting fingerprints are uniform over an extended geographic area or if they can be applied only to a specific watershed . Our research indicated that, using a single restriction enzyme (HindIII), the ribotyping procedure is not capable of differentiating E . coli isolates from the different animal species sampled in this study . Results indicate, however, that this procedure can still be used effectively to differentiate E . coli as being either human or animal derived when applied to organisms isolated from a large geographic region . Members of a Readily Enriched ß-Proteobacterial Clade Are Common in Surface Waters of a Humic Lake. Ulrike Burkert, 2003.Humic lakes are systems often characterized by irregular high input of dissolved organic carbon (DOC) from the catchment . We hypothesized that specific bacterial groups which rapidly respond to changes in DOC availability might form large populations in such habitats . Seasonal changes of microbial community composition were studied in two compartments of an artificially divided bog lake with contrasting DOC inputs . These changes were compared to community shifts induced during short-term enrichment experiments . Inocula from the two compartments were diluted 1:10 into water from the more DOC-rich compartment, and inorganic nutrients were added to avoid microbial N and P limitation . The dilutions were incubated for a period of 2 weeks . The microbial assemblages were analyzed by cloning and sequencing of 16S rRNA genes and by fluorescence in situ hybridization with specific oligonucleotide probes . ß-Proteobacteria from a cosmopolitan freshwater lineage related to Polynucleobacter necessarius (beta II) were rapidly enriched in all treatments . In contrast, members of the class Actinobacteria did not respond to the enhanced availability of DOC by an immediate increase in growth rate, and their relative abundances declined during the incubations . In lake water members of the beta II clade seasonally constituted up to 50% of all microbes in the water column . Bacteria from this lineage annually formed a significantly higher fraction of the microbial community in the lake compartment with a higher allochthonous influx than in the other compartment . Actinobacteria represented a second numerically important bacterioplankton group, but without clear differences between the compartments . We suggest that the pelagic microbial community of the studied system harbors two major components with fundamentally different growth strategies .
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