Prokaryotic rRNA Gene Research Articles

Composition of Eukaryotic and Prokaryotic rRNA Gene Phylotypes in Guts of Adults and Fingerlings of Mugil cephalus, Inhabiting an Egyptian Mediterranean Estuary

To understand the contribution of gut microflora to the feeding and health of Mugil cephalus in a Mediterranean estuary, we have explored and evaluated the diversity of rRNA genes in gut contents of both of adults and fingerlings. Bulk DNAs were extracted from the fish guts, followed by PCR, cloning and sequencing of eukaryote 18S rRNA gene; bacterial and archaeal 16S rRNA genes. Rarefaction analyses recorded 11, 18 and 13 phylotype groups of rRNA genes for eukaryotes, bacteria and archaea, respectively, in the adult guts. The fingerling guts contained 6 and 11 phylotype groups of rRNA genes for eukartyotes and bacteria, respectively, while lacked archaea. Adult and fingerling guts were dominated by zooplankton-like 18S rRNA gene phylotypes, belonging to those of rotifers, genus Brachionus and copepods, genus Apocyclops. Both of diatoms, genus Cyclotella- and fish-like rRNA gene phylotypes were recorded only in adult guts. Phylotypes, which belonged to uncultured proteobacteria and cyanobacteria, covered most of the bacterial 16S rRNA gene composition of adult guts. Bacteroidetes-like phylotypes characterized the fingerling guts. The study showed the first record of uncultured thaumarchaeote-like 16S rRNA genes in the fish guts, opening a window for exploring thaumarchaeote biological significances in fish metabolism. The fish guts represented a reservoir for geographic distant species and reflected the plankton ecosystem variability at the studied estuary. The pollution in the estuary could shape a fraction of the fish gut microbiota. To our knowledge, this work presented the first complete profile of rRNA gene diversities for all known microbiome domains in fish guts.

Cross-Kingdom Amplification Using Bacteria -Specific Primers: Complications for Studies of Coral Microbial Ecology

PCR amplification of pure bacterial DNA is vital to the study of bacterial interactions with corals. Commonly used Bacteria-specific primers 8F and 27F paired with the universal primer 1492R amplify both eukaryotic and prokaryotic rRNA genes. An alternative primer set, 63F/1542R, is suggested to resolve this problem.

Gene conversion drives within genic sequences: concerted evolution of ribosomal RNA genes in bacteria and archaea.

Multiple copies of a given ribosomal RNA gene family undergo concerted evolution such that sequences of all gene copies are virtually identical within a species although they diverge normally between species. In eukaryotes, gene conversion and unequal crossing over are the proposed mechanisms for concerted evolution of tandemly repeated sequences, whereas dispersed genes are homogenized by gene conversion. However, the homogenization mechanisms for multiple-copy, normally dispersed, prokaryotic rRNA genes are not well understood. Here we compared the sequences of multiple paralogous rRNA genes within a genome in 12 prokaryotic organisms that have multiple copies of the rRNA genes. Within a genome, putative sequence conversion tracts were found throughout the entire length of each individual rRNA genes and their immediate flanks. Individual conversion events convert only a short sequence tract, and the conversion partners can be any paralogous genes within the genome. Interestingly, the genic sequences undergo much slower divergence than their flanking sequences. Moreover, genomic context and operon organization do not affect rRNA gene homogenization. Thus, gene conversion underlies concerted evolution of bacterial rRNA genes, which normally occurs within genic sequences, and homogenization of flanking regions may result from co-conversion with the genic sequence.