SS2.05 Phylogenetic and Physiologic Successions in Aquatic Bacterial Communities
Date: Monday, June 10, 2002
Time: 4:00:00 PM
Location: Carson C
 
MacGregorBJ, Max Planck Institute for Marine Microbiology, Bremen, Germany, bmacgreg@mpi-bremen.de
Brüchert, V, , Max Planck Institute for Marine Microbiology, Bremen, Germany, vbrucher@mpi-bremen.de
Fleischer, S, , Max Planck Institute for Marine Microbiology, Bremen, Germany, sfleisch@mpi-bremen.de
Amann, R, , Max Planck Institute for Marine Microbiology, Bremen, Germany, ramann@mpi-bremen.de
 
RNA AS A BIOMARKER: ISOLATION OF SMALL-SUBUNIT RIBOSOMAL RNA FOR STABLE ISOTOPIC CHARACTERIZATION
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Small-subunit ribosomal RNA (SSU rRNA) has several characteristics making it a good candidate biomarker compound. It is found in bacteria, archaea, and eukaryotes; it is quickly degraded extracellularly, so that SSU rRNA extracted from a sample likely derives from the currently active population; it includes both conserved and variable regions, allowing the design of capture probes at various levels of phylogenetic discrimination; and rRNA sequences from uncultured or newly isolated species can be classified by comparison with the public database. We have developed a method for isolation of specific classes of rRNAs from mixtures of total RNA, employing biotin-labeled oligonucleotide probes and streptavidin-coated paramagnetic beads. We have also found that the stable carbon isotope composition of Escherichia coli total RNA and SSU rRNA reflect that of whole cells and of the growth substrate for cells grown on LB, M9 glucose, and M9 acetate media. SSU rRNA is therefore a promising biomarker for following the flow of carbon (and potentially nitrogen) in natural microbial populations, in particular where natural or introduced substrates have strong isotopic signatures.