The giant sulfur bacteria - single-cell 16S rRNA sequencing reveals the presence of introns and a new family structure


***Tuesday August 14, 2012
***Redfield Auditorium 1:30PM
Dr. Verna Salman
Max Planck Institute

The group of giant sulfur bacteria includes prominent marine benthic organisms like Beggiatoa, Thiomargarita and Thioploca, of which some have already been discovered more than a century ago owing to their enormous cell size and intriguing white appearance. They occur in organic-rich sulfidic habitats like upwelling areas or vent sites. Traditionally, they have always been classified according to their conspicuous morphologies, as both 16S rRNA gene sequencing and cultivation have remained difficult for this particular group of bacteria.

We hand-picked more than 100 individual cells and filaments and sequenced their 16S rDNA-ITS region. During this phylogenetic study, we identified up to four different self-splicing introns in 77% of the investigated 16S rRNA gene sequences, sometimes enlarging the gene to more than 3.5 kb. Remarkably, introns have never been identified in bacterial 16S rRNA genes before, although being the most frequently sequenced gene today. It is tempting to speculate that also other groups of bacteria have intron-inserted 16S rRNA genes, which would bear general problems for diversity studies as these elongated genes cause systematic biases during amplification in the polymerase chain reaction. This amplification bias leads to the exclusion of intron-containing genes from a heterogeneous population and thus excludes the analysis of particular groups of organisms. The far-reaching consequences of this finding for future studies in microbial ecology, the standard procedures of analyzing rRNA genes and microbial genome evolution are intriguing.

The 16S-based phylogenetic analysis of the group of large sulfur bacteria further on revealed that the morphologies of individual cells was not a suitable criterion for the determination of taxonomic units at it did not reflect the phylogenetic relationship within the family. Accordingly, we proposed a morphology-independent but 16S-based reclassification of the family, forming ten instead of three genera and introducing nine novel species. This novel nomenclature is a useful guidance for the work with large sulfur bacteria and simplifies communication.