You are here:
Detection and Composition of Bacterial Communities in Waters using RNA-based Methods
Citation:
Santodomingo, J. Detection and Composition of Bacterial Communities in Waters using RNA-based Methods. Presented at UC Medical School seminar, Cincinnati, OH, March 16, 2016.
Impact/Purpose:
In this seminar, I'll be presenting the work that we have conducted using RNA-methods to determine the presence and activity in different waters, including surface waters and samples collected from nitrifying enrichments.
Description:
In recent years, microbial water quality assessments have shifted from solely relying on pure culture-based methods to monitoring bacterial groups of interest using molecular assays such as PCR and qPCR. Furthermore, coupling next generation sequencing technologies with ribosomal RNA gene (rDNA) sequence analyses have allowed us to describe the structure of natural and engineered microbial communities at different trophic levels. Most studies have relied on using DNA as the PCR and sequencing template. Unfortunately, this approach does not discriminate between active and dead cells, information that is relevant from both public health and ecosystem function standpoints. The use of RNA-based detection methods has recently been proposed as RNA is rather unstable outside of the cell and degrades much faster than DNA in nonactive/dead cells. In theory, RNA-based methods can also take advantage of the higher number of rRNA copies in physiologically active cells to increase bacterial detection ratyes. The objective of this seminar is to discuss some of the latest results from our laboratory on the use of RNA-based methods as an alternate approach for the detection of active bacterial members of a microbial community. Specifically, we have compared bacteria detection rates using RNA- vs DNA-based qPCR assays, and evaluated the use of rRNA/rDNA ratios to access the metabolic status of different bacterial groups in different water matrices, including environmental waters, drinking waters, and wastewater bioreactors. Limitations and future research needs of the use of molecular for environmental monitoring will also be discussed.
