Molecular Evolution of Reductive Dehalogenases

Koshlan Mayer-Blackwell
PhD Student
Research Blurb: 

Idiosyncratic combinations of reductive dehalogenase (rdh) genes are a distinguishing genomic feature of closely related organohalogen-respiring bacteria. This feature can be used to deconvolute the population structure of organohalogen-respiring bacteria in complex environments and to identify relevant subpopulations, which is important for tracking interspecies dynamics needed for successful site remediation. Here we report the development of a nanoliter qPCR platform to identify organohalogen-respiring bacteria and populations by quantifying major orthologous reductive dehalogenase gene groups. The qPCR assays can be operated in parallel within a 5184-well nanoliter qPCR (nL-qPCR) chip at a single annealing temperature and buffer condition. We developed a robust bioinformatics approach to select from thousands of computationally proposed primer pairs those that are specific to individual rdh gene groups and compatible with a single amplification condition. We validated hundreds of the most selective qPCR assays and examined their performance in a trichloroethene-degrading bioreactor, revealing population structures as well as their unexpected shifts in abundance and community dynamics.

 

Nanoliter qPCR Platform for Highly Parallel, Quantitative Assessment of Reductive Dehalogenase Genes and Populations of Dehalogenating Microorganisms in Complex Environments

 
Koshlan Mayer-Blackwell †, Mohammad F. Azizian ‡, Christina Machak §, Elena Vitale , Giovanna Carpani , Francesca de Ferra , Lewis Semprini ‡, and Alfred M. Spormann *†

 

Full Email Address: 
Department or Organization: 
Civil And Environmental Engineering
Phone Number: 
(801) 450.6054
(801) 450.6054
Profile Photo: 
Member Date: 
October, 2010
0 April 21, 2011