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Design and Validation of ureC-based Primers for Groundwater Detection of Urea-Hydrolyzing Bacteria 

Authors: Tina L. T. Gresham a;  Peter P. Sheridan a;  Mary E. Watwood b;  Yoshiko Fujita c; Frederick S. Colwell d
Affiliations:   a Department of Biological Sciences, Idaho State University, Pocatello, ID, USA
b Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
c Biotechnology Department, Idaho National Laboratory, Idaho Falls, ID, USA
d College of Oceanic and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
DOI: 10.1080/01490450701459283
Publication Frequency: 8 issues per year
Published in: journal Geomicrobiology Journal, Volume 24, Issue 3 & 4 April 2007 , pages 353 - 364
Formats available: HTML (English) : PDF (English)
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Abstract

Polymerase chain reaction primers based on the ureC gene are described for use in detecting diverse groundwater urea-hydrolyzing bacteria. Six degenerate primers were designed and evaluated for their ability to detect the gene encoding the large catalytic subunit of urease, ureC. Five combinations of these primers were tested pair-wise and displayed an overlapping detection range for bacterial isolates. Pair L2F/L2R exhibited the greatest detection range for described bacterial species and for bacterial isolates from groundwater samples belonging to the bacterial divisions Firmicutes, Actinobacteria, and the agr, β, and γ subdivisions of Proteobacteria. Primers L2F/L2R exhibited a greater detection range than previously described ureC-specific primers, and amplified novel ureC sequences from groundwater isolates in the genera Hydrogenophaga, Acidovorax, Janthinobacterium, and Arthrobacter. A comparative phylogenetic analysis of ureC and 16S rRNA genes was performed to determine the utility of groundwater ureC sequence information as a phylogenetic marker for ureolytic species. Our results were consistent with previous analyses of urease genes which demonstrated that the ureC gene has undergone lateral transfer and is not a robust phylogenetic marker. However, the ureC-specific primers, L2F/L2R, demonstrate a broad detection range for ureolytic species, and can serve to enhance functional diversity analyses of ureolytic bacteria.
Keywords: bioremediation; groundwater; molecular ecology; primer design
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