Design and validation of ureC-based primers for groundwater detection of urea-hydrolyzing bacteria

Tina L T Gresham, Peter P. Sheridan, Maribeth E Watwood, Yoshiko Fujita, Frederick S. Colwell

Research output: Contribution to journalArticle

23 Citations (Scopus)

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 α, 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.

Original languageEnglish (US)
Pages (from-to)353-364
Number of pages12
JournalGeomicrobiology Journal
Volume24
Issue number3-4
DOIs
StatePublished - Apr 2007

Fingerprint

Groundwater
urea
Urea
Bacteria
Comamonadaceae
Genes
bacterium
groundwater
Urease
gene
phylogenetics
Arthrobacter
Proteobacteria
Gene encoding
Actinobacteria
Polymerase chain reaction
rRNA Genes
Catalytic Domain
polymerase chain reaction
Polymerase Chain Reaction

Keywords

  • Bioremediation
  • Groundwater
  • Molecular ecology
  • Primer design

ASJC Scopus subject areas

  • Earth and Planetary Sciences (miscellaneous)
  • Microbiology
  • Environmental Science(all)
  • Environmental Chemistry

Cite this

Design and validation of ureC-based primers for groundwater detection of urea-hydrolyzing bacteria. / Gresham, Tina L T; Sheridan, Peter P.; Watwood, Maribeth E; Fujita, Yoshiko; Colwell, Frederick S.

In: Geomicrobiology Journal, Vol. 24, No. 3-4, 04.2007, p. 353-364.

Research output: Contribution to journalArticle

Gresham, Tina L T ; Sheridan, Peter P. ; Watwood, Maribeth E ; Fujita, Yoshiko ; Colwell, Frederick S. / Design and validation of ureC-based primers for groundwater detection of urea-hydrolyzing bacteria. In: Geomicrobiology Journal. 2007 ; Vol. 24, No. 3-4. pp. 353-364.
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