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 language | English (US) |
|---|---|
| Pages (from-to) | 353-364 |
| Number of pages | 12 |
| Journal | Geomicrobiology Journal |
| Volume | 24 |
| Issue number | 3-4 |
| DOIs | |
| State | Published - Apr 2007 |
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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 journal › Article
}
TY - JOUR
T1 - Design and validation of ureC-based primers for groundwater detection of urea-hydrolyzing bacteria
AU - Gresham, Tina L T
AU - Sheridan, Peter P.
AU - Watwood, Maribeth E
AU - Fujita, Yoshiko
AU - Colwell, Frederick S.
PY - 2007/4
Y1 - 2007/4
N2 - 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.
AB - 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.
KW - Bioremediation
KW - Groundwater
KW - Molecular ecology
KW - Primer design
UR - http://www.scopus.com/inward/record.url?scp=34547505379&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=34547505379&partnerID=8YFLogxK
U2 - 10.1080/01490450701459283
DO - 10.1080/01490450701459283
M3 - Article
VL - 24
SP - 353
EP - 364
JO - Geomicrobiology Journal
JF - Geomicrobiology Journal
SN - 0149-0451
IS - 3-4
ER -