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APPLIED AND ENVIRONMENTAL MICROBIOLOGY
Vol. 75, No. 20, 2009; Pages: 6478–6487


Diversity, Abundance, and Consistency of Microbial Oxygenase Expression and Biodegradation in a Shallow Contaminated Aquifer

Jane M. Yagi and Eugene L. Madsen*

Department of Microbiology, Cornell University, B57A Wing Hall, Ithaca, NY 14853.


Abstract

The diversity of Rieske dioxygenase genes and short-term temporal variability in the abundance of two selected dioxygenase gene sequences were examined in a naphthalene-rich, coal tar waste-contaminated subsurface study site. Using a previously published PCR-based approach (S. M. Ní Chadhain, R. S. Norman, K. V. Pesce, J. J. Kukor, and G. J. Zylstra, Appl. Environ. Microbiol. 72:4078–4087, 2006) a broad suite of genes was detected, ranging from dioxygenase sequences associated with Rhodococcus and Sphingomonas to 32 previously uncharacterized Rieske gene sequence clone groups. The nag genes appeared frequently (20% of the total) in two groundwater monitoring wells characterized by low (~102 ppb; ~1 M) ambient concentrations of naphthalene. A quantitative competitive PCR assay was used to show that abundances of nag genes (and archetypal nah genes) fluctuated substantially over a 9-month period. To contrast short-term variation with long-term community stability, in situ community gene expression (dioxygenase mRNA) and biodegradation potential (community metabolism of naphthalene in microcosms) were compared to measurements from 6 years earlier. cDNA sequences amplified from total RNA extracts revealed that nah- and nag-type genes were expressed in situ, corresponding well with structural gene abundances. Despite evidence for short-term (9-month) shifts in dioxygenase gene copy number, agreement in field gene expression (dioxygenase mRNA) and biodegradation potential was observed in comparisons to equivalent assays performed 6 years earlier. Thus, stability in community biodegradation characteristics at the hemidecadal time frame has been documented for these subsurface microbial communities.

Keywords:Pseudomonas spp., nah genes, Burkholderia spp., phn genes,Ralstonia,Comamonas spp,physiology.


Corresponding author: Tel (607) 255-2417, Fax (607) 255-3904.

E-mail: elm3@cornell.edu

 

 
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