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Applied and Environmental Microbiology, October 2009, p. 6478-6487, Vol. 75, No. 20
0099-2240/09/$08.00+0     doi:10.1128/AEM.01091-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Diversity, Abundance, and Consistency of Microbial Oxygenase Expression and Biodegradation in a Shallow Contaminated Aquifer{triangledown} ,{dagger}

Jane M. Yagi and Eugene L. Madsen*

Department of Microbiology, Wing Hall, Cornell University, Ithaca, New York 14853

Received 12 May 2009/ Accepted 11 August 2009

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 µM) 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.

* Corresponding author. Mailing address: Department of Microbiology, Cornell University, B57A Wing Hall, Ithaca, NY 14853. Phone: (607) 255-2417. Fax: (607) 255-3904. E-mail: elm3{at}cornell.edu

{triangledown} Published ahead of print on 21 August 2009.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, October 2009, p. 6478-6487, Vol. 75, No. 20
0099-2240/09/$08.00+0     doi:10.1128/AEM.01091-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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