title: Diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer.
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 ( approximately 10(2) ppb; approximately 1 muM) 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.
authors.affiliation: Department of Microbiology, Cornell University, B57A Wing Hall, Ithaca, NY 14853, USA.
authors.forename: Jane M
authors.initials: JM
authors.lastname: Yagi
authors.forename: Eugene L
authors.initials: EL
authors.lastname: Madsen
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D001483:Base Sequence; D001673:Biodegradation, Environmental; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D049308:Dioxygenases / Q000235:genetics*; D015870:Gene Expression; D005798:Genes, Bacterial; D014644:Genetic Variation; D008969:Molecular Sequence Data; D009281:Naphthalenes / Q000378:metabolism*; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D013997:Time Factors; D014871:Water Microbiology; D014874:Water Pollutants, Chemical / Q000378:metabolism*
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial; D009281:Naphthalenes; D014874:Water Pollutants, Chemical; C031721:naphthalene; D049308:Dioxygenases
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