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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. Ni 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 (similar to 10{sup 2} ppb; similar to 1 {mu} 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) shiftsmore » 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.« less

Authors:
;  [1]
  1. Cornell University, Ithaca, NY (United States). Dept. of Microbiology
Publication Date:
OSTI Identifier:
21240387
Resource Type:
Journal Article
Resource Relation:
Journal Name: Applied and Environmental Microbiology; Journal Volume: 75; Journal Issue: 20
Country of Publication:
United States
Language:
English
Subject:
01 COAL, LIGNITE, AND PEAT; COAL TAR; AQUIFERS; CONTAMINATION; GENES; BIODEGRADATION; NAPHTHALENE; GROUND WATER; WATER POLLUTION; OXYGENASES; BIOASSAY

Citation Formats

Yagi, J.M., and Madsen, E.L.. Diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer. United States: N. p., 2009. Web. doi:10.1128/AEM.01091-09.
Yagi, J.M., & Madsen, E.L.. Diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer. United States. doi:10.1128/AEM.01091-09.
Yagi, J.M., and Madsen, E.L.. Thu . "Diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer". United States. doi:10.1128/AEM.01091-09.
@article{osti_21240387,
title = {Diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer},
author = {Yagi, J.M. and Madsen, E.L.},
abstractNote = {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. Ni 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 (similar to 10{sup 2} ppb; similar to 1 {mu} 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.},
doi = {10.1128/AEM.01091-09},
journal = {Applied and Environmental Microbiology},
number = 20,
volume = 75,
place = {United States},
year = {Thu Oct 15 00:00:00 EDT 2009},
month = {Thu Oct 15 00:00:00 EDT 2009}
}