Denitrifying bacteria from the terrestrial subsurface exposed to mixed waste contamination

Journal Article · Fri Jan 01 00:00:00 EST 2010 · Applied and Environmental Microbiology

DOI:https://doi.org/10.1128/AEM.03069-09· OSTI ID:985281

Green, Stefan ^[1]; Prakash, Om ^[1]; Gihring, Thomas ^[1]; Akob, Denise M. ^[1]; Jasrotia, Puja ^[1]; Jardine, Philip M ^[2]; Watson, David B ^[2]; Brown, Steven D ^[2]; Palumbo, Anthony Vito ^[2]; Kostka, Joel ^[1]

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1. Florida State University
2. ORNL

In terrestrial subsurface environments where nitrate is a critical groundwater contaminant, few cultivated representatives are available with which to verify the metabolism of organisms that catalyze denitrification. In this study, five species of denitrifying bacteria from three phyla were isolated from subsurface sediments exposed to metal radionuclide and nitrate contamination as part of the U.S. Department of Energy s Oak Ridge Integrated Field Research Challenge (OR-IFRC). Isolates belonged to the genera Afipia and Hyphomicrobium (Alphaproteobacteria), Rhodanobacter (Gammaproteobacteria), Intrasporangium (Actinobacteria) and Bacillus (Firmicutes). Isolates from the phylum Proteobacteria were confirmed as complete denitrifiers, whereas the Gram-positive isolates reduced nitrate to nitrous oxide. Ribosomal RNA gene analyses reveal that bacteria from the genus Rhodanobacter comprise a diverse population of circumneutral to moderately acidophilic denitrifiers at the ORIFRC site, with a high relative abundance in areas of the acidic source zone. Rhodanobacter species do not contain a periplasmic nitrite reductase and have not been previously detected in functional gene surveys of denitrifying bacteria at the OR-IFRC site. Sequences of nitrite and nitrous oxide reductase genes were recovered from the isolates and from the terrestrial subsurface by designing primer sets mined from genomic and metagenomic data and from draft genomes of two of the isolates. We demonstrate that a combination of cultivation, genomic and metagenomic data are essential to the in situ characterization of denitrifiers and that current PCR-based approaches are not suitable for deep coverage of denitrifying microorganisms. Our results indicate that the diversity of denitrifiers is significantly underestimated in the terrestrial subsurface.

• Research Organization: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
• Sponsoring Organization: USDOE Office of Science (SC)
• DOE Contract Number: DE-AC05-00OR22725
• OSTI ID: 985281
• Journal Information: Applied and Environmental Microbiology, Vol. 76, Issue 10; ISSN 0099-2240
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE
ABUNDANCE
BACILLUS
BACTERIA
CONTAMINATION
CULTIVATION
DENITRIFICATION
FUNCTIONALS
GENES
METABOLISM
MICROORGANISMS
NITRATES
NITRITES
NITROUS OXIDE
OXIDOREDUCTASES
RADIOISOTOPES
RIBOSOMAL RNA
SEDIMENTS
WASTES
nitrite reductase
nitrous oxide reductase
uranium contamination
Rhodanobacter