Appl Environ Microbiol 69: 3476–3483Ĭheneby, D, Hallet, S, Mondon, M, Martin-Laurent, F, Germon, JC, Philippot, L (2003) Genetic characterization of the nitrate reducing community based on narG nucleotide sequence analysis. Appl Environ Microbiol 64: 3769–3775īraker, G, Tiedje, JM (2003) Nitric oxide reductase ( norB) genes from pure cultures and environmental samples. Appl Environ Microbiol 67: 1893–1901īraker, G, Fesefeldt, A, Witzel, KP (1998) Development of PCR primer systems for amplification of nitrite reductase genes ( nirK and nirS) to detect denitrifying bacteria in environmental samples. Appl Environ Microbiol 63: 3662–3668īraker, G, Ayala-del Rio, HL, Devol, AH, Fesefeldt, A, Tiedje, JM (2001) Community structure of denitrifiers, bacteria, and archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase ( nirS) and 16S rRNA genes.

On the basis of 16S rRNA gene clone libraries retrieved from 13C-DNA, these unidentified nir sequences might be identified by examining the nir gene in candidates for true denitrifiers (e.g., the families Comamonadaceae, Hyphomicrobiaceae, Methylophilaceae, and Rhodobacteraceae).Īndreasen, K, Nielsen, PH (1997) Application of microautoradiography to the study of substrate uptake by filamentous microorganisms in activated sludge. However, most of the nirS or nirK sequences retrieved from 13C-DNA were clustered in some unidentified groups. Furthermore, we characterized nitrite reductase genes ( nirS and nirK) as functional marker genes for denitrifier communities in acetate- or methanol-assimilating populations and detected the nirS or nirK sequence related to that of some known pure cultures, such as Alcaligenes, Hyphomicrobium, and Thauera. Rarefaction curves for clones retrieved from 13C-DNA showed that the diversity levels for methanol-assimilating bacteria were considerably lower than those for acetate-assimilating bacteria.

When methanol was used as the carbon source, 16S rRNA gene sequences retrieved from 13C-DNA were affiliated with Methylophilaceae (e.g., Methylophilus, Methylobacillus, and Aminomonas) and Hyphomicrobiaceae. When acetate was used as the carbon source, 16S rRNA gene sequences retrieved from 13C-labeled DNA were closely related to the 16S rRNA genes of Comamonadaceae (e.g., Comamonas and Acidovorax) and Rhodocyclaceae (e.g., Thauera and Dechloromonas) of the Betaproteobacteria, and Rhodobacteraceae (e.g., Paracoccus and Rhodobacter) of the Alphaproteobacteria. Most of the acetate- or methanol-assimilating bacteria identified by SIP have been known as denitrifiers in wastewater treatment systems. We analyzed how growth of bacterial populations was stimulated by acetate or methanol as the external carbon source in nitrogen-removal systems. A sludge sample obtained from wastewater treatment systems was incubated in a denitrifying batch reactor fed with synthetic wastewater containing acetate or methanol as the main carbon source and nitrate as the electron acceptor. Stable-isotope probing (SIP) was used to identify acetate- or methanol-assimilating bacteria under nitrate-reducing conditions in activated sludge.

Analytic rarefaction software