Differential responses of nirK‐ and nirS‐carrying bacteria to denitrifying conditions in the anoxic rice field soil

Abstract

Denitrification occurs actively in rice field soils. In the present study, the responses of nirK and nirS denitrifier communities to nitrate addition in the anoxic rice soil were determined through molecular analyses of nitrite reductase genes nirK and nirS and 16S rRNA genes. Denitrification occurred rapidly when nitrate was added at the beginning of anoxic incubation (experiment I). The structure of nirK-type denitrifiers did not change; but their abundance as determined by quantitative (real-time) PCR increased in nitrate treatments compared with control. Both the structure and abundance of nirS denitrifiers remained unaffected in experiment I. The rate of denitrification was slowed down when nitrate was added 20 days after the onset of anoxic incubation (experiment II). The structure and abundance of nirK-type denitrifier community did not respond to nitrate addition; but the nirS community changed substantially in this experiment. The copy number of nirS genes increased by an order of magnitude in the treatments of 5 mM and 10 mM nitrate compared with control. The terminal restriction fragment length polymorphism (T-RFLP) analysis of nirS genes revealed that the 100 bp T-RF substantially increased in the nitrate treatments. Cloning and sequence analysis indicated that this T-RF had similarity of up to 90% with Herbaspirillum sp. T-RFLP profiles of the bacterial 16S rRNA genes also showed that Herbaspirillum sp. increased after nitrate amendments. Collectively, the nirK-type denitrifiers were probably active at the beginning of anaerobic incubation, while the nirS denitrifiers, especially those related with Herbaspirillum sp. probably were more active when anaerobic condition was fully developed.

Microbial functional diversity enhances predictive models linking environmental parameters to ecosystem properties

“…This agrees with what was observed by correlations in the original data set (Enwall et al 2010) and in other studies reporting either a significant and/or stronger correlation between denitrification activity and nirS abundance when compared to nirK (Philippot et al 2009, Graham et al 2010. It has been suggested that nirS-and nirK-type denitrifier communities occupy different ecological niches (e.g., Santoro et al 2006, Desnues et al 2007, Smith and Ogram 2008, Yuan et al 2012) and coexisting nirS and nirK communities are likely not under the same community assembly rules (Jones and Hallin 2010). In another experimental agricultural system, Hallin et al (2012) observed that denitrification process rates could be maintained over a range of temperatures and salinity levels and this functional operating range was expanded for bacterial communities that assembled under certain soil management practices and contained key genotypes.…”

Resource effects on denitrification are mediated by community composition in tidal freshwater wetlands soils

“…In general, NO 3 – fertilization increased denitrifier nirS population size (Fig. A), consistent with Kong and colleagues () and Yuan and colleagues (), most likely because of the greater availability of NO 3 – to serve as a terminal electron acceptor. Fertilization was also found to affect nirS ‐denitrifier community composition, manifesting as clear and consistent shifts on the PCoA diagram (Fig.…”

Nitrogen removal and spatial distribution of denitrifier and anammox communities in a bioreactor for mine drainage treatment

“…The abundance of nirS decreased with distance from the inlet while the greatest nirK abundance occurred in the central region of the bioreactor. This agrees with previous studies suggesting that nirS and nirK type denitrifiers have different niche preferences (Jones and Hallin, 2010), which would explain why they would respond differently to changing environmental conditions, as reported by others (Desnues et al, 2007;Enwall et al, 2010;Santoro et al, 2006;Smith and Ogram, 2008;Yuan et al, 2012). Since NO 3 À concentrations decreased to below detection limits in the outlet during the second half of the operational period, nirS abundance may have reflected substrate availability.…”