Abundance of narG , nirS , nirK , and nosZ Genes of Denitrifying Bacteria during Primary Successions of a Glacier Foreland

Abstract

Quantitative PCR of denitrification genes encoding the nitrate, nitrite, and nitrous oxide reductases was used to study denitrifiers across a glacier foreland. Environmental samples collected at different distances from a receding glacier contained amounts of 16S rRNA target molecules ranging from 4.9 ؋ 10 5 to 8.9 ؋ 10 5 copies per nanogram of DNA but smaller amounts of narG, nirK, and nosZ target molecules. Thus, numbers of narG, nirK, nirS, and nosZ copies per nanogram of DNA ranged from 2.1 ؋ 10 3 to 2.6 ؋ 10 4 , 7.4 ؋ 10 2 to 1.4 ؋ 10 3 , 2.5 ؋ 10 2 to 6.4 ؋ 10 3 , and 1.2 ؋ 10 3 to 5.5 ؋ 10 3 , respectively. The densities of 16S rRNA genes per gram of soil increased with progressing soil development. The densities as well as relative abundances of different denitrification genes provide evidence that different denitrifier communities develop under primary succession: higher percentages of narG and nirS versus 16S rRNA genes were observed in the early stage of primary succession, while the percentages of nirK and nosZ genes showed no significant increase or decrease with soil age. Statistical analyses revealed that the amount of organic substances was the most important factor in the abundance of eubacteria as well as of nirK and nosZ communities, and copy numbers of these two genes were the most important drivers changing the denitrifying community along the chronosequence. This study yields an initial insight into the ecology of bacteria carrying genes for the denitrification pathway in a newly developing alpine environment.Primary successional ecosystems, such as glacier forelands and volcanoes, present an ideal opportunity to study the biological colonization of substrates. Since the ice covers of many glaciers have receded over the past century, glacier forelands have released substrates for soil development. Autotrophic colonizers are expected to be important in the initial stages of primary community assembly. Organic substrates for microbial growth, however, might also come from allochthonous dead organic matter and living invertebrates in these environments. Hodkinson et al. (8) therefore recently proposed a previously unrecognized heterotrophic phase which should allow the initial establishment of functional communities. Accordingly, future studies in microbial ecology must account for both autotrophic and heterotrophic colonization along primary successional gradients such as glacier forelands, land lifts, floodplains, landslides, and volcanoes. In the past few years, studies have focused mainly on the composition and activities of the soil microbiota in primary succession of receding glaciers (19,21,24,25). Only a few studies have employed molecular tools to understand the diversity of archaeal and bacterial community structures along the forefields of receding glaciers (2,13,20). Analyses of activity and genetic structures of the nitrate reducer community at the Rotmoosferner glacier have shown that N cycling processes as well as microbial community composition depend on the successional age (...

Response of denitrification genes nirS, nirK, and nosZ to irrigation water quality in a Chinese agricultural soil

“…The abundance of nosZ gene was the highest one among the three functional genes in this study. This result was higher than those of previously reported: nosZ density of 3×10 6 -2.8×10 8 copies g −1 dry soil (Kandeler et al 2006;Dandie et al 2008;Hallin et al 2009). But Chronakova et al (2009) found the nosZ gene copy number was in a range of 9.1×10 7 -7.5×10 9 copies g −1 soil in an upland pasture soil.…”

“…Environmental factors affected the abundance of the bacterial denitrification genes greatly (Kandeler et al 2006;Yoshida et al 2009). Significantly positive correlations between the soil NO 3 − and the quantity of nirK gene (R=0.682, P<0.05), and between the soil organic matter content and the quantity of nirS gene (R=0.614, P<0.05), were found in this study.…”

Contrasting denitrifier communities relate to contrasting N2O emission patterns from acidic peat soils in arctic tundra

“…Pyrosequencing and quantitative kinetic real-time PCR of denitrification-associated genes substantiated the previous conclusion (Figure 4, Tables 4 and 5). narG copy numbers of cryoturbated peat soil were higher than or in the same range as in agricultural soils or glacier forelands Kandeler et al, 2006;Bru et al, 2007), and significantly higher than in unturbated peat soil (Table 5). Such findings are in agreement with the high in situ concentrations of nitrate in cryoturbated peat soil (Repo et al, 2009), and the inability of unturbated peat soil to cope with high nitrate concentrations (Figure 2).…”

Addition of activated switchgrass biochar to an aridic subsoil increases microbial nitrogen cycling gene abundances

“…Gene abundances were likewise corrected for gene copy per organism: 1 copy per organism for nifH, nirK, nirS, and nosZ (Hall et al, 2008;Kandeler et al, 2006); 2 copies per organism for amoA (Chain et al, 2003); and 3.6 copies per organism for the 16S rRNA gene (Klappenbach et al, 2001). Relative abundances (from non-log transformed qPCR values) were calculated for each sample as a ratio of the abundance of each N-cycling gene to 16S rRNA gene abundance.…”