Abundance And Diversity Of Denitrifying Bacteria In Agricultural Soils

Nitrogen fertilizer is not only a beneficial and often limiting substrate for plants but also is subject to a complex array of biogeochemical cycles which can lead to the production of nitrous oxide (N2O), a potent greenhouse gas which contributes to global climate change and ozone layer depletion. The major microbial processes responsible for N2O production are denitrification and nitrification. This dissertation aimed to investigate whether the abundance and diversity of the genes for denitrification, nirS, nirK and nosZ, measured by quantitative (Q) PCR and pyrosequencing, could be used to predict denitrification rates and N2O produced from denitrification. Emerging and classic techniques for determination of sources of N2O are discussed along with the importance of validating these techniques against the quantification of the nitrification and denitrification functional genes responsible for N 2O production through QPCR.;The effect of various organic carbon amendments on nitrate removal, abundance of the denitrifying bacterial community and N2O production was investigated in constructed denitrification beds. The nitrate removal rate was dependent on the quantity of bio-available carbon, which differed among carbon sources. Increasing the temperature enhanced growth of nirS containing bacteria and bacteria that lacked the nosZ gene, potentially explaining the greater N2O emission in warmer environments. The combination of maize cobs and woodchips are recommended to enhance NO3 removal while minimizing N2O production and TOC release from denitrification beds.;In an almond orchard fertilized with nitrate, despite low fluxes of N 2O, small but significant increases in nirS gene copies, nirS:16S rRNA, nirK:16S rRNA and nirS:nirK gene ratios were detected. In microcosms under reduced oxygen conditions, nosZ gene copy numbers and nirK:16S rRNA gene ratios increased, whereas there was no apparent effect on nirS or nirK gene copy numbers. We also found decreases in nirS and nirK at higher acetate and nitrate concentrations and a general preference for nirS over nirK in the microcosms. The estimated cell densities based on nitrate lost compared to gene copy numbers suggest that nirS and nirK genes accurately represent the denitrifying microbial community and that the amplified nosZ genes may not.;A field site was established in a table grape vineyard that had a strong contrast in the magnitude of N2O fluxes between the berm, where the vines grow, and the alley, the row between the berms. The abundance of the nirS and nirK genes were positively correlated with N 2O production in both field and denitrification enzyme activity incubations; however, no such relationships were observed with the nosZ gene. The high N2O produced in the berm appeared to select for nirS containing denitrifiers, as evidenced by higher nirS:nirK gene ratios in berm samples and the ratio of Sigmanir:nos was predictive of N2O production. Higher diversity was recorded in the berm than alley for all genes, nirS, nirK, nosZ and 16SrRNA, and positively correlated with N2O production. Specific bacterial phylogenetic groups were associated with complete or incomplete denitrification. In conclusion, the abundance and diversity of denitrifying populations may be useful in predicting N2O emissions in some environments, particularly as we learn more about the factors that govern these populations and their activities.