published_or_final_version / abstract / Civil Engineering / Master / Master of Philosophy

Nitrous oxide (N2O) is a potent greenhouse gas mainly emitted from agriculture. In the biological process of denitrification, intermediates of the nitrogen cycle are reduced under oxygen limiting conditions thereby releasing N2O. Denitrification is influenced by various environmental factors and both bacteria and fungi are capable of denitrification. The ultimate aim of this thesis was to determine the significance of fungal and bacterial denitrification in arable soil and to investigate influences of soil pH and physical disturbance on potential denitrification rates and denitrifying communities. Long-term pH plots combined with a disturbance gradient have been utilised to investigate fungal and bacterial denitrification distinguished by application of selective inhibitors. Highest N2O production was measured from slightly acidic soil and soil with reduced disturbance. Fungi and bacteria contributed to N2O production with bacterial denitrification as dominant source. Fungal denitrification remained unaffected by soil pH and disturbance whereas bacterial denitrification was influenced by these factors. Bacterial denitrification was positively correlated with concentrations of fatty acids which suggested that these fatty acids were common to bacteria involved in N2O production in the soils investigated here. Bacterial community structure changed with soil pH and disturbance whereas fungal community structure was only influenced by disturbance. Bacterial denitrifier communities (nitrite reductases nirK and nirS) changed over the pH gradient but only the nirK community was affected by disturbance. This indicated that groups of bacterial denitrifiers follow different ecological strategies. Gene abundance of nirK and nirS was also correlated to concentrations of the fatty acids associated with denitrifying bacteria in the soils investigated here. In conclusion, fungal denitrification was significant in arable soil but remained unchanged by soil pH and disturbance. Therefore, fungal denitrification is important in agricultural ecosystems and should be considered when developing mitigation strategies for N2O production especially under conditions favourable for fungal denitrification.

Thesis (doctoral)--Swedish University of Agricultural Sciences, 2006. / Thesis documentation sheet inserted. Appendix reprints three papers and manuscripts co-authored with others. Includes bibliographical references. Also partially issued electronically via World Wide Web in PDF format; online version lacks appendix.

Thesis (M.S.)--University of North Carolina Wilmington, 2007. / Includes bibliographical references (leaves: 120-121)

Thesis (M.Tech.: Biotechnology)-Dept. of Biotechnogy, Durban Institute of Technology, 2005 xvi, 85 leaves : ill. ; 31 cm / Atmospheric nitrogen pollution is on the increase and human activities are directly or indirectly responsible for the generation of the various nitrogen polluting compounds. This can lead to the two major problems of eutrophication and groundwater pollution. Therefore, the removal of nutrients such as nitrogen and phosphorus from wastewater is important. Nitrogen removal from wastewater is achieved by a combination of nitrification and denitrification. Thus, there is a need to identify and characterise heterotrophic denitrifying bacteria involved in denitrification in wastewater treatment systems. The aim of this study, therefore, was to characterise heterotrophic denitrifying bacteria through detailed biochemical and molecular analysis, to facilitate the understanding of their functional role in wastewater treatment systems. Drysdale (2001) isolated heterotrophic denitrifiers to obtain a culture collection of 179 isolates. This culture collection was used to screen for nitrate and nitrite reduction using the colorimetric biochemical nitrate reduction test. The isolates were thereafter Gram stained to assess their gram reaction, cellular and colonial morphology. Based on these results identical isolates were discarded and a culture collection of approximately 129 isolates remained. The genetic diversity of the culture collection was investigated by the analysis of polymerase chain reaction (PCR)-amplified 16S ribosomal DNA (rDNA) fragments on polyacrylamide gels using denaturing gradient gel electrophoresis (DGGE). Thus DNA fragments of the same length but different nucleotide sequences were effectively separated and microbial community profiles of eight predominant isolates were created. Batch experiments were conducted on these eight isolates, the results of which ultimately confirmed their characterisation and placed them into their four functional groups i.e. 3 isolates were incomplete denitrifiers, 2 isolates were true denitrifiers, 2 isolates were sequential denitrifiers and 1 isolate was an exclusive nitrite reducer.

Thesis (M.Tech.: Biotechnology)-Dept. of Biotechnogy, Durban Institute of Technology, 2005 xvi, 85 leaves : ill. ; 31 cm / Atmospheric nitrogen pollution is on the increase and human activities are directly or indirectly responsible for the generation of the various nitrogen polluting compounds. This can lead to the two major problems of eutrophication and groundwater pollution. Therefore, the removal of nutrients such as nitrogen and phosphorus from wastewater is important. Nitrogen removal from wastewater is achieved by a combination of nitrification and denitrification. Thus, there is a need to identify and characterise heterotrophic denitrifying bacteria involved in denitrification in wastewater treatment systems. The aim of this study, therefore, was to characterise heterotrophic denitrifying bacteria through detailed biochemical and molecular analysis, to facilitate the understanding of their functional role in wastewater treatment systems. Drysdale (2001) isolated heterotrophic denitrifiers to obtain a culture collection of 179 isolates. This culture collection was used to screen for nitrate and nitrite reduction using the colorimetric biochemical nitrate reduction test. The isolates were thereafter Gram stained to assess their gram reaction, cellular and colonial morphology. Based on these results identical isolates were discarded and a culture collection of approximately 129 isolates remained. The genetic diversity of the culture collection was investigated by the analysis of polymerase chain reaction (PCR)-amplified 16S ribosomal DNA (rDNA) fragments on polyacrylamide gels using denaturing gradient gel electrophoresis (DGGE). Thus DNA fragments of the same length but different nucleotide sequences were effectively separated and microbial community profiles of eight predominant isolates were created. Batch experiments were conducted on these eight isolates, the results of which ultimately confirmed their characterisation and placed them into their four functional groups i.e. 3 isolates were incomplete denitrifiers, 2 isolates were true denitrifiers, 2 isolates were sequential denitrifiers and 1 isolate was an exclusive nitrite reducer.

Diversity of the soil microbial community and its functional aspects were investigated in man-influenced environments, such as colliery spoil heaps in post mining sites and upland pasture used for outdoor cattle husbandry. The study was based on the cultivation of bacteria and streptomycetes as well as culture-independent approaches. Cultivated bacteria and streptomycetes were characterized by phenotypic and genotypic means. The culture-independent approaches were based on an analysis of environmental DNA in terms of both qualitative and quantitative parameters.