Les rivières reçoivent de l'azote de leurs bassins versants et elles constituent les derniers sites de transformations des nutriments avant leur livraison aux zones côtières. Les transformations de l’azote inorganique dissous en azote gazeux sont très variables et peuvent avoir un impact à la fois sur l’eutrophisation des côtes et les émissions de gaz à effet de serre à l’échelle globale. Avec l’augmentation de la charge en azote d’origine anthropique vers les écosystèmes aquatiques, les modèles d’émissions de gaz à effet de serre prédisent une augmentation des émissions d’oxyde nitreux (N2O) dans les rivières. Les mesures directes de N2O dans le Lac Saint-Pierre (LSP), un élargissement du Fleuve Saint-Laurent (SLR) indiquent que bien qu’étant une source nette de N2O vers l'atmosphère, les flux de N2O dans LSP sont faibles comparés à ceux des autres grandes rivières et fleuves du monde. Les émissions varient saisonnièrement et inter-annuellement à cause des changements hydrologiques. Les ratios d’émissions N2O: N2 sont également influencés par l’hydrologie et de faibles ratios sont observés dans des conditions de débit d'eau plus élevée et de charge en N élevé. Dans une analyse effectuée sur plusieurs grandes rivières, la charge hydraulique des systèmes semble moduler la relation entre les flux de N2O annuels et les concentrations de nitrate dans les rivières. Dans SLR, des tapis de cyanobactéries colonisant les zones à faible concentration de nitrate sont une source nette d’azote grâce à leur capacité de fixer l’azote atmosphérique (N2). Étant donné que la fixation a lieu pendant le jour alors que les concentrations d'oxygène dans la colonne d'eau sont sursaturées, nous supposons que la fixation de l’azote est effectuée dans des micro-zones d’anoxie et/ou possiblement par des diazotrophes hétérotrophes. La fixation de N dans les tapis explique le remplacement de près de 33 % de la perte de N par dénitrification dans tout l'écosystème au cours de la période d'étude. Dans la portion du fleuve Hudson soumis à la marée, la dénitrification et la production de N2 est très variable selon le type de végétation. La dénitrification est associée à la dynamique en oxygène dissous particulière à chaque espèce durant la marée descendante. La production de N2 est extrêmement élevée dans les zones occupées par les plantes envahissantes à feuilles flottantes (Trapa natans) mais elle est négligeable dans la végétation indigène submergée. Une estimation de la production de N2 dans les lits de Trapa durant l’été, suggère que ces lits représentent une zone très active d’élimination de l’azote. En effet, les grands lits de Trapa ne représentent que 2,7% de la superficie totale de la portion de fleuve étudiée, mais ils éliminent entre 70 et 100% de l'azote total retenu dans cette section pendant les mois d'été et contribuent à près de 25% de l’élimination annuelle d’azote. / Rivers receive nitrogen (N) from their watershed and are the final sites of nutrient processing before delivery to coastal waters. Transformations of dissolved inorganic N (DIN) to gaseous N are highly variable and can impact both coastal eutrophication and greenhouse gas emissions. With anthropogenic N loading to aquatic ecosystems on the rise, nitrous oxide (N2O) emission from rivers should increase. Direct measurements of N2O from lake St. Pierre (LSP), an enlargement of the St. Lawrence River (SLR) indicate that although LSP is a net atmospheric source of N2O to the atmosphere fluxes are low compared to others rivers. Emissions are seasonally and inter-annually highly variable due to changes in hydrological conditions. N2O: N2 is also influenced by hydrology and lower ratios are observed in conditions of higher water discharge and elevated N charge into the ecosystem. In a cross system analysis, hydraulic load mitigates the relation between annual N2O flux and nitrate concentrations in rivers. In SLR, cyanobacterial mats colonizing low nitrate areas are a net source of N with high negative di-nitrogen (N2) fluxes. Given that fixation occurred during daylight and that oxygen concentrations in the water column were supersaturated, we hypothesize that N2 fixation is performed by the dominant cyanobacteria in anoxic micro-zone of the mat and/ or possibly by heterotrophic diazotrophs. Our estimates indicate that N fixation in the mats account for the replacement of up to 33% of the N loss via denitrification in the entire ecosystem during the study period. In the tidal Hudson River N2 production is highly variable between vegetated shallows and was associated with species-driven differences in dissolved oxygen (DO) dynamics during the ebb tide. N2 production was extremely high in invasive floating-leaved plants (Trapa natans) but was insignificant in submersed native vegetation. An estimate of summertime N2 production in Trapa beds suggests that these beds are a major seasonal hotspot for N removal. Large Trapa beds represent only 2.7% of the total area of the tidal Hudson but they remove between 70 and 100% of the total N retained in this section of the river during summer months and contribute to as much as 25% of the annual N removal.

Agricultural management is essential for achieving optimum crop production and maintaining soil quality. Soil microorganisms are responsible for nutrient cycling and are an important consideration for effective soil management. The overall goal of the present research was to better understand microbial communities in agricultural soils as they relate to soil management practices. For this, we evaluated the differential impact of two contrasting drainage practices on microbial community composition and characterized active denitrifiers from selected agricultural sites. Field drainage is important for crop growth in arable soils. Controlled and uncontrolled tile drainage practices maintain water in the field or fully drain it, respectively. Because soil water content influences nutrient concentration, moisture, and oxygen availability, the effects of these two disparate practices on microbial community composition was compared in paired fields that had diverse land management histories. Libraries of the 16S rRNA gene were generated from DNA from 168 soil samples collected from eight fields during the 2012 growing season. Paired-end sequencing using next-generation sequencing was followed by read assembly and multivariate statistical analyses. Results showed that drainage practice exerted no measureable effect on the bacterial communities. However, bacterial communities were impacted by plant cultivar and applied fertilizer, in addition to sampled soil depth. Indicator species were only recovered for depth; plant cultivar or applied fertilizer type had no strong and specific indicator species. Among indicator species for soil depth (30-90 cm) were Chloroflexi (Anaerolineae), Betaproteobacteria (Janthinobacterium, Herminiimonas, Rhodoferax, Polaromonas), Deltaproteobacteria (Anaeromyxobacter, Geobacter), Alphaproteobacteria (Novosphingobium, Rhodobacter), and Actinobacteria (Promicromonospora). Denitrification in agricultural fields transforms nitrogen applied as fertilizer, reduces crop production, and emits N2O, which is a potent greenhouse gas. Agriculture is the highest anthropogenic source of N2O, which underlines the importance of understanding the microbiology of denitrification for reducing greenhouse gas emissions by altered management practices. Existing denitrifier probes and primers are biased due to their development based mostly on sequence information from cultured denitrifiers. To circumvent this limitation, this study investigated active and uncultivated denitrifiers from two agricultural sites in Ottawa, Ontario. Using DNA stable-isotope probing, we enriched nucleic acids from active soil denitrifiers by exposing intact replicate soil cores to NO3- and 13C6-glucose under anoxic conditions using flow-through reactors, with parallel native substrate controls. Spectrophotometric chemistry assays and gas chromatography confirmed active NO3- depletion and N2O production, respectively. Duplicate flow-through reactors were sacrificed after one and four week incubation periods to assess temporal changes due to food web dynamics. Soil DNA was extracted and processed by density gradient ultracentrifugation, followed by fractionation to separate DNA contributed by active denitrifiers (i.e., “heavy” DNA) from that of the background community (i.e., “light” DNA). Light and heavy DNA samples were analyzed by paired-end sequencing of 16S rRNA genes using next-generation sequencing. Multivariate statistics of assembled 16S rRNA genes confirmed unique taxonomic representation in heavy fractions from flow-through reactors fed 13C6-glucose, which exceeded any site-specific or temporal shifts in putative denitrifiers. Based on high relative abundance in heavy DNA, labelled taxa affiliated with the Betaproteobacteria (71%; Janthinobacterium, Acidovorax, Azoarcus, Dechloromonas), Alphaproteobacteria (8%; Rhizobium), Gammaproteobacteria (4%; Pseudomonas), and Actinobacteria (4%; Streptomycetaceae). Metagenomic DNA from the original soil and recovered heavy fractions were subjected to next-generation sequencing and the results demonstrated enrichment of denitrification genes with taxonomic affiliations to Brucella, Ralstonia, and Chromobacterium in heavy fractions of flow-through reactors fed 13C6-glucose. The vast majority of heavy-DNA-associated nitrite-reductase reads annotated to the copper-containing form (nirK), rather than the heme-containing enzyme (nirS). Analysis of recovered nirK genes demonstrated low sequence identity across common primer-binding sites used for the detection and quantification of soil denitrifiers, indicating that these active denitrifiers would not have been detected in molecular surveys of these same soils.

The aim of this thesis was to identify the denitrifying microbial communities in activated sludge from full-scale treatment plants and from small-scale reactors exposed to acetate or methanol as external carbon sources. Biological denitrification is currently the most widely used, sustainable and cost-effective process to remove nitrogen from wastewater. Increasingly strict effluent discharge standards are posing significant challenges to plant operators to reduce effluent NO3--N concentrations to levels as low as 2-3 mg L-1 or even lower. The lack of sufficient influent carbon in many municipal wastewater treatment plants makes it very difficult to achieve such low NO3--N concentrations in the effluent. An effective solution to the problem is to introduce additional external carbon sources to enhance denitrification. The selection of external carbon sources is not purely based on costs but is also dependent on the possible microbial transformations that these carbon sources may bring about in activated sludge. The most common carbon source used is methanol due to its low cost, but it has been found to cause long delays until an improvement in denitrification performance is observed. On the other hand, acetate has been found to improve denitrification almost instantaneously when added, but it has a significantly higher cost. In this study, methanol and acetate utilising denitrifiers were investigated in activated sludge with and without enrichment in laboratory scale bioreactors. The relevant denitrifiers were identified and evaluated in situ using culture independent methods particularly stable isotope probing (SIP), 16S rDNA cloning, fluorescence in situ hybridisation (FISH) and microautoradiography (MAR). Activated sludge collected from a biological nutrient removal plant exhibiting good denitrification was enriched in an anoxically-operated sequencing batch reactor (SBR) by feeding methanol as the sole carbon source and nitrate as the electron acceptor. The SBR was operated over a duration of 7 months and the SBR denitrification rate improved from 0.02 mg NO3--N mg mixed liquor volatile suspended solids (MLVSS)-1 h-1 to a steady-state value of 0.06 mg NO3-N mg MLVSS-1 h-1. At steady state operation the enriched biomass was subjected to SIP with 13C-methanol to biomark the denitrifiers capable of utilising methanol under anoxic conditions. The separated 12C-DNA and 13C-DNA fractions from the SIP experiment were individually subjected to full cycle rRNA analysis. The dominant 16S rRNA gene phylotype (Group-A clones) in the 13C-library was closely related to the obligate methylotrophs Methylobacillus and Methylophilus in the order Methylophilales of the Betaproteobacteria (96-97% sequence identities), while the most abundant clone groups in the 12C-library mostly belonged to the family Saprospiraceae in the Bacteroidetes phylum. Oligonucleotide probes were designed for FISH to target the Group-A clones and Methylophilales (probes DEN67 and MET1216, respectively) and the Saprospiraceae clones (probe SAP553). Application of these probes on SBR biomass over the enrichment period demonstrated a strong correlation between the level of SBR denitrification and relative abundance of DEN67-targeted bacteria in the SBR community. By contrast, no correlation was found between denitrification rate and the relative abundances of the well known denitrifying genera Hyphomicrobium and Paracoccus nor the Saprospiraceae-clones visualised by FISH in the SBR biomass. FISH combined with microautoradiography independently confirmed that the DEN67-targeted cells were the dominant bacterial group capable of anoxic [14C] methanol uptake in the enriched biomass. As observed in full-scale operations, the methanol-fed SBR experienced a lag period of several weeks before denitrification performance increased. Using FISH quantification, it was shown that this coincided with the lag phase in the growth of the DEN67-targeted denitrifying population. It was therefore concluded that the Methylophilales bacteria dominant in our SBR system are likely to be important in full-scale methanol-fed denitrifying sludges. The acetate utilising microbial consortium in activated sludge was investigated without prior enrichment using stable isotope probing (SIP). 13C-acetate was used in SIP to biomark the DNA of the denitrifiers. The extracted 13C-DNA fraction was subjected to a full cycle rRNA analysis. The dominant 16S rRNA gene phylotypes in the 13C-library were closely related to bacterial families Comamonadaceae and Rhodocyclaceae of class Betaproteobacteria (96-97% sequence identities). Seven oligonucleotide probes (DEN444, DEN220, DEN581, DEN441, DEN124, DEN220a and DEN1454) for use in FISH was designed to specifically target the identified phylotypes. Application of these probes on the sludge of a continuously fed denitrifying sequencing batch reactor (CFDSBR) operated over a duration of 16 days indicated a strong correlation between the level of CFDSBR denitrification and relative abundance of all probe-targeted bacteria in the CFDSBR community. FISH combined with microautoradiography (FISH-MAR) further confirmed that the DEN581- and DEN124-targeted cells dominating the CFDSBR were capable of taking up [14C] acetate under anoxic conditions. The initial occurrence of the DEN444- and DEN1454-targeted bacteria and the final dominance of DEN581- and DEN124-targeted bacteria in the CFDSBR community were likely related to the changing in-reactor nitrite concentrations during the first few days of CFDSBR operation. Hence, the DEN444- and DEN1454-targeted bacteria were hypothesised to have low affinities for nitrite while DEN124- and DEN581-targeted bacteria have higher nitrite affinities. However, it was clear that all probe-targeted bacteria were denitrifiers capable of utilising acetate as a carbon source. The rapid increase in numbers of the probe-targeted organisms positively correlates with the immediate increase in denitrification rates. The rapid response and community shifts observed when acetate was used to enhance denitrification suggest that an intermittent application of acetate is quite effective to temporarily enhance the denitrification capacity of a treatment plant. However, the importance of a bacterial impact assessment of activated sludge subjected to intermittent acetate supplementation is recommended prior to the wide use of acetate in the wastewater industry. The acetate utilising denitrifying microbial communities investigated in the previous chapter were characterised according to their eco-physiological properties using the r- and K-selection criteria. The electron donor (acetate) and acceptor (nitrite) affinities of these probe-identified denitrifiers were used as traits for this characterisation. The substrate to microorganism (S/M) ratio was manipulated to provide high and low substrate concentrations in the reactor to create conditions favourable for r- and K-strategists, respectively. Two factors, namely feeding regimes and sludge retention times, were studied to achieve the desired S/M ratios and enable r/K characterisation. The high substrate affinities and high specific growth rates of two probe-identified denitrifiers (DEN124 and DEN581) did not enable resolution of these two organisms with the feeding regimes used in this study. However, the application of different sludge retention times as a control strategy to maintain constant high and low in-reactor S/M ratios enabled characterisation of the two probe-targeted denitrifiers DEN124 and DEN581 as K- and r-strategists, respectively. The in-reactor S/M ratios applied in this study did not facilitate the characterisation of populations targeted by probes DEN444 and DEN1454. The minor fluctuations of the S/M ratios during a cycle in the SBR operation was considered as a drawback, but conclusive results could still be obtained from the study. A chemostat reactor operation with constant loading and variable flow rates is suggested as an alternative. Conclusively, this study was able to identify specific groups of denitrifying microorganisms in activated sludge when exposed to acetate and methanol. Unlike most previous studies, which relied on culture dependent methods, this study adopted a pure culture independent approach to identify microorganisms in relation to their function, i.e. denitrification. Moreover, acetate denitrifiers were in situ characterised based on eco-physiological properties. The identification of denitrifying communities in this study has paved the way to a larger research project on the optimisation of denitrification processes with external acetate, methanol and other carbon supplements. As such, this study has contributed significantly to the understanding of the denitrification processes by linking process data with microbial investigations.

The aim of this thesis was to identify the denitrifying microbial communities in activated sludge from full-scale treatment plants and from small-scale reactors exposed to acetate or methanol as external carbon sources. Biological denitrification is currently the most widely used, sustainable and cost-effective process to remove nitrogen from wastewater. Increasingly strict effluent discharge standards are posing significant challenges to plant operators to reduce effluent NO3--N concentrations to levels as low as 2-3 mg L-1 or even lower. The lack of sufficient influent carbon in many municipal wastewater treatment plants makes it very difficult to achieve such low NO3--N concentrations in the effluent. An effective solution to the problem is to introduce additional external carbon sources to enhance denitrification. The selection of external carbon sources is not purely based on costs but is also dependent on the possible microbial transformations that these carbon sources may bring about in activated sludge. The most common carbon source used is methanol due to its low cost, but it has been found to cause long delays until an improvement in denitrification performance is observed. On the other hand, acetate has been found to improve denitrification almost instantaneously when added, but it has a significantly higher cost. In this study, methanol and acetate utilising denitrifiers were investigated in activated sludge with and without enrichment in laboratory scale bioreactors. The relevant denitrifiers were identified and evaluated in situ using culture independent methods particularly stable isotope probing (SIP), 16S rDNA cloning, fluorescence in situ hybridisation (FISH) and microautoradiography (MAR). Activated sludge collected from a biological nutrient removal plant exhibiting good denitrification was enriched in an anoxically-operated sequencing batch reactor (SBR) by feeding methanol as the sole carbon source and nitrate as the electron acceptor. The SBR was operated over a duration of 7 months and the SBR denitrification rate improved from 0.02 mg NO3--N mg mixed liquor volatile suspended solids (MLVSS)-1 h-1 to a steady-state value of 0.06 mg NO3-N mg MLVSS-1 h-1. At steady state operation the enriched biomass was subjected to SIP with 13C-methanol to biomark the denitrifiers capable of utilising methanol under anoxic conditions. The separated 12C-DNA and 13C-DNA fractions from the SIP experiment were individually subjected to full cycle rRNA analysis. The dominant 16S rRNA gene phylotype (Group-A clones) in the 13C-library was closely related to the obligate methylotrophs Methylobacillus and Methylophilus in the order Methylophilales of the Betaproteobacteria (96-97% sequence identities), while the most abundant clone groups in the 12C-library mostly belonged to the family Saprospiraceae in the Bacteroidetes phylum. Oligonucleotide probes were designed for FISH to target the Group-A clones and Methylophilales (probes DEN67 and MET1216, respectively) and the Saprospiraceae clones (probe SAP553). Application of these probes on SBR biomass over the enrichment period demonstrated a strong correlation between the level of SBR denitrification and relative abundance of DEN67-targeted bacteria in the SBR community. By contrast, no correlation was found between denitrification rate and the relative abundances of the well known denitrifying genera Hyphomicrobium and Paracoccus nor the Saprospiraceae-clones visualised by FISH in the SBR biomass. FISH combined with microautoradiography independently confirmed that the DEN67-targeted cells were the dominant bacterial group capable of anoxic [14C] methanol uptake in the enriched biomass. As observed in full-scale operations, the methanol-fed SBR experienced a lag period of several weeks before denitrification performance increased. Using FISH quantification, it was shown that this coincided with the lag phase in the growth of the DEN67-targeted denitrifying population. It was therefore concluded that the Methylophilales bacteria dominant in our SBR system are likely to be important in full-scale methanol-fed denitrifying sludges. The acetate utilising microbial consortium in activated sludge was investigated without prior enrichment using stable isotope probing (SIP). 13C-acetate was used in SIP to biomark the DNA of the denitrifiers. The extracted 13C-DNA fraction was subjected to a full cycle rRNA analysis. The dominant 16S rRNA gene phylotypes in the 13C-library were closely related to bacterial families Comamonadaceae and Rhodocyclaceae of class Betaproteobacteria (96-97% sequence identities). Seven oligonucleotide probes (DEN444, DEN220, DEN581, DEN441, DEN124, DEN220a and DEN1454) for use in FISH was designed to specifically target the identified phylotypes. Application of these probes on the sludge of a continuously fed denitrifying sequencing batch reactor (CFDSBR) operated over a duration of 16 days indicated a strong correlation between the level of CFDSBR denitrification and relative abundance of all probe-targeted bacteria in the CFDSBR community. FISH combined with microautoradiography (FISH-MAR) further confirmed that the DEN581- and DEN124-targeted cells dominating the CFDSBR were capable of taking up [14C] acetate under anoxic conditions. The initial occurrence of the DEN444- and DEN1454-targeted bacteria and the final dominance of DEN581- and DEN124-targeted bacteria in the CFDSBR community were likely related to the changing in-reactor nitrite concentrations during the first few days of CFDSBR operation. Hence, the DEN444- and DEN1454-targeted bacteria were hypothesised to have low affinities for nitrite while DEN124- and DEN581-targeted bacteria have higher nitrite affinities. However, it was clear that all probe-targeted bacteria were denitrifiers capable of utilising acetate as a carbon source. The rapid increase in numbers of the probe-targeted organisms positively correlates with the immediate increase in denitrification rates. The rapid response and community shifts observed when acetate was used to enhance denitrification suggest that an intermittent application of acetate is quite effective to temporarily enhance the denitrification capacity of a treatment plant. However, the importance of a bacterial impact assessment of activated sludge subjected to intermittent acetate supplementation is recommended prior to the wide use of acetate in the wastewater industry. The acetate utilising denitrifying microbial communities investigated in the previous chapter were characterised according to their eco-physiological properties using the r- and K-selection criteria. The electron donor (acetate) and acceptor (nitrite) affinities of these probe-identified denitrifiers were used as traits for this characterisation. The substrate to microorganism (S/M) ratio was manipulated to provide high and low substrate concentrations in the reactor to create conditions favourable for r- and K-strategists, respectively. Two factors, namely feeding regimes and sludge retention times, were studied to achieve the desired S/M ratios and enable r/K characterisation. The high substrate affinities and high specific growth rates of two probe-identified denitrifiers (DEN124 and DEN581) did not enable resolution of these two organisms with the feeding regimes used in this study. However, the application of different sludge retention times as a control strategy to maintain constant high and low in-reactor S/M ratios enabled characterisation of the two probe-targeted denitrifiers DEN124 and DEN581 as K- and r-strategists, respectively. The in-reactor S/M ratios applied in this study did not facilitate the characterisation of populations targeted by probes DEN444 and DEN1454. The minor fluctuations of the S/M ratios during a cycle in the SBR operation was considered as a drawback, but conclusive results could still be obtained from the study. A chemostat reactor operation with constant loading and variable flow rates is suggested as an alternative. Conclusively, this study was able to identify specific groups of denitrifying microorganisms in activated sludge when exposed to acetate and methanol. Unlike most previous studies, which relied on culture dependent methods, this study adopted a pure culture independent approach to identify microorganisms in relation to their function, i.e. denitrification. Moreover, acetate denitrifiers were in situ characterised based on eco-physiological properties. The identification of denitrifying communities in this study has paved the way to a larger research project on the optimisation of denitrification processes with external acetate, methanol and other carbon supplements. As such, this study has contributed significantly to the understanding of the denitrification processes by linking process data with microbial investigations.

The aim of this thesis was to identify the denitrifying microbial communities in activated sludge from full-scale treatment plants and from small-scale reactors exposed to acetate or methanol as external carbon sources. Biological denitrification is currently the most widely used, sustainable and cost-effective process to remove nitrogen from wastewater. Increasingly strict effluent discharge standards are posing significant challenges to plant operators to reduce effluent NO3--N concentrations to levels as low as 2-3 mg L-1 or even lower. The lack of sufficient influent carbon in many municipal wastewater treatment plants makes it very difficult to achieve such low NO3--N concentrations in the effluent. An effective solution to the problem is to introduce additional external carbon sources to enhance denitrification. The selection of external carbon sources is not purely based on costs but is also dependent on the possible microbial transformations that these carbon sources may bring about in activated sludge. The most common carbon source used is methanol due to its low cost, but it has been found to cause long delays until an improvement in denitrification performance is observed. On the other hand, acetate has been found to improve denitrification almost instantaneously when added, but it has a significantly higher cost. In this study, methanol and acetate utilising denitrifiers were investigated in activated sludge with and without enrichment in laboratory scale bioreactors. The relevant denitrifiers were identified and evaluated in situ using culture independent methods particularly stable isotope probing (SIP), 16S rDNA cloning, fluorescence in situ hybridisation (FISH) and microautoradiography (MAR). Activated sludge collected from a biological nutrient removal plant exhibiting good denitrification was enriched in an anoxically-operated sequencing batch reactor (SBR) by feeding methanol as the sole carbon source and nitrate as the electron acceptor. The SBR was operated over a duration of 7 months and the SBR denitrification rate improved from 0.02 mg NO3--N mg mixed liquor volatile suspended solids (MLVSS)-1 h-1 to a steady-state value of 0.06 mg NO3-N mg MLVSS-1 h-1. At steady state operation the enriched biomass was subjected to SIP with 13C-methanol to biomark the denitrifiers capable of utilising methanol under anoxic conditions. The separated 12C-DNA and 13C-DNA fractions from the SIP experiment were individually subjected to full cycle rRNA analysis. The dominant 16S rRNA gene phylotype (Group-A clones) in the 13C-library was closely related to the obligate methylotrophs Methylobacillus and Methylophilus in the order Methylophilales of the Betaproteobacteria (96-97% sequence identities), while the most abundant clone groups in the 12C-library mostly belonged to the family Saprospiraceae in the Bacteroidetes phylum. Oligonucleotide probes were designed for FISH to target the Group-A clones and Methylophilales (probes DEN67 and MET1216, respectively) and the Saprospiraceae clones (probe SAP553). Application of these probes on SBR biomass over the enrichment period demonstrated a strong correlation between the level of SBR denitrification and relative abundance of DEN67-targeted bacteria in the SBR community. By contrast, no correlation was found between denitrification rate and the relative abundances of the well known denitrifying genera Hyphomicrobium and Paracoccus nor the Saprospiraceae-clones visualised by FISH in the SBR biomass. FISH combined with microautoradiography independently confirmed that the DEN67-targeted cells were the dominant bacterial group capable of anoxic [14C] methanol uptake in the enriched biomass. As observed in full-scale operations, the methanol-fed SBR experienced a lag period of several weeks before denitrification performance increased. Using FISH quantification, it was shown that this coincided with the lag phase in the growth of the DEN67-targeted denitrifying population. It was therefore concluded that the Methylophilales bacteria dominant in our SBR system are likely to be important in full-scale methanol-fed denitrifying sludges. The acetate utilising microbial consortium in activated sludge was investigated without prior enrichment using stable isotope probing (SIP). 13C-acetate was used in SIP to biomark the DNA of the denitrifiers. The extracted 13C-DNA fraction was subjected to a full cycle rRNA analysis. The dominant 16S rRNA gene phylotypes in the 13C-library were closely related to bacterial families Comamonadaceae and Rhodocyclaceae of class Betaproteobacteria (96-97% sequence identities). Seven oligonucleotide probes (DEN444, DEN220, DEN581, DEN441, DEN124, DEN220a and DEN1454) for use in FISH was designed to specifically target the identified phylotypes. Application of these probes on the sludge of a continuously fed denitrifying sequencing batch reactor (CFDSBR) operated over a duration of 16 days indicated a strong correlation between the level of CFDSBR denitrification and relative abundance of all probe-targeted bacteria in the CFDSBR community. FISH combined with microautoradiography (FISH-MAR) further confirmed that the DEN581- and DEN124-targeted cells dominating the CFDSBR were capable of taking up [14C] acetate under anoxic conditions. The initial occurrence of the DEN444- and DEN1454-targeted bacteria and the final dominance of DEN581- and DEN124-targeted bacteria in the CFDSBR community were likely related to the changing in-reactor nitrite concentrations during the first few days of CFDSBR operation. Hence, the DEN444- and DEN1454-targeted bacteria were hypothesised to have low affinities for nitrite while DEN124- and DEN581-targeted bacteria have higher nitrite affinities. However, it was clear that all probe-targeted bacteria were denitrifiers capable of utilising acetate as a carbon source. The rapid increase in numbers of the probe-targeted organisms positively correlates with the immediate increase in denitrification rates. The rapid response and community shifts observed when acetate was used to enhance denitrification suggest that an intermittent application of acetate is quite effective to temporarily enhance the denitrification capacity of a treatment plant. However, the importance of a bacterial impact assessment of activated sludge subjected to intermittent acetate supplementation is recommended prior to the wide use of acetate in the wastewater industry. The acetate utilising denitrifying microbial communities investigated in the previous chapter were characterised according to their eco-physiological properties using the r- and K-selection criteria. The electron donor (acetate) and acceptor (nitrite) affinities of these probe-identified denitrifiers were used as traits for this characterisation. The substrate to microorganism (S/M) ratio was manipulated to provide high and low substrate concentrations in the reactor to create conditions favourable for r- and K-strategists, respectively. Two factors, namely feeding regimes and sludge retention times, were studied to achieve the desired S/M ratios and enable r/K characterisation. The high substrate affinities and high specific growth rates of two probe-identified denitrifiers (DEN124 and DEN581) did not enable resolution of these two organisms with the feeding regimes used in this study. However, the application of different sludge retention times as a control strategy to maintain constant high and low in-reactor S/M ratios enabled characterisation of the two probe-targeted denitrifiers DEN124 and DEN581 as K- and r-strategists, respectively. The in-reactor S/M ratios applied in this study did not facilitate the characterisation of populations targeted by probes DEN444 and DEN1454. The minor fluctuations of the S/M ratios during a cycle in the SBR operation was considered as a drawback, but conclusive results could still be obtained from the study. A chemostat reactor operation with constant loading and variable flow rates is suggested as an alternative. Conclusively, this study was able to identify specific groups of denitrifying microorganisms in activated sludge when exposed to acetate and methanol. Unlike most previous studies, which relied on culture dependent methods, this study adopted a pure culture independent approach to identify microorganisms in relation to their function, i.e. denitrification. Moreover, acetate denitrifiers were in situ characterised based on eco-physiological properties. The identification of denitrifying communities in this study has paved the way to a larger research project on the optimisation of denitrification processes with external acetate, methanol and other carbon supplements. As such, this study has contributed significantly to the understanding of the denitrification processes by linking process data with microbial investigations.

The aim of this thesis was to identify the denitrifying microbial communities in activated sludge from full-scale treatment plants and from small-scale reactors exposed to acetate or methanol as external carbon sources. Biological denitrification is currently the most widely used, sustainable and cost-effective process to remove nitrogen from wastewater. Increasingly strict effluent discharge standards are posing significant challenges to plant operators to reduce effluent NO3--N concentrations to levels as low as 2-3 mg L-1 or even lower. The lack of sufficient influent carbon in many municipal wastewater treatment plants makes it very difficult to achieve such low NO3--N concentrations in the effluent. An effective solution to the problem is to introduce additional external carbon sources to enhance denitrification. The selection of external carbon sources is not purely based on costs but is also dependent on the possible microbial transformations that these carbon sources may bring about in activated sludge. The most common carbon source used is methanol due to its low cost, but it has been found to cause long delays until an improvement in denitrification performance is observed. On the other hand, acetate has been found to improve denitrification almost instantaneously when added, but it has a significantly higher cost. In this study, methanol and acetate utilising denitrifiers were investigated in activated sludge with and without enrichment in laboratory scale bioreactors. The relevant denitrifiers were identified and evaluated in situ using culture independent methods particularly stable isotope probing (SIP), 16S rDNA cloning, fluorescence in situ hybridisation (FISH) and microautoradiography (MAR). Activated sludge collected from a biological nutrient removal plant exhibiting good denitrification was enriched in an anoxically-operated sequencing batch reactor (SBR) by feeding methanol as the sole carbon source and nitrate as the electron acceptor. The SBR was operated over a duration of 7 months and the SBR denitrification rate improved from 0.02 mg NO3--N mg mixed liquor volatile suspended solids (MLVSS)-1 h-1 to a steady-state value of 0.06 mg NO3-N mg MLVSS-1 h-1. At steady state operation the enriched biomass was subjected to SIP with 13C-methanol to biomark the denitrifiers capable of utilising methanol under anoxic conditions. The separated 12C-DNA and 13C-DNA fractions from the SIP experiment were individually subjected to full cycle rRNA analysis. The dominant 16S rRNA gene phylotype (Group-A clones) in the 13C-library was closely related to the obligate methylotrophs Methylobacillus and Methylophilus in the order Methylophilales of the Betaproteobacteria (96-97% sequence identities), while the most abundant clone groups in the 12C-library mostly belonged to the family Saprospiraceae in the Bacteroidetes phylum. Oligonucleotide probes were designed for FISH to target the Group-A clones and Methylophilales (probes DEN67 and MET1216, respectively) and the Saprospiraceae clones (probe SAP553). Application of these probes on SBR biomass over the enrichment period demonstrated a strong correlation between the level of SBR denitrification and relative abundance of DEN67-targeted bacteria in the SBR community. By contrast, no correlation was found between denitrification rate and the relative abundances of the well known denitrifying genera Hyphomicrobium and Paracoccus nor the Saprospiraceae-clones visualised by FISH in the SBR biomass. FISH combined with microautoradiography independently confirmed that the DEN67-targeted cells were the dominant bacterial group capable of anoxic [14C] methanol uptake in the enriched biomass. As observed in full-scale operations, the methanol-fed SBR experienced a lag period of several weeks before denitrification performance increased. Using FISH quantification, it was shown that this coincided with the lag phase in the growth of the DEN67-targeted denitrifying population. It was therefore concluded that the Methylophilales bacteria dominant in our SBR system are likely to be important in full-scale methanol-fed denitrifying sludges. The acetate utilising microbial consortium in activated sludge was investigated without prior enrichment using stable isotope probing (SIP). 13C-acetate was used in SIP to biomark the DNA of the denitrifiers. The extracted 13C-DNA fraction was subjected to a full cycle rRNA analysis. The dominant 16S rRNA gene phylotypes in the 13C-library were closely related to bacterial families Comamonadaceae and Rhodocyclaceae of class Betaproteobacteria (96-97% sequence identities). Seven oligonucleotide probes (DEN444, DEN220, DEN581, DEN441, DEN124, DEN220a and DEN1454) for use in FISH was designed to specifically target the identified phylotypes. Application of these probes on the sludge of a continuously fed denitrifying sequencing batch reactor (CFDSBR) operated over a duration of 16 days indicated a strong correlation between the level of CFDSBR denitrification and relative abundance of all probe-targeted bacteria in the CFDSBR community. FISH combined with microautoradiography (FISH-MAR) further confirmed that the DEN581- and DEN124-targeted cells dominating the CFDSBR were capable of taking up [14C] acetate under anoxic conditions. The initial occurrence of the DEN444- and DEN1454-targeted bacteria and the final dominance of DEN581- and DEN124-targeted bacteria in the CFDSBR community were likely related to the changing in-reactor nitrite concentrations during the first few days of CFDSBR operation. Hence, the DEN444- and DEN1454-targeted bacteria were hypothesised to have low affinities for nitrite while DEN124- and DEN581-targeted bacteria have higher nitrite affinities. However, it was clear that all probe-targeted bacteria were denitrifiers capable of utilising acetate as a carbon source. The rapid increase in numbers of the probe-targeted organisms positively correlates with the immediate increase in denitrification rates. The rapid response and community shifts observed when acetate was used to enhance denitrification suggest that an intermittent application of acetate is quite effective to temporarily enhance the denitrification capacity of a treatment plant. However, the importance of a bacterial impact assessment of activated sludge subjected to intermittent acetate supplementation is recommended prior to the wide use of acetate in the wastewater industry. The acetate utilising denitrifying microbial communities investigated in the previous chapter were characterised according to their eco-physiological properties using the r- and K-selection criteria. The electron donor (acetate) and acceptor (nitrite) affinities of these probe-identified denitrifiers were used as traits for this characterisation. The substrate to microorganism (S/M) ratio was manipulated to provide high and low substrate concentrations in the reactor to create conditions favourable for r- and K-strategists, respectively. Two factors, namely feeding regimes and sludge retention times, were studied to achieve the desired S/M ratios and enable r/K characterisation. The high substrate affinities and high specific growth rates of two probe-identified denitrifiers (DEN124 and DEN581) did not enable resolution of these two organisms with the feeding regimes used in this study. However, the application of different sludge retention times as a control strategy to maintain constant high and low in-reactor S/M ratios enabled characterisation of the two probe-targeted denitrifiers DEN124 and DEN581 as K- and r-strategists, respectively. The in-reactor S/M ratios applied in this study did not facilitate the characterisation of populations targeted by probes DEN444 and DEN1454. The minor fluctuations of the S/M ratios during a cycle in the SBR operation was considered as a drawback, but conclusive results could still be obtained from the study. A chemostat reactor operation with constant loading and variable flow rates is suggested as an alternative. Conclusively, this study was able to identify specific groups of denitrifying microorganisms in activated sludge when exposed to acetate and methanol. Unlike most previous studies, which relied on culture dependent methods, this study adopted a pure culture independent approach to identify microorganisms in relation to their function, i.e. denitrification. Moreover, acetate denitrifiers were in situ characterised based on eco-physiological properties. The identification of denitrifying communities in this study has paved the way to a larger research project on the optimisation of denitrification processes with external acetate, methanol and other carbon supplements. As such, this study has contributed significantly to the understanding of the denitrification processes by linking process data with microbial investigations.

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Made available in DSpace on 2014-12-17T15:03:27Z (GMT). No. of bitstreams: 1 WelitonFBF_DISSERT.pdf: 2010897 bytes, checksum: 9145c54f00922f08967d3beb644f5f73 (MD5) Previous issue date: 2011-07-28 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / The improper disposal of nitrogen in receiving water courses causes problems such as toxicity to living beings through the consumption of oxygen to meet the nitrogen demand, eutrophication and nitrate contamination of aquifers. For this reason it is often necessary to be carried out complementary treatment of wastewater to eliminate or reduce the concentration of this compound in the wastewater. The objective of this study is to evaluate the biological removal of nitrogen compounds using submerged aerated and anoxic filters as post-treatment of an anaerobic system, with low cost and innovative technology, which in previous studies has shown high removal efficiency of organic matter and great potential biological nitrogen compounds removal. The simple design with perforated hoses for air distribution and filling with plastic parts proved to be very efficient in relation to organic matter removal and nitrification. The system presented, in the best stage, efficiency in converting ammonia to nitrate by 71%, and produced a final effluent concentration below 10 mg / L of NH3-N. In addition, carbon concentration was removed by 77%, producing final effluent with 24 mg/L COD. However, denitrification in anoxic filter was not effective even with the addition of an external carbon source. There was a reduction of up to 56% of nitrogen caused by the process of simultaneous nitrification and denitrification (SND). The high voids space presented by this type of support material coupled with direct aeration of the sludge, allows the respiration of biomass retained between the endogenous phase, increased cell retention time and sludge retention capacity, producing a final effluent with turbidity less than 5 UT and total suspended solids around 5.0 mg/L / A disposi??o inadequada do nitrog?nio em corpos receptores gera problemas como: toxicidade para seres vivos; consumo de oxig?nio do meio para atender a demanda nitrogenada; eutrofiza??o; e contamina??o dos aqu?feros por nitrato. Por esta raz?o ? muitas vezes necess?rio que seja realizado tratamento complementar dos esgotos para eliminar, ou reduzir, a concentra??o deste composto nas ?guas residu?rias. O objetivo deste trabalho ? avaliar a remo??o biol?gica dos compostos nitrogenados utilizando filtros aerados submersos como p?s-tratamento de um sistema anaer?bio, com tecnologia inovadora, de baixo custo, que em estudos anteriores demonstrou grande efici?ncia na remo??o de mat?ria org?nica carbon?cea e grande potencial na remo??o biol?gica de compostos nitrogenados. A forma simples como o sistema foi concebido, com mangueiras perfuradas para distribui??o do ar e preenchimento com pe?as pl?sticas - condu?te cortado - mostrou-se bastante eficiente em rela??o ? remo??o de mat?ria org?nica e na nitrifica??o. O sistema apresentou, na melhor fase, efici?ncia na convers?o de nitrog?nio amoniacal em nitrato de 71%, e produziu efluente final com concentra??o de N-NH3 inferior a 10 mg/L. Al?m disso, observou-se uma redu??o de 77% na concentra??o de carbono, produzindo efluente final com 24 mg/L de DQO. Contudo a desnitrifica??o no filtro an?xico n?o se mostrou eficiente mesmo com a adi??o de uma fonte externa de carbono. Mesmo assim observou-se redu??o de at? 56% do nitrog?nio causado pelo processo de Nitrifica??o e Desnitrifica??o Simult?neas (SND). O grande ?ndice de vazios apresentado por este tipo de material suporte aliado ? aera??o direta do lodo, permite que a respira??o da biomassa retida entre na fase end?gena, aumentado o tempo de reten??o celular e a capacidade de reten??o de lodo, produzindo um efluente final com turbidez inferior a 5 UT e SST em torno de 5,0 mg/L

O escopo principal desse projeto foi o de criar um conjunto de ações integradas que permitissem minimizar os impactos de sistemas de saneamento in situ nos recursos hídricos subterrâneo. Sendo as fossas sépticas, mesmo as bem construídas, pouco efetivas onde há alta densidade populacional, foi desenvolvido e aplicado no loteamento Jardim Santo Antônio (situado na APA de Capivari-Monos, Parelheiros) um novo conceito de saneamento in situ: uma fossa alternativa melhorada com uso de barreiras reativas, que possibilitasse a degradação mais eficiente de nitrato e de microorganismos patogênicos. Para a degradação de microorganismos, o material reativo utilizado correspondeu ao BOF (Basic Oxygen Furnace - resíduo de altos fornos de fundição em siderúrgicas) e para a desnitrificação, a serragem. A barreira reativa para remoção de nitrato foi alvo de estudos desse projeto. Desenvolveu-se um questionário de avaliação de risco sanitário para uma área onde foram cadastrados 178 lotes, em um total de 218 poços e 182 fossas. A partir da análise dos dados por Cluster foi possível selecionar um conjunto de perguntas que estivessem mais relacionadas a riscos de contaminação por bactérias e nitrato. Observou-se que a relação entre as características de construção e operação dos poços pouco pode prever a contaminação por nitrato, o que evidencia que sua presença é de caráter regional, fruto de uma ocupação desordenada e densa. Em contrapartida, as perguntas tiveram maior relação com o parâmetro bactérias, o que implica em uma característica local (do poço em si). Antes da implantação da fossa alternativa melhorada, foram realizados experimentos de colunas de sedimentos em laboratório para se testar a eficiência de serragem na degradação de nitrato. Montaram-se 3 colunas: uma só com sedimentos da área, que correspondeu ao branco, e as outras duas com sedimentos e 10cm e 20cm de espessura de uma mistura de serragem (Cedrinho) com areia, respectivamente. Os resultados mostraram uma eficiência de degradação do nitrato de até 96,5% e 99,7% para as colunas de 10cm e 20cm. Foram instaladas duas fossas na área de estudo: a fossa alternativa melhorada com o uso de barreiras reativas (FA) e a fossa controle (FC), equivalente ao esgotamento usualmente empregado pela comunidade (ausência de materiais reativos). Na Fossa Alternativa, estruturada com as barreiras reativas contendo BOF (1m abaixo do tanque receptor do efluente) e serragem (abaixo do BOF, mas separada deste por 1m de pacote arenoso), é possível discriminar certos comportamentos ao longo de suas posições. O BOF que é rico em óxidos de cálcio e ferro confere ao efluente percolante uma condutividade elétrica mais acentuada e um pH muito básico, em torno de 12. Já a barreira com serragem caracterizou-se por concentrações de oxigênio dissolvido mais baixas e presença de C orgânico na forma dissolvida, condições necessárias para a ocorrência da desnitrificação do nitrato gerado perfil acima. No entanto, as concentrações de oxigênio não devem ter sido suficientemente baixas para uma maior eficiência na desnitrificação na barreira de serragem. Além disso, a eficiência pode ter sido comprometida pelo elevado pH que essa barreira foi submetida pelo efluente percolado antes no BOF, o que afetou a capacidade das bactérias desnitrificantes em suas reações metabólicas. Na Fossa Controle, os íons distribuíram-se ao longo do perfil de forma mais regular. A composição dessa fossa representa a fonte em si, com altas concentrações de N-amoniacal e de carbono orgânico dissolvido e baixas concentrações de oxigênio dissolvido. Para esse tipo de cenário, a nitrificação deve ocorrer na zona não-saturada abaixo da fossa, para que depois o nitrato possa alcançar o lençol freático. / The main purpose of this project was to create a set of integrated actions that could minimize impacts of septic systems on groundwater resources. Since the septic tanks, even the well-constructed ones, are not effective on areas where the population density is high, an alternative latrine improved with reactive barriers was developed and applied in Jardim Santo Antônio settlement (Parelheiros, São Paulo, SP). In order to degrade the microorganisms, the reactive material was BOF (Basic Oxygen Furnace) slag from steel producer facilities, and in order to enhance the denitrification, the material of the reactive barrier was sawdust. The sawdust barrier was the main issue in this project. A risk assessment questionnaire was developed and it was applied to an area where 178 residences were evaluated, totalizing 218 water wells and 182 latrines. A Cluster Analysis was used to select the questions that would be related to the risk of contamination by bacteria or nitrate. It was observed that the inapropriated construction and operation of the wells are poorly related to the level of nitrate contamination, what suggests that the nitrate contamination is a more regional problem. On the other hand, it was found a good relationship between the level of bacteria contaminations and the characteristics of construction and operation of the wells, what suggests that this contamination has a local factor. Before the installation of the enhanced septic tank, soil columns breakthrough experiments were conducted in laboratory to test the efficiency of sawdust in nitrate removal. Three soil columns were set up: one filled only with sediments of Jardim Santo Antonio settlement, and another two with the same kind of sediments and sawdust layers introduced with 10cm and 20cm thickness. The results showed an efficiency of sawdust to denitrification of 96,5% and 99,7%, respectively. Two septic tanks were installed in the study area: the alternative latrine enhanced with reactive barriers (AL), and the control latrine (CL), equivalent to the usual tanks founded on the area. In AL, structured with reactive barriers containing BOF (1m below the wastewater tank) and sawdust (under the BOF layer, but first separate from it by 1m of sand package), it\'s possible to discern few parameter behaviors. BOF, which is rich in calcium oxides and iron oxides, incrises the electrical conductivity and the pH of the effluent (~12). The sawdust barrier, in its turn, was characterized by low concentration of dissolved oxygen and by the presence of dissolved organic carbon, essential conditions denitrification ocurrence. The denitrification efficiency of the sawdust barrier was affected by the high pH observed in the effluent that crossed the BOF barrier, which perturbed the denitrifying bacteria performance. In CL, the vertical distribution of the ions was more regular. The samples from this system presented high levels of ammonium and DOC and low values for dissolved oxygen. For this case, the nitrification must happen in the unsaturated zone bellow the tank, so the nitrate formed can reach the groundwater.

Increasing nitrate concentration in ground water from improper disposal of sewage and excessive use of fertilizers is deleterious to human health as ingestion of nitrate contaminated water can cause methaemoglobinemia in infants and possibly cancer in adults. The permissible limit for nitrate in potable water is 45 mg/L. Unacceptable levels of nitrate in groundwater is an important environmental issue as nearly 80 % of Indian rural population depends on groundwater as source of drinking water. Though numerous technologies such as reverse osmosis, ion exchange, electro-dialysis, permeable reactive barriers using zero-valent iron exists, nitrate removal from water using affordable, sustainable technology, continues to be a challenging issue as nitrate ion is not amenable to precipitation or removable by mineral adsorbents. Tapping the denitrification potential of soil denitrifiers which are inherently available in the soil matrix is a possible sustainable approach to remove nitrate from contaminated drinking water. Insitu denitrification is a useful process to remove NO3–N from water and wastewater. In biological denitrification, nitrate ions function as terminal electron acceptor instead of oxygen; the carbon source serve as electron donor and the energy generated in the redox process is utilized for microbial cell growth and maintenance. In this process, microorganisms first reduce nitrate to nitrite and then produce nitric oxide, nitrous oxide, and nitrogen gas. The pathway for nitrate reduction can be written as: NO3-→ NO2-→ NO → N2O → N2. (i) Insitu denitrification process occurring in soil environments that utilizes indigenous soil microbes is the chosen technique for nitrate removal from drinking water in this thesis. As presence of clay in soil promotes bacterial activity, bentonite clay was mixed with natural sand and this mix, referred as bentonite enhanced sand (BES) acted as the habitat for the denitrifying bacteria. Nitrate reduction experiments were carried out in batch studies using laboratory prepared nitrate contaminated water spiked with ethanol; the batch studies examined the mechanisms, kinetics and parameters influencing the heterotrophic denitrification process. Optimum conditions for effective nitrate removal by sand and bentonite enhanced sand (BES) were evaluated. Heterotrophic denitrification reactors were constructed with sand and BES as porous media and the efficiency of these reactors in removing nitrate from contaminated water was studied. Batch experiments were performed at 40°C with sand and bentonite enhanced sand specimens that were wetted with nutrient solution containing 22.6 mg of nitrate-nitrogen and ethanol to give C/N ratio of 3. The moist sand and BES specimens were incubated for periods ranging from 0 to 48 h. During nitrate reduction, nitrite ions were formed as intermediate by-product and were converted to gaseous nitrogen. There was little formation of ammonium ions in the soil–water extract during reduction of nitrate ions. Hence it was inferred that nitrate reduction occurred by denitrification than through dissimilatory nitrate reduction to ammonium (DNRA). The reduction in nitrate concentration with time was fitted into rate equations and was observed to follow first order kinetics with a rate constant of 0.118 h-1 at 40°C. Results of batch studies also showed that the first order rate constant for nitrate reduction decreased to 5.3x10-2 h-1 for sand and 4.3 x10-2 h-1 for bentonite-enhanced sand (BES) at 25°C. Changes in pH, redox potential and dissolved oxygen in the soil-solution extract served as indicators of nitrate reduction process. The nitrate reduction process was associated with increasing pH and decreasing redox potential. The oxygen depletion process followed first order kinetics with a rate constant of 0.26 h-1. From the first order rate equation of oxygen depletion process, the nitrate reduction lag time was computed to be 12.8 h for bentonite enhanced sand specimens. Ethanol added as an electron donor formed acetate ions as an intermediate by-product that converted to bicarbonate ions; one mole of nitrate reduction generated 1.93 moles of bicarbonate ions that increased the pH of the soil-solution extract. The alkaline pH of BES specimen (8.78) rendered it an ideal substrate for soil denitrification process. In addition, the ability of bentonite to stimulate respiration by maintaining adequate levels of pH for sustained bacterial growth and protected bacteria in its microsites against the effect of hypertonic osmotic pressures, promoting the rate of denitrification. Buffering capacity of bentonite was mainly due to high cation exchange capacity of the clay. The presence of small pores in BES specimens increased the water retention capacity that aided in quick onset of anaerobiosis within the soil microsites. The biochemical process of nitrate reduction was affected by physical parameters such as bentonite content, water content, and temperature and chemical parameters such as C/N ratio, initial nitrate concentration and presence of indigenous micro-organisms in contaminated water. The rate of nitrate reduction process progressively increased with bentonite content but the presence of bentonite retarded the conversion of nitrite ions to nitrogen gas, hence there was significant accumulation of nitrite ions with increase in bentonite content. The dependence of nitrate reduction process on water content was controlled by the degree of saturation of the soil specimens. The rate of nitrate reduction process increased with water content until the specimens were saturated. The threshold water content for nitrate reduction process for sand and bentonite enhanced sand specimens was observed to be 50 %. The rate of nitrate reduction linearly increased with C/N ratio till steady state was attained. The optimum C/N ratio was 3 for sand and bentonite enhanced sand specimens. The activation energy (Ea) for this biochemical reaction was 35.72 and 47.12 kJmol-1 for sand and BES specimen respectively. The temperature coefficient (Q10) is a measure of the rate of change of a biological or chemical system as a consequence of increasing the temperature by 10°C. The temperature coefficient of sand and BES specimen was 2.0 and 2.05 respectively in the 15–25°C range; the temperature coefficients of sand and BES specimens were 1.62 and 1.77 respectively in the 25–40°C range. The rate of nitrate reduction linearly decreased with increase in initial nitrate concentration. The biochemical process of nitrate reduction was unaffected by presence of co-ions and nutrients such as phosphorus but was influenced by presence of pathogenic bacteria. Since nitrate leaching from agricultural lands is the main source of nitrate contamination in ground water, batch experiments were performed to examine the role of vadose (unsaturated soil) zone in the nitrate mitigation by employing sand and BES specimens with varying degree of soil saturation and C/N ratio as controlling parameters. Batch studies with sand and BES specimens showed that the incubation period required to reduce nitrate concentrations below 45 mg/L (t45) strongly depends on degree of saturation when there is inadequate carbon source available to support denitrifying bacteria; once optimum C/N ratio is provided, the rate of denitrification becomes independent of degree of soil saturation. The theoretical lag time (lag time refers to the period that is required for denitrification to commence) for nitrate reduction for sand specimens at Sr= 81 and 90%, C/N ratio = 3 and temperature = 40ºC corresponded to 24.4 h and 23.1 h respectively. The lag time for BES specimens at Sr = 84 and 100%, C/N ratio = 3 and temperature = 40ºC corresponded to 13.9 h and 12.8 h respectively. Though the theoretically computed nitrate reduction lag time for BES specimens was nearly half of sand specimens, it was experimentally observed that nitrate reduction proceeds immediately without any lag phase in sand and BES specimens suggesting the simultaneous occurrence of anaerobic microsites in both. Denitrification soil columns (height = 5 cm and diameter = 8.2 cm) were constructed using sand and bentonite-enhanced sand as porous reactor media. The columns were permeated with nitrate spiked solutions (100 mg/L) and the outflow was monitored for various chemical parameters. The sand denitrification column (packing density of 1.3 Mg/m3) showed low nitrate removal efficiency because of low hydraulic residence time (1.32 h) and absence of carbon source. A modified sand denitrification column constructed with higher packing density (1.52 Mg/m3) and ethanol addition to the influent nitrate solution improved the reactor performance such that near complete nitrate removal was achieved after passage of 50 pore volumes. In comparison, the BES denitrification column achieved 87.3% nitrate removal after the passage of 28.9 pore volumes, corresponding to 86 h of operation of the BES reactor. This period represents the maturation period of bentonite enhanced sand bed containing 10 % bentonite content. Though nitrate reduction is favored by sand bed containing 10 % bentonite, the low flow rate (20-25 cm3/h) impedes its use for large scale removal of nitrate from drinking water. Hence new reactor was designed using lower bentonite content of 5 % that required maturation period of 9.6 h. The 5 and 10 % bentonite-enhanced sand reactors bed required shorter maturation period than sand reactor as presence of bentonite contributes to increase in hydraulic retention time of nitrate within the reactor. On continued operation of the BES reactors, reduction in flow rate from blocking of pores by microbial growth on soil particles and accumulation of gas molecules was observed that was resolved by backwashing the reactors.