Thesis (M.Phil.)--Hong Kong University of Science and Technology, 2005. / Includes bibliographical references (leaves 96-105). Also available in electronic version.

Thesis (Ph.D.)--Montana State University--Bozeman, 2007. / Typescript. Chairperson, Graduate Committee: John W. Peters. Includes bibliographical references (leaves 155-169).

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

The role of autotrophic production in different coastal habitats in the production of fish in estuaries is an important consideration in coastal management and conservation. In the estuarine waters of the Australian east coast, many economically important fish species occur over mudflats lacking conspicuous vegetation. I used stable isotope analysis to examine where such fish ultimately derived their nutrition, in the subtropical waters of southern Moreton Bay, Queensland, Australia. I first tested traditional processing methodologies of autotroph samples, in this case of mangrove leaves, and examined variability in mangrove isotope values at different spatial scales. Mangrove leaves processed using time-consuming grinding showed no significant difference in isotope values than coarsely broken leaf fragments. Isotope values of green leaves were not meaningfully different from yellow or brown leaves that would normally be the leaves that actually dropped on to the sediment. Future analyses therefore can use green leaves, since they are more abundant and therefore more easily collected, and can simply be processed as whole leaf fragments rather than being ground to a powder. Carbon and nitrogen isotope values varied at several spatial scales. The proportion of variability partitioned at different scales varied depending on the species of mangrove and element (C or N) analysed. To properly represent a geographic area, isotope analysis should be done on leaves collected at different locations and, especially, from different trees within locations. The autotrophic source(s) supporting food webs leading to fish production on mudflats might be either in situ microphytobenthos or material transported from adjacent habitats dominated by macrophytes. I tested the importance of these sources by measuring ?13C values of 22 fish species and six autotroph taxa (microphytobenthos on mudflats, and seagrass, seagrass epiphytic algae, mangroves, saltmarsh succulents and saltmarsh grass in adjacent habitats) in Moreton Bay. I calculated the distribution of feasible contributions of each autotroph to fishes. All fish ?13C values lay in the enriched half of the range for autotrophs. For over 90% of fishes, the top three contributing autotrophs were seagrass, epiphytes and saltmarsh grass, with median estimates of approximately 60-90% from these sources combined. Seagrass was typically ranked as the main contributor based on medians, while epiphytic algae stood out based on 75th percentile contributions. The other three sources, including MPB, were ranked in the top three contributors for only a single fish. Organic matter from seagrass meadows is clearly important at the base of food webs for fish on adjacent unvegetated mudflats, either through outwelling of particular organic matter or via a series of predator-prey interactions (trophic relay). Modelling results indicate that saltmarsh grass (Sporobolus) also had high contributions for many fish species, but this is probably a spurious result, reflecting the similarity in isotope values of this autotroph to seagrass. Carbon from adjacent habitats and not in situ microphytobenthos dominates the nutrition for this suite of 22 fishes caught over mudflats. The ultimate autotrophic sources supporting production of three commercially important fish species from Moreton Bay were re-examined by further analysing carbon and nitrogen stable isotope data. Mean isotope values over the whole estuary for fish and autotroph sources were again modelled to indicate feasible combinations of sources. Variability in isotope values among nine locations (separated by 3-10 km) was then used as a further test of the likelihood that sources were involved in fish nutrition. A positive spatial correlation between isotope values of a fish species and an autotroph indicates a substantial contribution from the autotroph. Spatial correlations were tested with a newly developed randomisation procedure using differences between fish and autotroph values at each location, based on carbon and nitrogen isotopes combined in two-dimensional space. Both whole estuary modelling and spatial analysis showed that seagrass, epiphytic algae and particulate organic matter in the water column, potentially including phytoplankton, are likely contributors to bream (Acanthopagrus australis) nutrition. However, spatial analysis also showed that mangroves were involved (up to 33% contribution), despite a very low contribution based on whole estuary modelling. Spatial analysis for sand whiting (Sillago ciliata) demonstrated the importance of two sources, mangroves and microalgae on the mudflats, considered unimportant based on whole estuary modelling. No spatial correlations were found between winter whiting (Sillago maculata) and autotrophs, either because fish moved among locations or relied on different autotrophs at different locations. Spatial correlations between consumer and source isotope values provide a useful analytical tool for identifying the role of autotrophs in foodwebs, and were used here to demonstrate that organic matter from adjacent habitats, and in some cases also in situ production of microalgae, were important to fish over mudflats. Whilst recognising that production from several habitats is implicated in the nutrition of fishes over mudflats in Moreton Bay, clearly the major source is from seagrass meadows. Organic matter deriving from seagrass itself and/or algae epiphytic on seagrass is the most important source at the base of fisheries food webs in Moreton Bay. The importance of seagrass and its epiphytic algae to production of fisheries species in Moreton Bay reinforces the need to conserve and protect seagrass meadows from adverse anthropogenic influences.

La dénitrification autotrophe à l’aide de composés réduit de soufre est une approche intéressante pour le traitement biologique des contaminations azotées et des effluents pauvre en matière organique. La dénitrification autotrophe utilise des composés inorganiques comme sources d'énergie et de carbone. L'absence de matière organique élimine le besoin de post-traitements pour éliminer l'excès de carbone organique et limite la formation sous-produits d’oxydation dans le cadre de la production d’eau potable. Les eaux usées provenant des industries métallurgiques et minières ont généralement un faible pH, des températures basses et des concentrations élevées en métaux lourds. L'élimination biologique de l'azote est un défi parce que les bactéries dénitrifiantes prospèrent habituellement à pH neutre et à températures ambiantes (20-30 °C).Le but de cette thèse était de développer un procédé robuste de dénitrification à base de soufre dans des bioréacteurs à pH acide, températures psychrophiles (< 20 °C) et concentrations élevées en nickel. Le procédé a été optimisé au préalable avec des essais biologiques étudiant l'influence de la source de soufre (S2O32-, S0 biogénique et le synthétisé chimiquement), de la taille des particules de S0 (poudre et lentilles), de la culture dénitrifiante (cultures pures et mixtes de Thiobacillus) et de la température (6-30 °C) sur la cinétique de la dénitrification. L'utilisation de S2O32- et d’une culture pure de T. denitrificans ont permis d’atteindre des rendements de dénitrification les plus élevés. Le soufre élémentaire biogénique a été testé pour la première fois comme donneur d'électrons pour la dénitrification, montrant des taux de dénitrification 1.7 fois plus élevés que ceux obtenue avec de la poudre de S0 synthétisé chimiquement. Les taux de la dénitrification avec le S2O32- augmentent exponentiellement avec la température et les calculs avec l'équation d'Arrhenius donnent une énergie d'activation apparente Ea de 76.6 kJ/mol.Deux réacteurs à lit fluidisé (FBR) ont été utilisés pour étudier la dénitrification avec S2O32- à différents pH (5.25-7.00) et températures décroissantes (3-20 °C). Des rendements de dénitrification > 99% ont été observés pour eaux usés présentant des pH compris entre 5.75 et 5.30. L'addition d'une unité de carbonatation fournissant au biofilm du CO2 comme source de carbone supplémentaire, permettant une dénitrification complète à un pH de 4.75. Dans le même FBR, des taux de charge d'azote élevés (jusqu'à 3,3 kg N-NO3-/m3 d) avec le thiosulfate ont été maintenu à des températures aussi basses que 3 °C. L'impact de deux composés du Nickel (NiEDTA2- et NiCl2) sur la dénitrification à base de soufre a été étudiée dans deux FBR en parallèle à 20 (± 2) °C et des concentrations de nickel variant dans la gamme de 5-200 mg Ni/L. Dans des bioessais discontinues, 25-100 mg Ni/L de NiCl2 ont inhibée l'élimination de NO3- de 7-16%, alors qu'aucune inhibition n'a été observée avec NiEDTA2-. L'EDTA non complexée a inhibée la dénitrification à des concentrations supérieures à 100 mg/L. Les deux composés de Ni ont montré aucun effet négatif sur la dénitrification en FBR aux concentrations testées. Le bilan massique du nickel, la caractérisation de la phase solide et la modélisation thermodynamique ont révélé que des précipités de nickel ont été principalement éliminés avec l'effluent. Les phosphates, sulfures et oxydes de nickel ont été déterminés comme les principaux précipités de nickel et étaient principalement amorphe.Les FBRs se sont révélés être bioprocédés robustes pour l'élimination de l'azote à pH acide, pour des températures psychrophiles et des concentrations élevées de nickel. Les résultats de cette étude sont d'un grand intérêt pour le traitement des eaux souterraines et minières contaminés par les nitrates dans les régions froides du monde et également pour les eaux usées industrielles acides et chargées en métaux lourds / Autotrophic denitrification driven by reduced sulfur compounds is a promising and cost-effective biological nitrogen removal process, recommended for the treatment of organic-deficient waters, e.g. groundwater and several industrial wastewaters. Autotrophic denitrifiers utilize inorganic compounds as sources of energy and carbon. The lack of organics eliminates the need of post-treatments to remove excess organic carbon and limits the formation of harmful organic byproducts (e.g. trihalomethanes, THM), resulting in a clean and safe treatment also for drinking water. Wastewaters from mining and metal-finishing industry commonly feature low pH and temperatures as well as high heavy metal concentrations. Nitrogen removal from these waters is a technical challenge, since denitrifying bacteria usually thrives at circumneutral pH and ambient temperatures (20-30°C).The aim of this study was to develop a robust and efficient sulfur-based denitrification bioreactor process able to tolerate acidic pH, psychrophilic temperatures (< 20°C) and high nickel concentrations. The process was preliminary optimized in batch bioassays investigating the influence of sulfur source, i.e. thiosulfate (S2O32-) and biogenic and chemically synthesized elemental sulfur (S0), S0 particle size (powder and lentils), denitrifying culture (pure and mixed cultures of Thiobacillus) and temperature (6-30°C) on denitrification kinetics. The use of S2O32- and a pure culture of Thiobacillus denitrificans resulted in the highest denitrification rates. Biogenic S0 was tested for the first time as electron donor for autotrophic denitrification, showing 1.7-fold faster NO3- removal than that achieved with chemically synthesized S0 powder. The rates of thiosulfate-driven denitrification exponentially increased with temperature, being modeled according to the Arrhenius equation with an apparent activation energy Ea of 76.6 kJ/mol and a temperature coefficient Q10 of 3.0.Fluidized-bed reactors (FBRs) were used to investigate continuous thiosulfate-driven denitrification under decreasing feed pH (5.25-7.00) and temperatures (3-20°C). Denitrification efficiencies > 99% were observed at feed and effluent pH as low as 5.75 and 5.30, respectively. At lower feed pH values, the denitrification activity rapidly decreased due to an inorganic carbon deficiency. The addition of a carbonation unit providing CO2 as supplemental carbon source to the FBR biofilm allowed complete denitrification even at a pH of 4.75. In the same FBR, high-rate (up to 3.3 kg N-NO3-/m3 d) thiosulfate-driven denitrification was maintained at temperatures as low as 3°C. The impact of two Ni compounds, i.e. NiEDTA2- and NiCl2, on sulfur-based denitrification was investigated in a parallel FBR at 20 (±2)°C and feed Ni concentrations in the range of 5-200 mg Ni/L. Preliminary batch bioassays were carried out to assess Ni and free EDTA toxicity on sulfur-based denitrification. In batch bioassays, 25-100 mg Ni/L of NiCl2 inhibited NO3- removal by 7-16%, whereas no inhibition was observed with NiEDTA2-. Free EDTA inhibited sulfur-based denitrification at concentrations exceeding 100 mg/L. Both Ni compounds showed no detrimental effects on sulfur-based denitrification in FBR at the tested concentrations. Nickel mass balance, solid-phase characterization and thermodynamic modeling revealed that nickel precipitates were mostly washed out with the effluent, due to the slow Ni precipitation kinetics and high upflow velocities in the FBR. Nickel phosphate, sulfide and oxide were indicated as the main nickel precipitates and were mostly amorphous.FBRs were shown to be powerful and robust biofilm systems for nitrogen removal under acidic pH, psychrophilic temperatures and high nickel concentrations. The results of this study are of great interest for the treatment of NO3- contaminated ground and mining waters in cold regions (e.g. Canadian and Scandinavian regions) as well as acidic and heavy-metal-laden wastewaters

Hydrogen sulfide (H2S), a major odorous component emitted from construction and demolition debris landfills, has received increasing attention. Besides its unpleasant odor, long-term exposure to a very low concentration of H2S can cause a public health issue. Although cover materials such as soil and compost are recommended to be used routinely to control an odor problem from the landfills, the problem still remains. Autotrophic denitrification may have environmental applications including treatment of water, groundwater, wastewater or gaseous streams contaminated with sulfur and/or nitrogen compounds. However, there have been no studies reported in the literature on H2S removal using autotrophic denitrification from landfills. This study, therefore, investigated the application of autotrophic denitrification incorporated into landfill covers in order to evaluate the feasibility of controlling H2S emissions generated from landfills. Research was investigated by two techniques, microcosm and laboratory-scale column studies. The microcosm experiments were conducted to evaluate the kinetics of autotrophic denitrification in various cover materials with H2S-nitrate as electron donor-acceptor couple. Cover materials including soil, compost and sand were tested and nitrate was added. Based on the microcosm study results, the addition of nitrate into soil and compost can stimulate indigenous autotrophic denitrifying bacteria which are capable of H2S oxidation biologically under anoxic conditions. Results also demonstrated that some amount of H2S can be removed physically and chemically by soil or compost. There was no H2S removal observed in sand microcosms. Rapid H2S oxidation to sulfate was achieved, especially in soil. Zero-order kinetics described the H2S oxidation rate in soil and compost microcosms. The rates of sulfide oxidation under autotrophic denitrification in soil and compost were 2.57 mg H2S/d-g dry soil and 0.17 mg H2S/d-g dry compost, respectively. To further explore H2S removal in a landfill biocover, two sets of column experiments were run. The first set of columns contained seven cm of soil. The autotrophic column was prepared with 1.94 mg KNO3/g dry soil; an identical control column was prepared without nitrate. A gas stream was introduced to the columns with a H2S concentration of 930 ppm. The second set contained seven cm of soil, with both an autotrophic (0.499 mg KNO3/g dry soil) and a control column. Influent H2S concentration was 140 ppm for the second set. Column studies supported the results of microcosm studies; removal of H2S was observed in all columns due to the capacity for soil to absorb H2S, however autotrophic columns removed significantly more. The higher concentration of H2S resulted in partial oxidation to elemental sulfur, while sulfate was found at levels predicted by stoichiometric relationships at the lower concentration. H2S oxidation in the column with higher loading was found to follow zero-order kinetics. The rate of H2S oxidation was 0.46 mg H2S removed/d-g dry soil. Economic comparison of cover systems including autotrophic denitrification, soil amended with lime, fine concrete, and compost covers were analyzed. Based on a case-study landfill area of 0.04 km2, the estimated H2S emissions of 80,900 kg over the 15-year period and costs of active cover system components (ammonium nitrate fertilizer, lime, concrete and compost), autotrophic denitrification cover was determined to be the most cost-effective method for controlling H2S emissions from landfills.

Nitrification is a biological oxidation of NH3 to NO2- and then to NO3-. Understanding how the nitrifier community responds to agricultural management is essential because the community composition is complex and functional distinction of subgroups occurs. Better managing nitrifiers could benefit the environment by increasing nitrogen (N) fertilizer use efficiency, decreasing NO3- leaching, and reducing NO and N2O emissions. This study examined how long-term N fertilization and tillage influenced nitrifier density, ratios, nitrification rates, and the community structure of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and nitrite-oxidizing bacteria (NOB). The study site was a long-term (>40 years) continuous maize (Zea mays L.) experiment with three N fertilization rates (0, 168, and 336 kg ha-1) and either no-tillage (NT) or plow tillage (PT). Most Probable Number method was used to estimate the density of AOB and NOB; the shaken slurry method was used to measure potential nitrification rates; PCR-denaturing gradient gel electrophoresis (DGGE) was used to analyze nitrifier communities. Tillage, fertilization, and their interaction all significantly influenced the AOB and NOB densities, the ratio of AOB to NOB, and potential nitrification rate. Nitrifier densities and potential nitrification rates increased with increased N fertilization; NOB density increased faster than AOB density with fertilization. The influence of tillage on nitrification was different for different fertilization rates. The trends for nitrifier density and potential nitrification rate were not consistent. Nitrifier community structure was influenced by sample season, N fertilization rates, tillage, and their interaction. Different nitrifier groups had different responses to the treatments. The AOB became more diverse with increasing N input; tillage rather than N fertilizer played a dominant role affecting the AOA community; two NOB genera had different responses to N fertilization rates: Nitrobacter diversity increased with more N applied; Nitrospira was the opposite. Unique bands/members were discovered in different treatments, manifesting environmental selection. Long-term field trials were useful in better understanding how soil management influenced the relationship between nitrifier densities, nitrification rates, and community structure, which may facilitate new approaches to optimize nitrification and provide new clues to discover which environmental factors most influence the nitrifier community in agroecosystems.

Le procédé à biofilm R3F / MBBR est une technologie récente en France qui vient s'ajouter à la gamme des procédés biologiques de traitement de la matière organique et azotée des eaux usées. Sa valeur ajoutée repose sur sa compacité grâce au développement d'une quantité importante de biomasse bactérienne dans un ouvrage à emprise au sol faible. Ainsi, le procédé R3F / MBBR s'avère être une solution intéressante pour le traitement de l'azote dans un contexte de contrainte foncière importante. Le principe de la technologie est l'emploi de biomédias, supports plastiques de quelques centimètres, sur lesquels un biofilm bactérien se développe. Ces biomédias sont mis en suspension dans le réacteur par insufflation d'air ou par brassage mécanique. Aujourd'hui, la modélisation est devenue un outil précieux d'aide au dimensionnement. S'il existe beaucoup de modèles de biofilm aujourd'hui, peu de travaux de recherche ont abouti à l'élaboration d'un modèle dynamique R3F / MBBR à destination de l'ingénierie et capable de simuler le procédé en conditions réelles. Ainsi, l'objectif principal de cette thèse est la construction d'un modèle dynamique utilisable en ingénierie. La validation d'un tel modèle avec des données de terrain n'ayant pas encore été faite, ce point constituera une originalité. Pour ce faire, le fonctionnement d'une unité pilote R3F alimentée par des eaux résiduaires urbaines a été étudié. Le suivi du pilote pendant près de 2 ans en régime pseudo-permanent a d'abord permis d'évaluer les performances de 3 biomédias, travail là encore jamais réalisé. Ensuite, le régime dynamique, par l'application d'à-coups de charge hydraulique à une charge surfacique appliquée donnée, a été étudié. Une campagne de mesure intensive pendant une période de 4 jours en régime dynamique a servi de base pour le calage du modèle. Une période de 30 jours en régime pseudo-permanent a servi de base pour la validation du modèle.Ce travail de modélisation a abouti à l'élaboration d'un protocole de calage qui informe des paramètres à mesurer, et à modifier pour obtenir un modèle dynamique du procédé R3F / MBBR capable de simuler son fonctionnement en conditions réelles. Des protocoles de mesure ont également été élaborés pour estimer la valeur des paramètres à mesurer. Des simulations prédictives réalisées avec le modèle nouvellement calé ont ensuite permis d'évaluer le procédé dans de nouvelles conditions de fonctionnement. Une étude critique du modèle a abouti à la détermination de faiblesses qui limitent la qualité des simulations. Pour ces faiblesses, des propositions d'amélioration ont été apportées. / The R3F / MBBR biofilm process is a relatively recent technology in France able to treat organic and nitrogen matters from domestic wastewaters. Its advantage is its compactness due to the development of a significant quantity of bacterial biomass in a tank with low surface area. Thus, the R3F / MBBR process is a relevant solution for nitrogen treatment in a difficult property context. The principle of this technology is the plastic carriers of few centimeters use, on which a bacterial biofilm grows. These carriers freely move in the tank thanks to a air flow rate or a mixing. Nowadays, modeling has become a relevant tool for design. Lots of biofilm models exist but few research works have led to the carrying out of a R3F / MBBR dynamic model for engineering and able to simulate the process in real conditions. Thus, the principal objective of this thesis is the achievement of a R3F / MBBR dynamic model useful in engineering. The validation of such a model with experimental measurements has never been carried out and will represent an original point. The operating of a R3F pilot-scale wastewater plant fed with domestic wastewater has been studied. The follow-up of the pilot-scale unit, during almost 2 years, has first allowed evaluating the performances of 3 carriers in steady state, a work that has never been achieved. Then, the dynamic state has been studied in applying peak-loads but conserving the daily loading. During 4 days, an intensive measurement campaign in dynamic state has been used to calibrate the model. Another 30 days in steady state has been used to validate the model. This modeling work has led to a calibration protocol which informs about the parameters to measure, and to adjust in order to obtain a R3F / MBBR dynamical model able to simulate its operating in real conditions. Some measurement protocols have also been created to estimate the value of parameters to measure. Some predictive simulations carried out with the calibrated model have then allowed assessing the process in new operating conditions. A critical study of the model has led to the identification of some weaknesses which limit the quality of simulations. Thus, propositions to enhance the model have been brought.

Projected climate change may alter soil carbon dioxide (CO2) efflux from terrestrial ecosystems; yet disentangling effect of plant species from climate drivers remains a key challenge. We explored the effects of the dominant plant species, warming, and precipitation distribution on soil CO2 efflux, its underlying components, and mycorrhizal abundance in southern post oak savannah. Post oak savannah in the south-central US are dominated by three contrasting plant functional types: Schizachyrium scoparium (Michx.) Nash. (little bluestem) a C4 grass, Quercus stellata Wangenh.(post oak)a C3 deciduous tree, and Juniperus virginiana L. (eastern redcedar) a C3 evergreen tree. Monocultures and tree-grass plots were warmed using infrared heaters and precipitation events were manipulated to intensify summer drought and augment cool season precipitation. Soil CO2 efflux, the root, bacterial and hyphal components of CO2 efflux, and mycorrhizal abundance were measured. Soil CO2 efflux varied with seasonal changes in soil VWC and temperature, with higher soil CO2 efflux rates in the spring and lower rates in both the cooler winter season and at the end of the dry summer period. There was no relationship between root length density or root mass density and soil CO2 efflux during the short term precipitation distribution campaigns. Partitioning of root, fungal, and bacterial component contribution to soil CO2 efflux indicated a substantial contribution of bacterial respiration to soil CO2 efflux within this system. There was no relationship between microbial biomass [microbial dissolved organic carbon (DOC)] and soil CO2 efflux, or root length (or mass) density and microbial biomass. This suggests that species and climatic effects on root and microbial activity drive soil CO2 efflux. As plant species within this system differed in their association with mycorrhizal fungi and had a strong effect on the individual components of soil CO2 efflux, we conclude that shifts in vegetation cover and growth and the response of vegetation to long term warming and potential future extreme precipitation events (e.g., large preciptation events, prolonged drought) will be major drivers of changes in soil carbon (C) dynamics and associated soil CO2 efflux.

In an effort to develop cost-effective technologies for the removal of ammonium nitrogen from dairy waste, a novel biological wastewater treatment process, utilizing anaerobic ammonium oxidation (anammox), referred to as Oxygen-Limited Autotrophic Nitrification and Denitrification (OLAND) was examined. Due to the potential use of OLAND-based systems in dairy manure management, a detailed water quality assessment of a modern dairy farm manure treatment-system was conducted. The Johnson Highland Dairy Farm, Glade Spring, Virginia, was selected for this assessment and a comprehensive analysis of the wastewater characteristics throughout the confined animal feeding operation was completed. The results suggest that ammonia concentrations in the anaerobic storage facility was high enough to justify use of treatment technologies that reduce ammonia loads in stored dairy waste. A lightly loaded Fixed Film Bioreactor (FFBR), in which the OLAND process was desired to occur, was then constructed in the laboratory and monitored over 51 days. Of particular interest was the time taken to achieve stable performance of this OLAND system. Furthermore, a protocol was developed to determine whether OLAND based metabolism was occurring. Ammonium nitrogen removal efficiency in the FFBR throughout the 51-day monitoring period was high, averaging approximately 95 % for the length of the study. From day 32 to 51, simultaneous removal of both ammonium and nitrite with a low level of concomitant nitrate production was observed, a key indicator of possible anammox activity. Stoichiometric ratios calculated for the FFBR compared favorably with those already established for OLAND systems. The developed protocol, incorporating anaerobic and aerobic batch experiments, to verify the occurrence of OLAND based metabolism did not yield expected results and described poorly what was being observed in the FFBR. Volatilization of ammonia during the experimental test was suspected and should be controlled when the protocol is performed in the future. / Master of Science