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The ability of Nakivubo wetland (which has performed tertiary water treatment for Kampala city for the past 40 years) to respond to pollution and to protect the water quality of Inner Murchison Bay of Lake Victoria was investigated. The aim of this study was to assess the capacity of Nakivubo wetland to remove nitrogen from the wastewater after its recent encroachment and modification, in order to optimize biological nitrogen removal processes using constructed wetland technology. Field studies were performed to assess the hydraulic loading, stability and water quality of this wetland. The distribution and activity of ammonium-oxidizing bacteria (AOB) in Nakivubo channel and wetland were also investigated, and the significance of the different matrices in biological nitrogen transformations within the two systems elucidated. Studies to optimize nutrient removal processes were carried out at pilot scale level both in container experiments and in the field using substrate-free constructed wetlands (CWs) planted with Cyperus papyrus and Miscanthidium violaceum which were adapted to the local ecological conditions. Results showed that Nakivubo wetland performs tertiary treatment for a large volume of wastewater from Kampala city, which is characterised by large quantities of nutrients, organic matter and to a lesser extent metals. Mass pollutant loads showed that wastewater effluent from a sewage treatment plant constituted a larger proportion of nitrogen and phosphorus and biochemical oxygen demand (BOD) discharged into the wetland. The upper section of Nakivubo wetland exhibited high removal efficiencies for BOD, whereas little or no ammonium-nitrogen and metals except Lead were removed by wetland. Studies further showed that nitrifying bacteria existed in the wetland but their activity was limited by oxygen depletion due to the high BOD in the wastewater and heterotrophic bacteria from the sewage treatment plant. Distributional studies indicated the presence of more AOB in surface sediments than the water column of the lower section of Nakivubo channel, an indication that nitrifiers settled with particulate matter prior to discharge into the wetland, and thus did not represent seeding of the wetland. The significant reductions in concentrations of BOD compared to ammonium and total nitrogen in the channel and wetland wastewater confirmed this finding. Whereas suspended nitrifiers upstream of Nakivubo channel equally influenced total nitrogen balance as those in surface sediments, epiphytic nitrification was more important than that of sediment/peat compartments in the wetland, and thus highlighted the detrimental impacts of wetland modification on the water quality Inner Murchison Bay and Lake Victoria as a whole. Performance assessment of pilot-scale container experiments and field-based CWs indicated highly promising treatment efficiencies, notably in papyrus-based treatments. Plant biomass productivity, nutrient storage, and overall system treatment performance were higher in papyrusbased constructed wetlands, and resulted in effluent that met national discharge limits. Thus, papyrus-based CWs were found to be operationally efficient in removing pollutants from domestic wastewater. / QC 20101028

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Vast amounts of carbon are stored forest soils, a product of decaying organic matter. Increased CO2 in the atmosphere is predicted to lead to increasing global temperatures, and more extreme moisture regimes. Such increases in mean temperature could accelerate the rate of organic matter decay in soils and lead to additional release of CO2 into the atmosphere, thus exacerbating climate change. However, due to its impact on plant metabolism, high atmospheric CO2 concentrations may also lead to greater condensed tannins (CT) and reduced nitrogen (N) content in leaf litter. This reduction in litter quality has the potential to slow decay of organic matter in soil and therefore offset the accelerated decay resulting from a warmer climate. My research aimed to quantify the effects of climate and litter chemistry, specifically CT and N, on litter decay, N mineralization and associated microbes in the field. Strings of litterbags were laid on the forest floor along climate transects of mature Douglas-fir stands of coastal British Columbia rain-shadow forests. In-situ climate was monitored alongside carbon and nitrogen loss over 3.58 years of decay along three transects located at different latitudes, each transect spanning the coastal Western Hemlock and Douglas-fir biogeoclimatic zones. Microbial communities in the decaying litter and in forest soils were also analyzed using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Microbial biogeography at field sites was partially influenced by climate, soil characteristics and spatial distance, but did not improve best fit decay models using climate and litter chemistry variables. Litter with greater initial CT and smaller N concentration slowed down early decay (0 - 0.58 yr) and net N mineralization. Warmer temperatures accelerated later decay (0.58 - 3.58 yr) and net N mineralization. Water-soluble CT were rapidly lost during decay, while other forms of CT were likely responsible for slower decay. The composition of fungal communities on decaying litter was affected by initial concentrations of CT and N. On a yearly basis, the slower decay of litter with high CT and reduced N content can offset accelerated rates of decay associated with warmer temperatures. Concurrent shifts in microbial communities and net N mineralization suggest potential benefits to trees. / Graduate / 2017-12-19

Une part importante de la détérioration des réseaux d’assainissement en matériau cimentaire est d’origine biologique. Dans ce contexte, les matériaux à base de ciment alumineux ont montré une meilleure durabilité que ceux à base de ciment Portland ordinaire, couramment utilisés. Les hypothèses de la littérature qui expliqueraient cette meilleure résistance sont centré sur l’aluminium (présent à plus de 50% dans les ciments alumineux pour seulement 5% dans les ciments Portland). L’objectif de cette thèse est de caractériser et hiérarchiser les mécanismes de résistance des matériaux cimentaires lors de la biodétérioration. Cela permettra de comprendre le rôle de l’aluminium dans les interactions entre les microorganismes et les matériaux cimentaires. Après des études en réacteur et des tests de biodétérioration de pâte de ciments en laboratoire, il semblerait que la principale cause de résistance est due à la réactivité des matrices cimentaires plus qu’à un effet inhibiteur de l’aluminium ou du matériau sur les microorganismes. / An important part of the deterioration observed in concrete sewer networks is due to biological activity. In this context, calcium aluminate cement (CAC) based material has shown a better durability than ordinary Portland cement, usually used in such context. In literature, hypothesis explaining the better resistance are focused on aluminium. The aim of the project is to characterize the role of aluminium in the interactions between cementitious material and microorganisms. Reactor study and Lab scale aggressive biodeterioration protocol of cementitious material revealed that the better resistance of CAC is due to their lower reactivity and not to a bacteriostatic effect of the material on the microorganisms.

Pelagic aggregates function as biological carbon pumps for transporting fixed organic carbon to sediments. In iron-rich (ferruginous) lakes, photoferrotrophic and chemolithoautotrophic bacteria contribute to CO2 fixation by oxidizing reduced iron, leading to the formation of iron-rich pelagic aggregates (iron snow). The significance of iron oxidizers in carbon fixation, their general role in iron snow functioning and the flow of carbon within iron snow is still unclear. Here, we combined a two-year metatranscriptome analysis of iron snow collected from an acidic lake with protein-based stable isotope probing to determine general metabolic activities and to trace 13CO2 incorporation in iron snow over time under oxic and anoxic conditions. mRNA-derived metatranscriptome of iron snow identified four key players (Leptospirillum, Ferrovum, Acidithrix, Acidiphilium) with relative abundances (59.6–85.7%) encoding ecologically relevant pathways, including carbon fixation and polysaccharide biosynthesis. No transcriptional activity for carbon fixation from archaea or eukaryotes was detected. 13CO2 incorporation studies identified active chemolithoautotroph Ferrovum under both conditions. Only 1.0–5.3% relative 13C abundances were found in heterotrophic Acidiphilium and Acidocella under oxic conditions. These data show that iron oxidizers play an important role in CO2 fixation, but the majority of fixed C will be directly transported to the sediment without feeding heterotrophs in the water column in acidic ferruginous lakes.

<p>This doctoral research comparatively assesses the biogeochemical properties of suspended aquatic flocs through a integrated field-laboratory approach; providing new insight into the linkages among floc associated bacteria, floc-reactive solid phases and trace metal uptake.</p> <p>Results show flocs to possess a distinct geochemistry, microbiology and composition from bed sedimentary materials in close proximity (III-oxyhydroxide minerals (FeOOH); resulting in localized floc-Fe-mineral precipitates and enhanced reactivity. Further, the Fe-enrichment of floc and of floc bio-mineral constituents in turn provides an important and novel lens through which to examine how environmental microbial communities, microbial metabolism and Fe^III/Fe^IIredox transformations interact. The results were the discovery of floc-hosted, Fe^III/II-redox cycling bacterial consortia across diverse oxygenated (O₂^Sat.=1-103%) aquatic systems, which were not predicted to sustain bacterial Fe-metabolism. Both environmental<em> </em>and experimentally-developed consortial aggregates constituted multiple genera of aero-intolerant Fe^III-reducing and Fe^II-oxidizing bacteria together with oxygen consuming organotrophic species. These findings highlight that the implementation of geochemical thermodynamic constraints alone as a guide to investigating and interpreting microbe-geosphere interactions may not accurately capture processes occurring <em>in situ.</em></p> <p><em> </em> Seasonal investigation of microbial Fe^III/II-redox transformations highlighted the interdependence of floc Fe-redox cycling consortia members, revealing that cold conditions and a turnover in putative Fe-reducing community membership extinguishes the potential for coupled Fe-redox cycling by wintertime floc bacteria. Further, the observed summer-winter seasonal turnover of <em>in situ</em> floc community membership corresponded with an overall shift from dominant Fe to S redox cycling bacterial communities. This significantly impacted observable floc Fe and TE (Cd, Pb) geochemistry, resulting in a shift in floc associated Fe-phases from dominantly Fe^(III)_(s) to Fe^(II)_(s), and, in turn, corresponded to a large decrease of TE uptake by flocs under ice.</p> / Doctor of Science (PhD)

Reconnu par leur effet toxique, inhibiteur et corrosif, les sulfures (S2-, SH-, SH2) sont un sous-produit indésirable de la digestion anaérobie des boues de station de traitement des eaux domestiques de la ville de Marrakech, Maroc (STEP). Ils proviennent essentiellement de la réduction "dissimilatrice" des composés soufrés (SO4 2-, SO3 2-, S2O4 2- ..) contenus dans ces boues. Ce processus est réalisé par un groupe bactérien anaérobie appelé bactéries sulfatoréductrices (BSR). Une fois dans le biogaz, les sulfures sous forme gazeuse réduisent en plus la durée de vie des installations et des équipements de la STEP. Elle est ainsi dotée d’installations biologiques et physico-chimiques lui permettant d’éliminer ces sulfures avant la transformation du biogaz en énergie électrique. Cependant, ces procédés sont onéreuses et grandes consommatrices d’énergies. D’où l’idée de minimiser la production des sulfures au sein même des digesteurs anaérobies. Pour cela, il était nécessaire d’abord de connaître les microorganismes à l'origine de la production des sulfures (BSR), ceux potentiellement impliqués dans leur élimination (bactéries sulfo-oxydantes), et d’un groupe de microorganismes fermentaires (Synergistetes) intervenant dans le bon fonctionnement de la digestion anaérobie. Ces études ont été menées à la fois sur des d'approches moléculaires et culturales. Les résultats obtenus, ont permis de comprendre comment ces groupes bactériens, d’intérêts écologique et économique importants, interviennent dans la digestion anaérobie des boues de la STEP permettant à la fois d’accélérer les processus d’oxydation de la matière organique combinée à la réduction des composés soufrés et de minimiser la concentration des en sulfure dans le biogaz. / Recognized by their toxic, inhibitory and corrosive effect, sulfides (S2-, SH-, H2S) are an undesirable by-product of the anaerobic digestion of from domestic wastewater treatment plants sludge in the city of Marrakech, Morocco (WWTP). They produced mainly by the dissimilatory reduction of sulfur compounds (SO42-, SO32-, S2O42-) contained in these sludges. This process is performed by an anaerobic bacterial group called sulfate reducing bacteria (SRB). Once in the biogas, the sulfides in gaseous form shorten in addition the lifetime of the installations and equipments of the WWTP. It is thus equipped with biological and physicochemical installations allowing it to eliminate these sulfides before the transformation of biogas into electrical energy. However, these processes are expensive and consume large amounts of energy. Hence the idea of minimizing the production of sulfides within anaerobic digesters. For this, it was first necessary to know the microorganisms originating of the production of sulfides (SRB), those potentially involved in their elimination (sulfur oxidizing bacteria), and a group of fermentative microorganisms (Synergistetes) involved in the good functioning of the anaerobic digestion. These studies were conducted on both molecular and cultural approaches. The results obtained allowed to understand how these bacterial groups, of great ecological and economic interest, are involved in the anaerobic digestion of sludge from the WWTP, which both accelerates the oxidation processes of the organic matter combined with the reduction of sulfur compounds and to minimize the concentration of sulfide in biogas.

Ecosystems currently face widespread biodiversity losses and other environmental disturbances, such as climate warming, related to increased anthropogenic activities. Within this context, scientists consider the effects of such changes on the biodiversity, and hence on the activity, of soil microorganisms. Indeed, soil microorganisms mediate a wide range of soil processes. Currently, knowledge on soil microbial diversity is still limited, partially due to technical limitations. The advent of molecular-based analyses now allows studying the soil microbial diversity. These advances in the study of soil microbial communities have lead to a growing evidence of the critical role played by the microbial community in ecosystem functioning. This relationship is supposed to be relevant for narrow processes, regulated by a restricted group of microorganisms, such as the nitrification process. This PhD thesis aimed at studying ammonia oxidizing bacteria (AOB) community structure and richness as an integrated part of soil functioning. This research aimed at investigating the effect of aboveground plant diversity on ammonia oxidizing bacteria diversity and function in forest and grassland soils with focus on the influence of (a) functional group identity of grassland plants (legumes, grasses, forbs), (b) grassland plant species richness and (c) tree species, on AOB diversity and function. Another objective of this research was to study the effect of a 3°C increase in air temperature on AOB diversity and function. The link between AOB diversity and function (potential nitrification) is also investigated. For grassland ecosystems, a microcosm experiment was realized. An experimental platform containing 288 assembled grassland communities was established in Wilrijk (Belgium). Grassland species were grown in 12 sunlit, climate controlled chambers. Each chamber contained 24 communities of variable species richness (S) (9 S=1, 9 S=3 and 6 S=9).The grassland species belonged to three functional groups: three species of each grasses (Dactylis glomerata L., Festuca arundinacea SCHREB., Lolium perenne L.), forbs (non-N-fixing dicots; Bellis perennis L., Rumex acetosa L., Plantagolanceolata L.), and legumes (N-fixing dicots; Trifolium repens L., Medicago sativa L., Lotus corniculatus L.). Half of these chambers were exposed to ambient temperature and the other half were exposed to (ambient +3°C) temperature. One ambient and one (ambient+3°C) chambers were destructively harvested 4, 16 and 28 months after the start of the experiment. The influence of plant functional group identity on the nitrification process and on AOB community structure and richness (AOB diversity) was assessed in soils collected from the first two destructive amplings (chapter 2). The effect of plant species richness on AOB diversity and function was considered for soils sampled after 16 and 28 months (chapter 3). AOB function was determined by potential nitrification. AOB community structure and richness were assessed by polymerase chain reaction followed by denaturing gradient gel electrophoresis (DGGE) and sequencing of excised DGGE bands. I found that functional group identity can affect AOB community structure. In particular, the presence of legumes, both in monoculture or in mixture with forbs and grasses, lead to AOB community composition changes towards AOB clusters tolerating higher ammonium concentrations. This change in AOB community structure was only linked to increased potential nitrification under monocultures of legumes, when ammonium was supposed to be not limiting. This study revealed that physiological attributes of AOB and resource availability may be important factors in controlling the nitrification process. This research showed that the impact of plant species richness on the nitrification process could be mediated by the interactions between plants and AOB, through competition for substrate. A 3°C increase in air temperature did not affect AOB community structure, richness or function. In forest ecosystems, we studied the effect of tree species in forest sites located in Belgian and in the Grand-Duchy of Luxembourg covered each by several deciduous or coniferous tree species (Fagus sylvatica L., Quercus petraea (Mattuschka) Lieblein, Picea abies (L.) Karst, Pseudotsuga menziesii (Mirbel) Franco). We investigated the influence of these tree species on microbial processes (chapter 5) related to C and N cycling, particularly with emphasize on the nitrification process and on the diversity of AOB (chapter 6). The results showed that the effect of tree species on net N mineralization was likely to be mediated through their effect on soil microbial biomass, reflecting their influence on organic matter content and carbon availability. Influence of tree species on nitrification (potential and relative) might be related to the presence of ground vegetation through its influence on soil ammonium and labile C availability. AOB community structure was more site-specific than tree specific. However, within sites, AOB community structure under broadleaved trees differed from the one under coniferous trees. The effect on tree species on AOB was likely to be driven by the influence of tree species on net N mineralization, which regulates the substrate availability for AOB. The results also demonstrated that the relationship between AOB diversity and function might be related both to AOB abundance and AOB community structure and richness. This thesis showed no clear relationship between AOB community structure or richness and AOB function. However, we revealed that aboveground grassland plant richness, grassland plant functional groups and tree species influence AOB community structure and richness. Actuellement, les écosystèmes sont soumis à dimportantes pressions anthropiques et environnementales, pouvant aboutir à des pertes massives de biodiversité. Les scientifiques sinterrogent sur limpact de ces perturbations sur la diversité et, par conséquent, sur lactivité des microorganismes du sol. En effet, ceux-ci régulent de nombreux processus du sol. Actuellement, de nombreuses lacunes subsistent dans la connaissance de la diversité microbienne du sol. Celles-ci peuvent être partiellement attribuées aux difficultés méthodologiques associées à l'étude des micro-organismes du sol. Lavènement des techniques moléculaires nous permet de combler ces lacunes. Les avancées réalisées dans l'étude des communautés microbiennes du sol ont mis en évidence le rôle crucial joué par les communautés microbiennes dans le fonctionnement des écosystèmes. De plus, il semblerait que les processus régulés par un groupe restreint dorganismes, tel le processus de nitrification, soient plus sensibles à toute altération de la communauté. Lobjectif de cette thèse était détudier la structure de la communauté ainsi que la richesse (nombre de bandes DGGE) des bactéries oxydant lammoniac (AOB) comme une partie intégrante du fonctionnement des sols. Notre étude se focalisait sur linfluence de (a) différents groupes fonctionnels de plantes (graminées, légumineuses, dicotylédones), (b) communautés de plantes présentant une richesse spécifique croissante et (c) différentes essences forestières, sur la diversité (structure de la communauté et richesse des AOB) et la fonction des AOB. Cette recherche étudiait également limpact dune augmentation de température de 3°C sur ces paramètres. Létablissement dun lien éventuel entre la diversité et la fonction (nitrification potentielle) des AOB a aussi été envisagé. Concernant les écosystèmes prairiaux, nous avons réalisé une étude en microcosmes. Une plateforme expérimentale comprenant 288 communautés artificielles de plantes a été établie à Wilrijk (Belgique). Cette plateforme consistait en 12 chambres, dont une moitié était à température ambiante et la seconde était à température ambiante augmentée de 3°C. Chaque chambre contient 24 communautés de plantes de richesse spécifique variable (9 S=1, 9 S=3 et 6 S=9). Les communautés de plantes sont créées avec 9 espèces de plantes appartenant à trois groupes fonctionnels : 3 espèces de graminées (Dactylis glomerata L., Festuca arundinacea SCHREB., Lolium perenne L.), de légumineuses (dicotylédones fixatrices dazote ;Trifolim repens L., Medicago sativa L., Lotus corniculatus L.), et de dicotylédones non fixatrices dazote (Bellis perennis L., Rumex acetosa L., Plantago lanceolata L.). Les sols issus dune chambre à température ambiante et dune chambre à température ambiante augmentée de 3°C ont été échantillonnés, respectivement, 4, 16 et 28 mois après le début de lexpérimentation. Linfluence des groupes fonctionnels de plantes sur le processus de nitrification ainsi que sur la structure de la communauté et la richesse des AOB a été mesuré sur les sols issus des deux premiers échantillonnages (chapitre 2). Nous avons mesuré leffet de la richesse croissante en plantes sur la diversité et lactivité des AOB sur les sols échantillonnés après 16 et 28 mois dexpérimentation (chapitre 3). La structure de la communauté ainsi que la richesse des AOB ont été évaluées à laide dune amplification spécifique par réaction de polymérisation en chaîne (PCR) de lADN génomique extrait du sol suivie par une séparation par électrophorèse sur gel dacrylamide en présence dun gradient dénaturant (DGGE). Nous avons identifié les différentes AOB présentes par séquençage des bandes DGGE excisées. Nos résultats ont montré que les différents groupes fonctionnels peuvent affecter la structure de la communauté des AOB. En particulier, la présence de légumineuses, aussi bien en monoculture quen mélange avec des graminées ou des dicotylédones non fixatrices dazote, provoque des changements au sein de la structure de la communauté des AOB, favorisant la présence de clusters tolérants des concentrations en ammonium plus élevées. Ces changements de la structure de la communauté des AOB sont liés à des augmentations de la production potentielle de nitrates (nitrification potentielle) quand lammonium est supposé être non limitant. Cette étude révèle que la physiologie des AOB ainsi que la disponibilité en substrat peuvent être des facteurs majeurs intervenant dans le contrôle du processus de nitrification. Cette recherche montre que linfluence de la richesse spécifique des plantes sur la nitrification pourrait dépendre des interactions entre les plantes et les AOB via la compétition pour le substrat. Une augmentation de la température de lair de 3°C na pas influencé les richesse, structure de la communauté ou les fonctions des AOB. Pour les écosystèmes forestiers, nous aborderons leffet de différentes essences forestières (Picea abies (L.) KARST, Fagus sylvatica L., Quercus petraea LIEBLEIN ; Pseudotsuga menziezii (MIRB.) FRANCO) dans différents peuplements au Grand Duché du Luxembourg et en Belgique. Nous avons étudié l'influence de ces essences forestières sur les processus microbiens (chapitre 5) liés aux cycles du carbone et de lazote, en particulier leur effet sur le processus de nitrification et la diversité des AOB (chapitre 6). Notre étude révèle que linfluence des essences forestières sur la minéralisation nette de lazote pourrait être attribuable à leur effet sur la biomasse microbienne, reflétant ainsi leur effet sur la teneur en matière organique et la disponibilité en carbone. Limpact des essences forestières sur la nitrification (à la fois sur la nitrification relative et sur la nitrification potentielle) serait conditionné par la présence de végétation au sol, en raison de linfluence de celle-ci sur la disponibilité en ammonium et en carbone labile. Nous avons observé que la structure de la communauté des AOB était plus spécifique aux sites quaux essences forestières. Cependant, au sein dun site, elle différait sous feuillus et sous conifères. Les essences forestières influenceraient la structure de la communauté des AOB au travers de limpact quelles ont sur la minéralisation nette de lazote qui régule, quant à elle, la disponibilité en ammonium. Cette recherche démontre que le lien observé entre la diversité et la fonction dépendrait la fois de labondance, de la structure de la communauté et de la richesse des AOB. Cette thèse na révélé aucune relation claire entre la structure de la communauté ou la richesse des AOB et leur fonction. Par contre, nous avons observé que la richesse spécifique et les groupes fonctionnels de plantes prairiales et les essences forestières affectent la structure de la communauté et la richesse des AOB.