L'éventail sous-marin profond du Congo, situé sur la marge continentale Congo-Angolaise (côte Ouest Africaine, Océan Atlantique Equatorial Sud) représente un écosystème sédimentaire marin profond unique.Celui-ci est caractérisé par de forts apports en matière organique provenant du fleuve Congo, qui se déversent le long du canyon et au travers de systèmes chenal Jevées actuels jusque dans les zones les plus profondes (5 000 m) où se développe le système des lobes.L'objectif de cette thèse est d'étudier la distribution spatiale et la diversité phylogénétique et fonctionnelle des communautés archéennes et bactériennes en relation avec les caractéristiques et les contraintes de I'environnement.Cette étude a permis de mettre en évidence une distribution géographique régionale et locale des communautés microbiennes contraintes par la distance des différents lobes par rapport à l'embouchure du chenal. La distribution des communautés microbiennes est liée à la disponibilité en accepteurs et donneurs d'électrons issus de la diagénèse précoce de la matière organique. La composition et l'identité taxonomique de ces communautés microbiennes sont comparables aux communautés rencontrées dans des sédiments marins et des zones d'émission de fluides froids riches en méthane.Cette étude révèle également des densités cellulaires relativement élevées de bactéries méthanotrophes aérobies associées à différents habitats sédimentaires particuliers, colonisés par des bivalves Vesicomyidae, des tapis microbiens et des sédiments réduits caractéristiques des environnements d'émissions de fluides froids riches en méthane et hydrogène sulfuré. Ces communautés sont non seulement apparentées à celles rencontrées dans des habitats d'émissions de fluides froids, mais également à celles des habitats terrestres, malgré la distance ~ 1000 km des côtes Africaines.Les travaux menés au cours de cette thèse montrent l'intérêt des études pluridisciplinaires pour comprendre la diversité et le fonctionnement des écosystèmes dans les lobes terminaux du système turbiditique du Congo et apportent de nouvelles informations sur la diversité des microorganismes peu explorée dans les éventails sous-marins profonds. / The Congo deep sea fan, located in the Congo-Angola continental margin (West African coast, Equatorial South Atlantic Ocean) represents a unique deep-sea sedimentary ecosystem. It is characterized by high organic matter inputs from the Congo River, that flow along a canyon and through presently active channel system-lifted into the deeper areas (5 000 m) where the lobes system develops.The aim of this thesis is to study the spatial distribution as well as the phylogenetic and functional diversity of archaeal and bacterial communities in relation with environmental characteristics and constraints of the terminal lobes of the Congo deep see fan, one of the largest submarine fan systems in the world.This study highlights geographical distribution of microbial communities constrained by the distal and proximal distance of the different lobes from the Congo river's channel mouth as well as linked to the electron donor and acceptor availability from organic matter diagenesis. This study revealed quite high abundance of aerobic methane oxidizing bacteria cells at peculiar sedimentary habitats dominated by Vesicomyid bivalves, microbial mats and reduced sediments typical of cold-seep environments. These communities are not only related to the ones encountered in cold seeps, but also to the ones in terrestrial habitats despite an approximately distance of 1000 km offshore the African coast.This thesis underlines the interest of pluridisciplinary studies to understand the ecosystem diversity and functioning in the terminal lobes of the Congo turbiditic system and provides further insights into the underexplored microbial diversity from deep-sea fans.

Les effondrements miniers en Lorraine (France) ont pour origine la rupture des piliers de soutien constitués de minerai de fer. Leur rupture n'est pas seulement due aux seules contraintes mécaniques qu’exerce le recouvrement mais également aux différentes transformations minéralogiques du minerai de fer, compromettant sa cohésion et sa résistance et par conséquent, la stabilité des piliers. On parle alors d’altération/vieillissement minéralogique du minerai de fer. Les mécanismes chimiques qui entrainent ces transformations minéralogiques sont désormais bien connus mais l’influence de l’activité bactérienne n’est pas encore bien comprise. Des travaux préliminaires ayant soulevé le rôle possible des activités microbiennes, ce travail de thèse s'est alors appliqué à identifier les métabolismes bactériens susceptibles de réagir avec le minerai de fer en conditions aérobie et anaérobie, et à en caractériser les effets physico-chimiques, minéralogiques et mécaniques. Les groupes métaboliques bactériens suspectés d’être impliqués dans ces réactions (activités ferri-réductrices, ferro-oxydantes et sulfato-réductrices) ont été identifiés dans les eaux de mine et incubés en présence du minerai de fer, en souche pure ou avec un consortium issu de l’eau de mine. Les bactéries ferri-réductrices (IRB), sulfato-réductrices (BSR) et acidophiles ferro-oxydantes ont été les seules qui, dans les conditions de laboratoire, ont impacté significativement le minerai en modifiant le ratio Fe(II)/Fe(III). Une phase ferro-carbonatée et de la pyrite se sont formées respectivement au cours des incubations avec les IRB et BSR, et ont été caractérisées par analyse du solide (spectroscopies infrarouge en réflexion diffuse (DRIFTS) et Mössbauer et par diffraction aux rayons X). Des bactéries nitrate-réductrices ont aussi été testées et aucune modification significative du ratio Fe(II)/Fe(III) du minerai de fer n’a été observée. Enfin, les propriétés mécaniques du minerai de fer ont été mesurées après les réactions d’oxydo-réduction biologiques et purement chimiques. Des modifications sensibles de ces propriétés mécaniques par rapport à l’état initial ont ainsi pu être mises en évidence. Sur la base de ces résultats, l’hypothèse de l’altération mécanique du minerai de fer par des activités microbiennes est donc tout à fait réaliste. / Mine collapses occurred in Lorraine (France) because of the failure of safety pillars made of iron ore. Their failure is not only due to the mechanic stresses applied by the overburden, but also due to the various mineralogical transformations in iron ore which decrease material cohesion and resistance and thus stability of pillars. This is called mineralogical alteration/ageing of iron ore. Chemical mechanisms inducing these mineralogical transformations are now well known but the influence of microbial activity is not well understood yet. Preliminary works have raised the possible role of microbial activity, then the focus of this work was to identify the various bacterial metabolisms capable of reacting with iron ore and to characterize the physico-chemical, mineralogical and mechanical effects. The bacterial metabolism groups possibly implied in these reactions (iron-reducing (IRB), iron-oxidizing and sulfate-reducing bacteria (SRB)) were identified from the mine water. As pure strain or as consortium, these bacteria were incubated with iron ore. Under laboratory conditions, only iron-reducing, sulfate-reducing and acidophilic iron-oxidizing bacteria impacted iron ore samples by modifying the Fe(II)/Fe(III) ratio. A ferrous-carbonate phase and pyrite were formed during incubations with IRB and SRB, respectively. These minerals were characterized from analysis of the solid phase (Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS), Mössbauer spectroscopy and X-ray diffraction). The impact nitrate-reducing bacteria was also tested but the Fe(II)/Fe(III) ratio of iron ore was not modified significantly. Finally, mechanical properties of iron ore were measured after microbial and purely chemical redox reactions. Discernible modifications of these mechanical properties were observed. From these results, the alteration of iron ore mechanical properties by bacterial activities is a realistic assumption.

Thesis (PhD (Chemical Engineering))--Cape Peninsula University of Technology, 2019 / Simultaneous nitrification and aerobic denitrification (SNaD) is a preferred method for single stage total nitrogen (TN) removal, which was recently proposed to improve wastewater treatment plant design. However, SNaD processes are prone to inhibition by toxicant loading with free cyanide (CN-) possessing the highest inhibitory effect on such processes, rendering these processes ineffective. Despite the best efforts of regulators to limit toxicant disposal into municipal wastewater sewage systems (MWSSs), free cyanide (CN-) still enters MWSSs through various pathways; hence, it has been suggested that CN- resistant or tolerant microorganisms be utilized for processes such as SNaD. To mitigate toxicant loading, organisms in SNaD have been observed to adopt a multiphase growth strategy to sequentially degrade CN- during primary growth and subsequently degrade TN during the secondary growth phase. However, CN- degrading microorganisms are not widely used for SNaD in MWSSs due to the inadequate application of suitable microorganisms (Chromobacterium violaceum, Pseudomonas aeruginosa, Thiobacillus denitrificans, Rhodospirillum palustris, Klebsiella pneumoniae, and Alcaligenes faecalis) commonly used in single-stage SNaD. The use of CN- degrading or resistant microorganisms for SNaD is a cost-effective method compared to the use of other methods of CN- removal prior to TN removal, as they involve multi-stage systems (as currently observed in MWSSs). The use of CN- degrading microorganisms, particularly when used as a consortium, presents a promising and sustainable resolution to mitigate inhibitory effects of CN- in SNaD. However, SNaD is known to be completely inhibited by CN- thus it is imperative to also study some thermodynamic parameters of SNaD under high CN- conditions to see the feasibility of the process. The Gibbs free energy is significant to understand the feasibility of SNaD, it is also vital to study Gibbs free energy to determine whether or not the biological reaction is plausible. The relationship between the rate of nitrification and Gibbs free energy was also investigated. The attained results showed that up to 37.55 mg CN-/L did not have an effect on SNaD. The consortia degraded CN- and achieved SNaD, with degradation efficiency of 92.9 and 97.7% while the degradation rate of 0.0234 and 0.139 mg/L/hr for ammonium-nitrogen (NH4-N) and CN- respectively. Moreover, all the free Gibbs energy was describing the individual processes were found to be negative, with the lowest Gibbs free energy being -756.4 and -1830.9 Kcal/mol for nitritation and nitratation in the first 48 h of the biological, reaction respectively. Additionally, a linear relationship between the rate of NH4-N and nitrite-nitrogen (NO2-N) degradation with their respective Gibbs free energy was observed. Linear model was also used to predict the relationship between NH4-N, NO2-N degradation and Gibbs free energy. These results obtained showed a good correlation between the models and the experimental data with correlation efficiency being 0.94 and 0.93 for nitritation, and nitratation, respectively. From the results found it can be deduced that SNaD is plausible under high cyanide conditions when cyanide degrading or tolerant microorganisms are employed. This can be a sustainable solution to SNaD inhibition by CN- compounds during wastewater treatment. Furthermore, a single strain was purified from the consortium and identified as Acinetobacter courvalinii. This bacterial strain was found to be able to perform sequential CN- degradation, and SNaD; an ability associated with multiphase growth strategy of the microorganism when provided with multiple nitrogenous sources, i.e. CN- and TN. The effect of CN- on nitrification and aerobic denitrification including enzyme expression, activity and protein functionality of Acinetobacter courvalinii was investigated. It was found that CN- concentration of up to 5.8 mg CN-/L did not affect the growth of Acinetobacter courvalinii. In cultures whereby the A. courvalinii isolate was used, degradation rates of CN- and NH4-N were found to be 2.2 mg CN-/L/h and 0.40 mg NH4-N/L/h, respectively. Moreover, the effect of CN- on NH4-N, nitrate-nitrogen (NO3-N) and NO2-N oxidizing enzymes was investigated, with findings indicating CN- did not affect the expression and activity of ammonia monooxygenase (AMO), but affected the activity of nitrate reductase (NaR) and nitrite reductase (NiR). Nevertheless, a slow decrease in NO2-N was observed after the addition of CN- thus confirming the activity of NaR and the activation of the denitrification pathway by the CN-. Moreover, five models’ (Monod, Moser, Rate law, Haldane, and Andrew’s model) ability to predict SNaD under CN- conditions, indicated that only Rate law, Haldane and Andrew’s models, were suited to predict both SNaD and CN- degradation. Due to low degradation rates of NH4-N and CN-, optimization of SNaD was essential. Therefore, response surface methodology was used to optimize the SNaD under CN- conditions. The physiological parameters that were considered for optimization were temperature and pH; with the result showing that the optimum for pH and temperature was 6.5 and 36.5oC respectively, with NH4-N and CN- degradation efficiency of 50 and 80.2%, respectively. Furthermore, the degradation kinetics of NH4-N and CN- were also studied under the optimum conditions in batch culture reactors, and the results showed that up to 70.6% and 97.3% of NH4-N and CN- were simultaneously degraded with degradation rates of 0.66 and 0.41 mg/L/h, respectively. The predictive ability of RSM was further compared with cybernetic models, and cybernetic models were found to better predict SNaD under CN- conditions. These results exhibited a promising solution in the management of inhibition effected of CN- towards SNaD at an industrial scale.

<p>This thesis is a collection of three research articles to quantify carbon fluxes and isotopic signature changes across global terrestrial ecosystems. Chapter 2, the first article of this thesis, focuses on the importance of an under-estimated methane soil sink for contemporary and future methane budgets in the pan-Arctic region. Methane emissions from organic-rich soils in the Arctic have been extensively studied due to their potential to increase the atmospheric methane burden as permafrost thaws. However, this methane source might have been overestimated without considering high affinity methanotrophs (HAM, methane oxidizing bacteria) recently identified in Arctic mineral soils. From this study, we find that HAM dynamics double the upland methane sink (~5.5 TgCH₄yr^-1) north of 50°N in simulations from 2000 to 2016 by integrating the dynamics of HAM and methanogens into a biogeochemistry model that includes permafrost soil organic carbon (SOC) dynamics. The increase is equivalent to at least half of the difference in net methane emissions estimated between process-based models and observation-based inversions, and the revised estimates better match site-level and regional observations. The new model projects double wetland methane emissions between 2017-2100 due to more accessible permafrost carbon. However, most of the increase in wetland emissions is offset by a concordant increase in the upland sink, leading to only an 18% increase in net methane emission (from 29 to 35 TgCH₄yr^-1). The projected net methane emissions may decrease further due to different physiological responses between HAM and methanogens in response to increasing temperature. This article was published in <i>Nature Climate Change</i> in March 2020.</p> <p>In Chapter 3, the second article of this thesis, I develop and validate the first biogeochemistry model to simulate carbon isotopic signatures (δ¹³C) of methane emitted from global wetlands, and examined the importance of the wetland carbon isotope map for studying the global methane cycle. I incorporated a carbon isotope-enabled module into an extant biogeochemistry model to mechanistically simulate the spatial and temporal variability of global wetland δ¹³C-CH₄. The new model explicitly considers isotopic fractionation during methane production, oxidation, and transport processes. I estimate a mean global wetland δ¹³C-CH₄ of -60.78‰ with its seasonal and inter-annual variability. I find that the new model matches field chamber observations 35% better in terms of root mean square estimates compared to an empirical static wetland δ¹³C-CH₄ map. The model also reasonably reproduces the regional heterogeneity of wetland δ¹³C-CH₄ in Alaska, consistent with vertical profiles of δ¹³C-CH₄ from NOAA aircraft measurements. Furthermore, I show that the latitudinal gradient of atmospheric δ¹³C-CH₄ simulated by a chemical transport model using the new wetland δ¹³C-CH₄ map reproduces the observed latitudinal gradient based on NOAA/INSTAAR global flask-air measurements. I believe this study is the first process-based biogeochemistry model to map the global distribution of wetland δ¹³C-CH₄, which will significantly help atmospheric chemistry transport models partition global methane emissions. This article is in preparation for submission to <i>Nature Geoscience</i>.</p> <p>Chapter 4 of this thesis, the third article, investigates the importance of leaf carbon allocation for seasonal leaf carbon isotopic signature changes and water use efficiency in temperate forests. Temperate deciduous trees remobilize stored carbon early in the growing season to produce new leaves and xylem vessels. The use of remobilized carbon for building leaf tissue dampens the link between environmental stomatal response and inferred intrinsic water use efficiency (iWUE) using leaf carbon isotopic signatures (δ¹³C). So far, few studies consider carbon allocation processes in interpreting leaf δ¹³C signals. To understand effects of carbon allocation on δ¹³C and iWUE estimates, we analyzed and modeled the seasonal leaf δ¹³C of four temperate deciduous species (<i>Acer saccharum, Liriodendron tulipifera, Sassafras albidum, </i>and <i>Quercus alba</i>) and compared the iWUE estimates from different methods, species, and drought conditions. At the start of the growing season, leaf δ¹³C values were more enriched, due to remobilized carbon during leaf-out. The bias towards enriched leaf δ¹³C values explains the higher iWUE from leaf isotopic methods compared with iWUE from leaf gas exchange measurements. I further showed that the discrepancy of iWUE estimates between methods may be species-specific and drought sensitive. The use of δ¹³C of plant tissues as a proxy for stomatal response to environmental processes, through iWUE, is complicated due to carbon allocation and care must be taken when interpreting estimates to avoid proxy bias. This article is in review for publication in <i>New Phytologist</i>.</p> <p> </p>

Partial Nitritation/Anammox process (deammonification process), by which occurs oxidation of ammonium to nitrogen gas by autotrophic bacteria in anaerobic conditions, considered to be cost-effective and environmentally friendly method of nitrogen removal. Present research work focuses on achieving a high nitrogen removal degree, thanks to Anammox bacteria, while providing the best performance of the ongoing process. Integrated fixed-film activated sludge (IFAS) reactor was supplied with the main stream of the wastewater after UASB reactor, characterized by low concentration of nitrogen and organic matter. The bacteria ability to accommodate, were tested in the biofilm and in the activated sludge, depending on the different stages in which the process were being conducted. Batch test, such as Specific Anammox Activity (SAA), Nitrate Uptake Rate (NUR) and Oxygen Uptake Rate (OUR), were used for the evaluation of activity of various groups of bacteria. On the basis of laboratory analysis verified the values obtained from the batch tests. It was determined that a high degree of nitrogen removal (92% of NH4-N) was achieved thanks to the dominant activity of the Anammox bacteria, with low participation of other groups of bacteria. It was also proved, that Anammox bacteria activity were overwhelming in the biofilm. Dominant role of Ammonium Oxidizing Bacteria (AOB) was associated with high activity of Anammox bacteria, which together satisfyingly out-competed Nitrite Oxidizing Bacteria (NOB) and heterotrophic bacteria. It has been shown that Anammox bacteria quickly adapt to the new conditions and they are able to assume a dominant role, even in the case of inoculation of the reactor with the sludge from SBR. This allows conclude, that in the case of operational problems, the reactor can be supplied from another source, in order not to inhibit the process.