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In this dissertation I am using M. truncatula as a model legume that forms indeterminate nodules with rhizobia under limited nitrogen conditions. I take advantage of an M. truncatula Tnt1 mutant population that provides a useful resource to uncover and characterize novel genes. Here, I focused on several objectives. First, I carried out forward and reverse genetic screening of M. truncatula Tnt1 mutant populations to uncover novel genes involved in symbiotic nitrogen fixation. Second, I focused on reverse genetic screening of two genes, identified as encoding blue copper proteins, and characterization of their mutants' potential phenotypes. Third, I further characterized a nodule essential gene, M. truncatula vacuolar iron transporter like 8 (MtVTL8), which encodes a nodule specific iron transporter. I characterized the expression pattern, expression localization and function of MtVTL8. Additionally, I characterized several residues predicted to be essential to function using a model based on the known crystal structure of Eucalyptus grandis vacuolar iron transporter 1 (EgVIT1), a homologous protein to MtVTL8. I identified several potential essential residues of the MtVTL8 protein, mutagenized them, and through complementation experiments in planta and in yeast assessed functionality of the resulting protein. This helped us to better understand the potential mechanism by which MtVTL8 functions.

Diazotrophs supply legumes such as soybean (Glycine max L. Merr) with nitrogen (N) needed for protein synthesis through biological nitrogen fixation (BNF). Through BNF, these bacteria such as Bradyrhizobium that reside in soybean root nodules, convert atmospheric nitrogen (N2) into ammonia (NH3/ NH4), a form that is biologically available for use by the plants, in return for photosynthate carbon from the plant. Abiotic stresses such as drought disrupt BNF and subsequently affects soybean yield. In addition, increasing demand for soybean is leading to supplementing its growth with synthetic N fertilizer. However, fertilizer application is known for its detrimental effects on the environment causing waterways eutrophication contributing to global warming. On the other hand, diazotrophs can supply soybean with up to 90% of N need. As such, improving the understanding and exploiting the relationship between soybean and diazotrophs is key to promoting the sustainable growing of soybean. This dissertation here investigates three main questions. First, how the soybean-diazotrophs respond to changes in water such as rainfall and irrigation. Second, how changes in these bacterial diazotrophs are related to levels of BNF, and N-related soybean molecular markers. Finally, as my colleagues and I found non-diazotrophs in the nodules of some soybean plants, I was curious about the role they are playing inside the nodules in concert with the diazotrophs. The main hypotheses tested in this dissertation are that root nodule bacterial community (bacteriome) would (1) vary by plant type, (2) respond to changes in water, and (3) be related to BNF. To answer the research questions, I devised the dissertation as follows. In Chapter 2, my colleagues and I used nine commercial cultivars of soybean that vary in drought tolerance and agronomic traits. We show that soybean sometimes, but not always, harbor a consortium of non-nitrogen fixing bacteria belonging to Pseudomonadaceae and Enterobacteriaceae families. However, as expected, nodules diazotrophs rather than non-diazotrophs responded most to changes in soil water status. In chapter 3, I used a collection of 24 genotypes of soybean that vary in their ability to fix nitrogen. The results revealed that the bacteriome diazotroph alpha diversity metrics, phylogenetic richness and evenness, was correlated with changes in BNF. Moreover, few N-related molecular markers were associated with some of the bacteria. However, we have also observed a strong effect of the environment on the diazotroph driven process of BNF (i.e. 39%-75%). For chapter 4, we sequenced three of the Pseudomonas spp. strains that were subsequently recovered again from a diversity of soybean nodules in field trials. I found that one of the strains has the ability to adapt to the nodule's unique hypoxic conditions, supporting Bradyrhizobium nodulation and possibly nodule iron. The results include the draft assembly of the proposed Pseudomonas nodulensis sp. nov. as a novel species of nodule adapted bacteria belonging to the P. fluorescens complex. The results of this dissertation contribute to the basic knowledge needed to advance sustainable breeding and management of soybean. Nodule diazotrophs are sensitive to water status e.g. drought, and other experiments have shown that the nodule bacteriome is the driver of BNF. Thus, improving the understanding and exploiting the nodule bacteriome will support developing more resilient cultivars of soybean that are efficient in BNF, and tolerant of stress. Identifying and testing diazotrophs and atypical nodule bacteria will provide a platform for developing new inoculants and biofertilizers. / Doctor of Philosophy / Soybean, the top harvested crop in the USA and 4th worldwide, is an important protein input of the livestock industry and an affordable alternative protein source for human consumption. Soybean depends on Nitrogen (N), provided by bacteria helpers, diazotrophs, that reside in nodules on soybean roots, to synthesize protein. While N makes up 80% of air, it is not suitable in its breathable form for use by most living organisms. Diazotrophs, converts this N to ammonium, a form more useful by soybean, through a process called biological nitrogen fixation (BNF). Root nodules provide a special habitat to support BNF, where soybean provides the diazotrophs with carbon as an energy source in return for the fixed ammonium. BNF is sensitive to environmental stress such as drought, which in turn affects soybean yield. While synthetic fertilizer supplementation may help reduce yield loss, it contributes to global warming and water systems pollution. Understanding the associations between soybean and diazotrophs has the potential to improve the sustainable growing of soybean. In this dissertation, we first determine the changes in the soybean root nodule bacteria in response to different water treatments. We then study how the bacterial community inside the nodules change based on different rates of BNF. After that, we look for the connections between soybean-based nitrogen molecular markers and these bacteria. Finally, we take a deeper look at how some different types of bacteria can help support N fixation. Our results have revealed that soybean hosts non-nitrogen fixing bacteria, and in high abundances. These bacteria seem to be supporting soybean growth. However, the soybean-diazotroph relationship is more sensitive to changes in water. We also found variation in nodule bacterial diversity that is related to N fixation. As well, we found that these, previously undescribed, non-nitrogen fixing bacteria are capable of living inside the nodules and they could help support the diazotrophs, under certain conditions. We provide some possible explanations to how these, previously undescribed and novel, bacteria may have adapted to the nodules. These results are very useful in the development of new inoculation products that would serve as biofertilizers for soybean, thus improving the sustainability of the agriculture industry.

Drought, salinity, and low soil fertility have negative impacts on agricultural productivity, resulting in food scarcity and nutritional insecurity, particularly in Sub-Saharan Africa. Mungbean [Vigna radiata (L.) R. Wilczek] has seen increased interest as a short-duration and drought tolerant legume crop, capable of atmospheric N₂ fixation. Mungbean is a protein and iron-rich legume and can be used as vegetable or grain for human consumption or multipurpose crop. At present, few studies have simultaneously explored the best agronomic practices for mungbean cultivation and evaluated its potential for increasing crop yields via intercropping systems and improving soil fertility through biological N₂ fixation. To understand the agronomic practices and soil physical properties limiting mungbean production, the impacts of two mungbean cultivars (Berken and OK2000) with and without inoculation with Bradyrhizobium spp. grown in loamy sand and silt loam soils on mungbean growth and yield were investigated under glasshouse conditions. Promising results from this study led to the introduction of mungbean into pearl millet systems in Senegal and evaluation of the effects of intercropping on growth, yields, land equivalent ratio (LER), canopy cover estimates, and normalized difference vegetation index (NDVI). Finally, we evaluated plant growth and N₂ fixation of five mungbean genotypes grown in two soil textures using the ¹⁵N natural abundance technique leading to recommendations for those with the greatest overall benefit to the cropping system. The literature review shows mungbean often proposed as a strategic crop for increasing legume diversification within current cropping systems and providing increased food security as well as market diversification and economic sustainability. The greenhouse study revealed that OK2000 cultivar produced significantly higher yield when inoculated and planted on a silt loam soil than other treatments, indicating the importance of inoculation and soil texture in mungbean establishment. Intercropping mungbean and millet significantly (p≤ 0.05) increased combined yields (35% to 100% increase) and LER compared to sole millet cropping systems. Canopy cover estimates and NDVI values significantly increased up to 60% and 30%, respectively, in millet-mungbean intercropping over millet alone. The N2 fixation study showed that %Ndfa of mungbean was higher when grown in the loamy sand soil (27% increase). However, soil N uptake (235 mg plant⁻¹) and amount of N fixed (67 mg plant⁻¹) were greater in the silt loam soil. Among genotypes, IC 8972-1 significantly (p≤ 0.05) derived less N from the atmosphere (23%) but took more soil N (155 mg plant⁻¹) which yielded significantly greater dry biomass (7.85 g plant⁻¹) and shoot N content (200 mg plant⁻¹). The results from the N₂ fixation study indicated that choice of mungbean genotype can contribute to reducing N needs of agricultural systems. Overall, this research project demonstrated that mungbean has the potential for diversifying smallholder agriculture and adding biologically fixed N into soils, in line with transformative adaptation strategies being promoted for sustainable agriculture. Further research and development programs on good cultural practices, adaptation to cropping systems, and nutritional benefits for human consumption can promote mungbean cultivation in SSA. / Doctor of Philosophy / Global population growth is expected to reach 9.8 billion in 2050 while climate change is predicted to reduce food production. Sustainable solutions are needed for increasing food availability and satisfying nutritional needs under changing climatic conditions. Mungbean is a viable option because it is a legume crop capable of restoring soil fertility and has low water requirements. Mungbean also contains high levels of protein and iron and can, therefore, provide a nutritious and healthy food. Although the agronomic benefits of mungbean have been studied, best cultural practices and its impact on farming systems and soil fertility are scattered. The objectives of this research were to identify the best agronomic practices for mungbean production, assess its effects when grown together with millet, and measure its nitrogen contribution to the soil. The results showed that selecting the best genotypes to be grown in a particular soil texture can significantly increase mungbean growth and yield. In addition, incorporation of mungbean into cereal-based farming systems demonstrated its capacity for improving agricultural production in a low-input environment. Assessment of nitrogen fixation by mungbean showed that it can naturally add nitrogen into the soils, the most limiting plant nutrient, reducing nitrogen application needs. Thus, the ability of mungbean to diversify farming systems, improve soil fertility, and deliver nutritious food will provide agronomic, environmental, and economic benefits to farmers, especially in food-insecure households. However, exploitation of the full potential of mungbean won't be achieved without understanding the major factors influencing mungbean cultivation and production.

Site-directed mutagenesis and gene replacement procedures were used to isolate mutant strains of <i>Azotobacter vinelandii</i> that produce altered MoFe proteins where the α-subunit residue-195 position, normally occupied by a histidine residue, was individually substituted by a variety of other amino acids. Structural studies have revealed that this histidine residue is associated with the FeMo-cofactor binding domain and probably provides an NH→S hydrogen bond to a central bridging sulfide located within FeMo-cofactor. The present study investigates the role of the α-histidine-195 residue in nitrogenase catalysis by examining the altered MoFe proteins. Comparisons of the catalytic and spectroscopic properties of altered MoFe proteins produced by the <i>Azotobacter vinelandii</i> mutant strains suggest that the α-histidine-195 residue has a structural role which serves to keep the FeMo-cofactor attached to the MoFe protein and to correctly position the FeMo-cofactor within the polypeptide matrix such that N₂ binding is accommodated. Substitution of the α-His-195 residue by a glutamine residue results in an altered MoFe protein that binds but does not reduce N₂, the physiological substrate. Stopped-flow spectroscopic analyses indicate that the α-195^gln MoFe protein is unable to reduce N₂ even though the altered MoFe protein can reach the redox state necessary for N₂ reduction. Although, N₂ is not a substrate for the altered MoFe protein, it is an inhibitor of both acetylene and proton reduction, both of which are otherwise effectively reduced by the altered MoFe protein. This result provides evidence that N₂ inhibits proton and acetylene reduction by simple occupancy of the active site. The α-195^gln MoFe protein catalyzes HD formation in the presence of N₂ and D₂. Moreover, N₂ binding at the active site of the altered MoFe protein is inhibited by the addition of D₂. These observations indicate that binding of nitrogen to the enzyme is necessary but its reduction is not required for the formation of HD. N₂ uncouples MgATP from proton reduction catalyzed by the α-195gln MoFe protein, but does so without lowering the overall rate of MgA TP hydrolysis. Thus, the quasi-unidirectional flow of electrons from the Fe protein to the MoFe protein that occurs during nitrogenase turnover is controlled, in part, by the substrate serving as an effective electron sink. N₂-induced uncoupling of ATP hydrolysis from substrate reduction by the α-195^gln MoFe protein is reversed by the addition of H₂ (D₂) in the assay atmosphere. This observation can successfully be explained if it-is assumed that the altered MoFe protein has a much greater binding affinity for H₂ (D₂) than for N₂. Substitution of the α-histidie-195 residue by glutamine also imparts hypersensitivity of acetylene reduction and N2 binding to inhibition by CO, indicating that the imidazole group of the α-histidine- 195 residue might protect an Fe contained within FeMo-cofactor from attack by CO. / Ph. D.

Many plants, especially grasses, have Nitrogen (N) as their growth-limiting nutrient. Large amounts of N fertilizer (>100 kg N ha-1) are used in managed systems to maximize crop productivity. However, the plant captures less than 50% of the (~12 million tons per year, U.S.) applied N-fertilizer. The remaining mobile N lost through leaching and denitrification accumulates in waterways and the atmosphere, respectively. Losses of fertilizers create environmental and economic concerns globally and create conditions that support the invasion of exotic plants in the natural landscapes. There is thus a need to come up with biological solutions to better manage nitrogen for plant growth and ecosystem sustainability. Microbial communities in the rhizosphere are known to potentially have beneficial effects on plant growth. Diazotrophs, for example, are bacteria that can convert the atmospheric nitrogen to ammonia, a process called 'nitrogen fixation.' Utilizing the natural process of associative nitrogen fixation to support most of the plant's N needs would substantially reduce fertilizer use and thus reduce production and environmental costs. The goal of this dissertation was to determine the structure and function of root-zone microbial communities for increasing productivity of native plants. Towards this end, we study the root-zone bacterial and fungal communities of native and exotic invasive plants. This study identifies that shifts in rhizosphere microbial communities are associated with invasion and highlights the importance of rhizosphere associated structure and function of microbes. A study of root-zone associated microbes in switchgrass (Panicum virgatum L.) - a U.S. native, warm-season, perennial, bioenergy crop indicates that high biomass yield and taller growth are associated with increased plant N-demand and supportive of bacteria with greater rates of N2-fixation in the rhizosphere. Another crucial outcome of the thesis is a better description of the core and cultivar-specific taxa that comprise the switchgrass root-zone associated microbiome. The work in this dissertation has brought us closer to designing N supply strategies by utilizing the natural microbial communities to balance the N-cycle in agroecosystems and support a sustainable environment. / Ph. D.

Nitrogenase fixation occurred in a number of habitats in and nearby several antarctic lakes. The observed acetylene reduction occurred in bluegreen algal mats in littoral areas that received maximal sunlight. The benthic bluegreen algal communities in reduced light under 5-6 m of permanent ice showed no detectable nitrogenase activity. The observed nitrogen fixation potential correlated with the presence of heterocystous bluegreen algae considered to be the major nitrogen fixing organisms in these habitats. The relatively low acetylene reduction rates suggest that a small but significant contribution of ammonia to these environments deficient in nitrogen may occur through nitrogen fixation. / Master of Science

Wave heights and periods of surface waves in the Baltic Sea have been modelled for a two-year period (1999-2000) with the wave model Hypas on an 11x11-km grid scale. There is a clear seasonal variation with higher waves during winter and lower during summer. This is mainly a reflection of the wind climate in the area where the winters are windier than the summers. The largest waves are found in the Skagerrak and over the deeper, eastern areas in the Baltic Proper. In the Baltic Sea, the surface waves influence the bottom sediment by initiating resuspension down to 80 m depths. This process is dependent not only on the waves but also on the varying grain size diameters. Fine and medium sand resuspend more often than other sediment types, and these sediments cover together about 25% of the Baltic Proper area. On average sediment is here resuspended 4-5 times per month with a duration for each event of 22 hours. The highest resuspension frequencies are found on the eastern and southern side of the Baltic Proper. During resuspension sediment grains are lifted up into the water mass and matters earlier bound in the sediment can be released. This may stimulate both production and degradation of organic matter.

In aquatic environments the availability of nitrogen (N) generally limits primary production. N2-fixing prokaryotes (diazotrophs) can convert N2 gas into ammonium and provide significant input of N into the oceans. Cyanobacteria are thought to be the main N2-fixers but diazotrophs also include a wide range of heterotrophic bacteria. However, their activity and regulation in the water column is largely unknown. In this thesis the distribution, diversity, abundance, and activity of marine and estuarine heterotrophic diazotrophs was investigated. With molecular methods targeting the nifH gene, encoding the nitrogenase enzyme for N2 fixation, it was shown that diverse nifH genes affiliating with heterotrophic bacteria were ubiquitous in surface waters from ten marine locations world-wide and the estuarine Baltic Sea. Through enrichment cultures of Baltic Sea surface water in anaerobic N-free medium, heterotrophic N2 fixation was induced showing that there was a functional N2-fixing community present and isolates of heterotrophic diazotrophs were obtained. In Sargasso Sea surface waters, transcripts of nifH related to heterotrophic bacteria were detected indicating heterotrophic N2-fixing activity. Nitrogenase expression is thought to be highly regulated by the availability of inorganic N and the presence of oxygen. Low oxygen zones within the water column can be found in association with plankton. The presence of diazotrophs as symbionts of heterotrophic dinoflagellates was investigated and nifH genes related to heterotrophic diazotrophs rather than the cyanobacterial symbionts were found, suggesting that a symbiotic co-existence prevailed. Oxic-anoxic interfaces could also be potential sites for heterotrophic N2 fixation. The Baltic Sea contains large areas of anoxic bottom water. At the chemocline and in anoxic deep water heterotrophic diazotrophs were diverse, abundant and active. These findings extend the currently known regime of N2 fixation to also include ammonium-rich anaerobic waters. The results of this thesis suggest that heterotrophic diazotrophs are diverse and widely distributed in marine and estuarine waters and that they can also be active. However, limits in the knowledge on their physiology and factors which regulate their N2 fixation activity currently prevent an evaluation of their importance in the global marine N budget.

L’azote est l’élément le plus abondant dans l’atmosphère terrestre avec un pourcentage atteignant 78 %. Composant essentiel pour la biosynthèse des matériels organiques cellulaires, il est inutilisable sous sa forme diatomique (N2) très stable par la plupart des organismes. Seules les bactéries dites diazotrophiques comme Rhodobacter capsulatus sont capables de fixer l’azote moléculaire N2 par le biais de la synthèse d’une enzyme, la nitrogénase. Cette dernière catalyse la réduction du N2 en ammonium (NH4) qui peut alors être assimilé par d’autres organismes. La synthèse et l’activité de la nitrogénase consomment beaucoup d’énergie ce qui implique une régulation rigoureuse et son inhibition tant qu’une quantité suffisante d’ammonium est disponible. Parmi les protéines impliquées dans cette régulation, la protéine d’intérêt AmtB est un transporteur membranaire responsable de la perception et le transport de l’ammonium. Chez R. capsulatus, il a été démontré que suite à l’addition de l’ammonium, l’AmtB inhibe de façon réversible (switch off/switch on) l’activité de la nitrogénase en séquestrant la protéine PII GlnK accompagnée de l’ajout d’un groupement ADP ribose sur la sous unités Fe de l’enzyme par DraT. De plus, la formation de ce complexe à lui seul ne serait pas suffisant pour cette inactivation, ce qui suggère la séquestration d’une troisième protéine, DraG, afin d’inhiber son action qui consiste à enlever l’ADP ribose de la nitrogénase et donc sa réactivation. Afin de mieux comprendre le fonctionnement de l’AmtB dans la régulation et le transport de l’ammonium à un niveau moléculaire et par la même occasion la fixation de l’azote, le premier volet de ce mémoire a été d’introduire une mutation ponctuelle par mutagénèse dirigée au niveau du résidu conservé W237 de l’AmtB. La production d’hydrogène est un autre aspect longtemps étudié chez R. capsulatus. Cette bactérie est capable de produire de l’hydrogène à partir de composés organiques par photofermentation suite à l’intervention exclusive de la nitrogénase. Plusieurs études ont été entreprises afin d’améliorer la production d’hydrogène. Certaines d’entre elles se sont intéressées à déterminer les conditions optimales qui confèrent une production maximale de gaz tandis que d’autres s’intéressent au fonctionnement de la bactérie elle même. Ainsi, le fait que la bioproduction de H2 par fermentation soit catalysée par la nitrogénase cela implique la régulation de l’activité de cette dernière par différents mécanismes dont le switch off par ADP ribosylation de l’enzyme. De ce fait, un mutant de R. capsulatus dépourvu d’AmtB (DG9) a été étudié dans la deuxième partie de cette thèse en termes d’activité de la nitrogénase, de sa modification par ADP ribosylation avec la détection des deux protéines GlnK et DraG qui interviennent dans cette régulation pour connaitre l’influence de différents acides aminés sur la régulation de la nitrogénase et pour l‘utilisation future de cette souche dans la production d’H2 car R. capsulatus produit de l’hydrogène par photofermentation grâce à cette enzyme. Les résultats obtenus ont révélé une activité de la nitrogénase continue et ininterrompue lorsque l’AmtB est absent avec une activité maximale quand la proline est utilisée comme source d’azote durant la culture bactérienne ce qui implique donc que l’abolition de l’activité de cette protéine entraine une production continue d’H2 chez R. capsulatus lorsque la proline est utilisée comme source d’azote lors de la culture bactérienne. Par ailleurs, avec des Western blots on a pu déterminer l’absence de régulation par ADP ribosylation ainsi que les expressions respectives de GlnK et DraG inchangées entre R. capsulatus sauvage et muté. En conclusion, la nitrogénase n’est pas modifiée et inhibée lorsque l’amtB est muté ce qui fait de la souche R. capsulatus DG9 un candidat idéal pour la production de biohydrogène en particulier lorsque du glucose et de la proline sont respectivement utilisés comme source de carbone et d'azote pour la croissance. / Nitrogen is the most abundant element in the Earth's atmosphere with a percentage of 78 %. This element is essential for the biosynthesis of cellular organic material and is unusable in its stable diatomic form (N2) by most organisms. Only bacteria called diazotrophs such as Rhodobacter capsulatus are able to fix molecular nitrogen N2 through the synthesis of the nitrogenase enzyme. The latter catalyzes the reduction of N2 to NH4 which can then be absorbed by other organisms. The synthesis and activity of nitrogenase consumes a lot of energy and therefore implies a strict regulation and its inhibition when a sufficient amount of ammonium is available. Among the proteins involved in this regulation, is the membrane transporter AmtB which is responsible for the sensing and transportation of ammonia. In R. capsulatus, it was shown that following the addition of ammonium, AmtB reversibly inhibits (switch off / switch on) nitrogenase activity by sequestering the PII protein GlnK accompanied by the addition of an ADP ribose group onto the Fe subunit of the enzyme by DraT. In addition, the formation of this complex alone would not be sufficient for this inactivation, suggesting the sequestration of a third protein, DraG is required to inhibit its action of removing the ADP ribose from the nitrogenase and therefore its reactivation. To better understand the role of the AmtB in the fixation of nitrogen, regulation and transport of ammonium at the molecular level, the first part of this study was to introduce a point mutation by directed mutagenesis in the conserved residue W237 of AmtB . Hydrogen production is another property of R. capsulatus that has been studied for a long time. This bacterium is capable of producing hydrogen from organic compounds following photofermentation and the exclusive enzymatic intervention of nitrogenase. Several studies have been undertaken to improve the production of hydrogen. Some of them were involved in determining the optimum conditions that give maximum gas production while others were interested in improving the growth of the bacterium itself. Thus, since the bio-production of H2 by fermentation is catalyzed by the nitrogenase, it is important to study the regulation of the activity of this enzyme by different mechanisms such as the switch off by ADP ribosylation. Therefore, a mutant of R. capsulatus (DG9) lacking AmtB was studied in the second part of this thesis for its nitrogenase activity, its modification by GlnK-DraG, and to see the effects of different amino acids used in the growth medium on the regulation and therefore the future use of this strain for the production of H2. The results showed a continuous and uninterrupted activity of the nitrogenase when AmtB was absent with a maximum activity when proline was used as a nitrogen source for bacterial growth. In addition, Western blots were used to demonstrate the effect of ADP ribosylation on regulation and that the expression of GlnK and DraG were unchanged between the wild –type and mutant R. capsulatus. In conclusion, nitrogenase is not modified or inhibited when mutated amtB what makes the R. capsulatus strain DG9 an ideal candidate for biohydrogen production especially when glucose and proline are respectively used as source carbon and nitrogen for growth.